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Comparative analysis of conserved elements between duplicated genes provides a powerful approach …


Biology Articles » Evolutionary Biology » Comparative Genomics » Comparative genomics using Fugu reveals insights into regulatory subfunctionalization » Tables

Tables
- Comparative genomics using Fugu reveals insights into regulatory subfunctionalization

Table 1
Co-ortholog nomenclature and genomic locations in the Fugu genome
Human gene*
Co-ortholog name
Fugu scaffold (S) location (kb)
Length (kb)§
Prop 'N's (%)
Fugu protein accession code¥
BCL11A
bcl11a.1
S113: 140.8-518.9
378.1
2.98
NEWSINFRUP00000142044

bcl11a.2
S62: 603.7-740.4
136.7
0.18
NEWSINFRUP00000144873
EBF1
ebf1.1
S97: 400.4-483.3
82.9
0.82
NEWSINFRUP00000127762

ebf1.2
S71: 999.3-1,091.7
92.4
1.90
NEWSINFRUP00000148373
FIGN
fign.1
S36: 382.6-486.8
104.2
0.16
NEWSINFRUP00000153680

fign.2
S46: 126.9-219.9
93
0.39
NEWSINFRUP00000177971
PAX2
pax2.1
S86: 541.7-669.8
128.1
0.29
-

pax2.2
S59: 768.9-898.3
132.7
3.59
-
SOX1
sox1.1
S42: 1,020-1,105
85
1.49
[Swiss-Prot: Q6WNU3_FUGRU]

sox1.2
S313: 107.2-174.9
67.7
8.9
[Swiss-Prot: Q6WNU2_FUGRU]
UNC4.1
unc4.1.1
S15: 761.1-825.5
61
0.32
NEWSINFRUP00000154395

unc4.1.2
S40: 1,435-1,537
102
0.96
NEWSINFRUG00000161008
ZNF503
znf503.1
S86: 7-220
213
3.64
NEWSINFRUP00000181530

znf503.2
S59, S29 (all)
148.5
3.22
NEWSINFRUP00000181454
*Name of human gene ortholog. Nomenclature of novel Fugu co-orthologs. Location and extent of Fugu genomic scaffold used in multiple alignment. §Length of Fugu genomic region used in multiple alignment. Proportion of Fugu genomic region that is made up of unfinished sequence (that is, runs of 'N's). ¥The protein accession code for each co-ortholog. These were derived either from Ensembl (v40.4b) or from SwissProt. Protein sequences for pax2.1 and pax2.2 were incomplete in both Ensembl and SwissProt and were reconstructed using alignments of full-length amino acid sequences from other species.
Table 2
Tajima relative rate tests of overlapping co-orthologous CNE in Fugu
Gene region*
No. of overlapping pairs
No. of CNE pairs with p > 0.05
No. of CNE pairs with p ≤ 0.05§
% of CNE pairs with p







Co-ortholog 1
Co-ortholog 2

BCL11A
20
15
1
4
25
EBF1
7
5
1
1
21
FIGN
28
21
5
2
25
PAX2
43
34
4
5
21
SOX1
6
5
0
1
17
UNC4.1
20
15
0
5
25
ZNF503
84
62
5
17
26
*Gene region. Total number of overlapping CNEs within gene region. Numbers of overlapping CNE pairs with no significant difference in substitution rates (that is, p values of > 0.05). §The number of overlapping CNEs that exhibit a significant difference in substitution rate (that is, p value ≤ 0.05) in the CNE sequence in the vicinity of one co-ortholog over that in the other. The percentage of overlapping CNEs with significantly different substitution rates in either co-ortholog as a proportion of the total number of overlapping CNEs.
Table 3
Co-ortholog CNEs that are also conserved in the vicinity of trans-dev paralogs in the human genome
Gene region
Co-ortholog 1
Co-ortholog 2
Gene paralog in the vicinity of the dCNE(s)
BCL11A
CRCNE00002445
CRCNE00004614
BCLL1B

CRCNE00002557
-


CRCNE00002548
CRCNE00004648


CRCNE00002544
CRCNE0004643



CRCNE0004644


CRCNE00002540
-

EBF1
CRCNE00010771
-
EFB3

-
CRCNE00010818


CRCNE00000027
CRCNE00010823


CRCNE00010778
CRCNE00010827


CRCNE00010787
-

EBF1
CRCNE00010772
CRCNE00010820
EBF1/2/3/4
PAX2
CRCNE00000064
CRCNE00000133
PAX8
PAX2
CRCNE00000071
CRCNE00000147
PAX5

CRCNE00000090
CRCNE00000165


CRCNE00000092
CRCNE00000167


CRCNE00000099
CRCNE00000174

SOX1
-
CRCNE00001926
SOX2
ZNF503
CRCNE00010112
CRCNE00004977
ZNF703

CRCNE00010147
CRCNE00004994


CRCNE00010126
CRCNE00005024


CRCNE00010167
-


CRCNE00010170
-


CRCNE00010187
-


CRCNE00010180
-


CRCNE00010176
CRCNE00005013



CRCNE00005015


CRCNE00010165
CRCNE00005011


CRCNE00010161
CRCNE00005008


CRCNE00010046
CRCNE00004906


CRCNE00010156
CRCNE00005003


CRCNE00010120
CRCNE00004986

CNEs in each co-ortholog are referred to by their CONDOR database identifiers [53]. Each CNE was considered duplicated if the human sequence they are conserved to shows significant hit to a sequence elsewhere in the genome through BLAST. Any gene in the vicinity (

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