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Putative Gene Deserts on Chromosome 7

Twenty regions on human chromosome 7 and the syntenic intervals in mouse devoid of genes (gene deserts)(Tables S7a, S7b). For this study a gene desert was defined as a region with no known, novel, or partial genes in a 500 kb region. The control regions examined are shown (Tables S7c, S7d, S7e). In addition to the randomly selected genomic regions (described in the published text), as an additional control, we examined the genomic intervals encompassed by large genes (>500 kb) on chromosome 7 (Table S7f). In all cases the only correlation was with low CpG density. The orthologous genes in mouse and syntenic anchor points were used to identify the equivalent regions in the murine genome. Table S7b shows the orthologous murine gene that flanks the region. If an orthologous gene was not yet defined, the nearest known gene flanking the region was selected (the closest EST or syntenic anchor marker to the boundary is also listed in brackets). When syntenic anchors are used, the corresponding region in the public mouse assembly (UCSC) can be identified by retrieving the syntenic anchor sequence from the chromosome 7 Genome Browser (http://www.chr7.org), and searching the mouse assembly. The best sequence alignment (using BLAT) will represent the border of the mouse region equivalent to the human gene desert. For our analysis of mouse, we examined both the UCSC (results shown in Table S7b) and the Celera assemblies separately. In 19 of 20 cases the results were equivalent. In one instance (human desert #7), a break in synteny occurred and UCSC placed both mouse segments on chromosome 5 (Table S7b), while Celera positioned them on chromosomes 12 and 5. Notwithstanding, using our criteria all 20 regions would still be characterized as deserts in mouse. The location of the human gene deserts along chromosome 7 can also be observed in the 'Structural Feature' track in the Genome Browser at http://www.chr7.org.

(Table S7a) Putative Gene Deserts on Chromosome 7

 

 

Gene Desert

Size (kb)

Location

Flanking Reference Genes

Genes and Models in Region

CpG Island

CpG Island/Mb

% Syntenic (>75%)

Repetitive Content

LINEs

SINEs

1

1850

7q11.22-q11.23

FLJ13195

AUTS2

2 predicted

1

0.5

4.20%

10.80%

25.80%

2

1740

7q31.1

THC1201470

IMMP2L

3 predicted; 1 pseudogene

0

0

4.60%

32.90%

5.20%

3

1700

7p12.2-p12.1

KIAA0633

FLJ40449

2 predicted; 1 putative; 1 pseudogene

4

2.4

2.90%

26.00%

8.10%

4

1690

7p22.1-p21.3

NXPH1

IMAGE:3605453

2 predicted; 1 putative; 1 pseudogene

3

1.8

4.70%

31.20%

5.30%

5

1640

7q31.31-q31.32

ANKRD7

hCT1816883

1 pseudogene

2

1.2

2.10%

32.20%

4.20%

6

1190

7p21.3

ARL4

ETV1

1 pseudogene

2

1.7

5.60%

24.00%

8.70%

7

1040

7q21.11-q21.13

IMAGE:5272175

GRM3

1 predicted

1

1

2.10%

33.80%

4.90%

8

990

7p12.3-p12.2

MGC26484

ZPBP

none

1

1

2.60%

31.00%

6.00%

9

950

7q31.33-q31.2

THC1079110

GRM8

1 predicted

0

0

3.10%

28.70%

5.10%

10

900

7q36.1-q36.2

ARP3BETA

DPP6

2 predicted

2

2.2

1.90%

24.30%

8.40%

11

850

7p13-p12.3

IGFBP3

PRO1866

2 predicted; 1 pseudogene

1

1.2

1.50%

31.40%

5.80%

12

810

7q31.2-q31.31

IMAGE:4276820

TFEC

1 putative

0

0

11.80%

19.90%

6.10%

13

770

7q21.2

FLJ32110

IMAGE:5295327

1 predicted

1

1.3

4.80%

33.60%

5.20%

14

730

7q31.2

GPR85

PPP1R3

none

1

1.4

4.10%

31.40%

5.10%

15

720

7q35

TPK1

THC1203597

3 pseudogenes

1

1.4

4.10%

29.70%

6.30%

16

660

7p14.1-p13

GLI3

MGC2821

1 predicted

0

0

4.10%

31.10%

6.50%

17

610

7q21.11

AIP1

GNAI1

1 predicted; 1 pseudogene

0

0

2.40%

30.00%

6.30%

18

540

7p21.2-p21.1

FERD3L

LOC221830

1 predicted

0

0

6.50%

35.40%

5.20%

19

540

7p14.1

BC033981

INHBA

none

0

0

6.60%

16.60%

9.70%

20

540

7q21.3-q22.1

DC11

TAC1

2 predicted

0

0

3.30%

28.70%

12.20%

 

Total (kb)

 

 

 

 

Average

0.8

4.20%

28.10%

7.50%

 

20460

 

 

 

 

Standard Deviation

0.8

2.30%

6.30%

4.70%

 

(Table S7b) Mouse Regions Syntenic to Gene Deserts on Chromosome 7 (Data shown is from analysis on UCSC mouse sequence)

Gene Desert

Mouse Size (kb)

Mouse Location

Flanking Reference Genes

Genes and Models in Region

CpG Island

CpG Island/Mb

% Syntenic (>75%)

Repetitive Content

LINEs

SINEs

1

1488

chr5

BC021509

Gats (hmSA93056)

none

1

0.7

6.40%

7.80%

16.20%

2

1951

chr12

Immp2l-pending

Dnajb9 (hmSA72264)

none

1

0.5

4.20%

31.50%

2.90%

3

2128

chr11

U26967

Sec61g (hmSA220916)

none

3

1.4

2.30%

33.80%

2.60%

4

2216

chr6

Ica1 (BB641832)

BC011114 (hmSA167586)

2 spliced EST clusters

4

1.8

3.80%

39.80%

2.30%

5

2019

chr6

AW214405 (hmSA16662)

Kcnd2 (hmSA15769)

none

1

0.5

1.80%

39.30%

2.20%

6

1138

chr12

Etv1

Arl4

none

0

0

5.80%

27.50%

4.00%

7

172

chr5

Cdk6 (hmSA322558)

Sema3a (BB451280)

none

0

0

4.80%

33.80%

3.40%

1117

chr5

Telomere (BB871298)

Png (hmSA322547)

none

3

2.7

1.90%

34.60%

2.60%

8

1239

chr11

Rpo2-3 (hmSA220133)

Zpbp

1 spliced EST cluster

3

2.4

2.10%

35.40%

2.50%

9

972

chr6

AI851169 (hmSA138658)

Gprc1h

none

0

0

3.20%

34.90%

2.30%

10

967

chr5

Xrcc2 (BI248187)

AF092507

none

0

0

1.80%

15.00%

4.50%

11

740

chr11

Igfbp3

Spin (hmSA193672)

none

1

1.4

1.80%

23.70%

2.90%

12

1003

chr6

Foxp2 (hmSA23596)

Tcfec

none

0

0

9.60%

25.10%

3.50%

13

1010

chr5

Tiarp-pending (hmSA318744)

Hspa8

1 known: M36516 (homology to chr19)

0

0

4.10%

32.70%

5.10%

14

833

chr6

GPR85

Ppp1r3a

none

0

0

4.10%

32.60%

3.20%

15

974

chr6

Tpk1

Rbpsuh (hmSA166085)

1 spliced EST cluster

1

1

3.80%

30.50%

4.20%

16

830

chr13

AW209491

Gli3

1 spliced EST cluster

1

1.2

3.40%

35.60%

2.90%

17

841

chr5

Cd36

Acvrip1-pending (hmSA354360)

1 spliced EST cluster

1

1.2

1.90%

32.40%

3.00%

18

493

chr12

BC017546 (BI689342)

Nato3-pending

none

1

2

7.40%

30.80%

3.70%

19

628

chr13

Inhba

AF397014 (hmSA45738)

none

1

1.6

6.20%

25.70%

2.40%

20

521

chr6

Dlx5 (BB645073)

Tac1

1 spliced EST cluster

0

0

3.50%

31.10%

3.10%

 

Total (kb)

 

 

 

 

Average

0.9

4.00%

30.20%

3.80%

 

23280

 

 

 

 

Standard Deviation

0.9

2.10%

7.60%

2.90%

 

 

(Table S7c) Random 1 Mb Control Regions (20 from Chromosome 7 and 5 from Other Chromosomes)

 

 

 

 

 

Size (kb)

Location

Flanking Genes

Genes and Models in Region

CpG Island

CpG Island/Mb

Syntenic Coverage

 Repetitive Content

LINEs

SINEs

1000

7q32.3

N/A

5 known; 5 putative; 3 predicted

6

6

5.00%

23.50%

17.70%

1000

7q22.1

N/A

5 known; 1 novel; 1 putative

11

11

5.30%

7.60%

35.30%

1000

7q21.2

N/A

6 known; 1 novel; 3 putative

10

10

5.70%

28.80%

12.50%

1000

7q11.23

N/A

4 known; 4 novel; 1 predicted

7

7

6.30%

17.30%

19.70%

1000

7q11.23

N/A

2 known

2

2

2.80%

14.30%

24.20%

1000

7p14.3

N/A

5 known

10

10

5.40%

21.00%

12.20%

1000

7p15.1

N/A

10 known; 3 predicted

6

6

8.00%

19.00%

9.10%

1000

7p15.2

N/A

18 known; 1 novel; 1 partial; 1 putative; 9 predicted; 1 pseudogene

36

36

14.50%

16.80%

14.50%

1000

7p22.1

N/A

14 known; 1 partial; 4 putative; 6 predicted

35

35

4.40%

8.10%

36.00%

1000

7q35

N/A

1 known; 1 putative; 2 pseudogenes

0

0

5.00%

20.60%

8.20%

1000

7p14.2

N/A

1 known; 1 putative; 4 predicted

3

3

6.00%

21.10%

9.30%

1000

7q21.3

N/A

5 known; 2 putative; 4 predicted

3

3

9.60%

25.90%

8.50%

1000

7q11.23

N/A

20 known; 2 predicted

35

35

5.30%

8.90%

42.40%

1000

7q32.1

N/A

8 known; 1 novel; 2 putative; 3 predicted

12

12

14.20%

15.50%

11.20%

1000

7q33

N/A

4 known; 1 partial; 2 putative; 1 predicted

2

2

7.60%

15.50%

11.50%

1000

7p21.3

N/A

1 known; 1 novel

2

2

5.40%

20.70%

6.70%

1000

7q21.11

N/A

2 known; 1 partial; 1 putative; 1 predicted

3

3

5.30%

18.30%

7.10%

1000

7q22.1

N/A

8 known; 3 predicted; 1 pseudogene

6

6

8.60%

22.10%

12.60%

1000

7p13

N/A

20 known; 4 putative; 3 predicted

22

22

7.20%

16.40%

23.10%

1000

7q31.32

N/A

5 known; 1 novel; 1 putative; 5 predicted

7

7

8.90%

20.70%

8.10%

1000

1p32.2

N/A

4 known

2

2

12.00%

16.50%

14.10%

1000

3p22.2

N/A

7 known

4

4

1.50%

31.50%

9.40%

1000

5p12

N/A

2 known

0

0

8.70%

31.80%

5.20%

1000

10q26.12

N/A

3 known

5

5

9.50%

14.60%

11.70%

1000

12q13.12

N/A

15 known

17

17

8.00%

12.50%

30.40%

Total

 

 

 

 

Average

9.8

7.20%

18.80%

16.00%

25000

 

 

 

 

Standard Deviation

10.9

3.10%

6.40%

10.20%

 

 

(Table S7d) Putative Gene Deserts on Other Chromosomes

 

 

 

 

Size (kb)

Location

Flanking Genes

Genes and Models in Region

CpG Island

CpG Island/Mb

Syntenic Coverage

Repetitive Content

LINEs

SINEs

1245

14q31.2

SEL1L

FLRT2

1 putative

12

9.6

4.00%

19.50%

6.90%

687

20q12

DDX35

MAFB

N/A

0

0

8.50%

20.60%

9.50%

2594

21q21.1

PRSS7

PRED14

1 predicted; 5 pseudogenes

0

0

2.80%

21.80%

6.40%

3269

21q21.2

PRED16

C21ORF42

1 predicted; 6 pseudogenes

0

0

1.90%

21.10%

7.80%

Total

 

 

 

Average

2.4

4.30%

20.80%

7.70%

7804

 

 

 

Standard Deviation

4.8

2.90%

1.00%

1.40%

 

 

(Table S7e) FRA7H Region on Chromosome 7

 

 

 

 

 

Size (kb)

Location

Flanking Genes

Genes and Models in Region 

CpG Island

CpG Island/Mb

Syntenic Coverage

Repetitive Content

LINEs

SINEs

375

7q32.3

BTEB5

MKLN1

5 putative; 1 predicted

1

2.7

2.40%

24.90%

15.50%

 

 

(Table S7f) Large Genes (>500 kb) on Chromosome 7

 

 

 

 

 

Size (kb)

Location

Large Gene

Genes and Models in Region

CpG Island

CpG Island/Mb

Syntenic Coverage

   Repetitive Content

LINEs

SINEs

2305

7q35

CNTNAP2

1 known; 1 putative

2

1

5.30%

18.40%

9.50%

1436

7q11.23

AIP1

1 known; 1 novel; 1 partial

0

0

6.50%

20.40%

8.40%

1194

7q11.23

AUTS2

1 known

3

3

11.70%

11.50%

13.70%

1018

7q36.3

PTPRN2

1 known; 1 novel; 2 predicted

35

34

2.40%

10.80%

4.30%

901

7q31.1

IMMP2L

2 known; 1 partial; 1 putative

1

1

8.60%

20.40%

7.40%

830

7q36.2

DPP6

1 known; 1 predicted

3

4

2.30%

11.10%

9.70%

812

7q33

SEC8

1 known; 1 putative

0

0

10.40%

17.50%

10.90%

805

7q32.1

GRM8

1 known

1

1

10.00%

21.10%

6.80%

727

7p14.1

C7orf10

1 known; 1 putative

0

0

7.00%

19.20%

15.30%

694

7p21.3

DGKB

1 known

0

0

7.60%

20.80%

6.30%

629

7q11.23

CALN1

1 known; 1 putative; 1 predicted

1

2

1.80%

17.20%

24.90%

611

7q21.2

PFTK1

1 known

1

2

7.50%

21.90%

7.90%

594

7p14.2

ELMO1

1 known; 1 putative

2

3

6.80%

15.80%

10.20%

581

7q11.23

WBSCR17

1 known; 1 novel

0

0

3.50%

13.70%

24.30%

546

7p15.1

PDE1C

1 known

2

4

3.40%

22.90%

8.20%

517

7q22.1

RELN

1 known; 1 predicted

1

2

10.90%

18.40%

9.70%

Total

 

 

 

Average

4

6.60%

17.60%

11.10%

14201

 

 

 

Standard Deviation

8.3

3.20%

3.90%

5.90%