Table 2

Coding/non-coding property of female-biased X-linked genes

A. CPC

B. nRNA db

C. BLAST x

Gene symbol

Refseq RNA

Coding/Non-coding

Score

RNA-db

NONCODE

Cov, Ident

RefSeq Protein





Known X-linked:

Xist

NR_001463.3

weak coding

0.45

Y

Y

6, 28

XP_001478155.1

Kdm5c

NM_013668.3

coding

17.40

N

N

73, 100

NP_038696.2

Eif2s3x

NM_012010.3

coding

3.63

N

N

39, 100

NP_036140.1

Kdm6a

NM_009483.1

coding

16.02

N

N

80, 100

NP_033509.1

Ddx3x

NM_010028.3

coding

9.69

N

N

38, 100

NP_034158.1

2010000I03Rik

NR_015508.1

weak coding

0.14

Y

Y

11,68

XP_0014781580.1

Novel X-linked:

2010308F09Rik

AK008545.1

noncoding

-1.13

N

N

20, 60

XP_001479963.1

D330035K16Rik

AK084720.1

noncoding

-1.21

N

N

18, 24

NP_035953.3

5530601H04Rik

AK164650.1

weak coding

0.83

Y

Y

2, 78

XP_001478711.1

2610029G23Rik

NM_026312.4

coding

3.05

N

N

22, 100

NP_080588.1

D930009K15Rik

AK148627.1

noncoding

-1.22

Y

Y

5, 29

NP_032530.1


A: Coding potential calculation (CPC) and coding/non-coding classification based on sequence composition [27].

B: Genes that are annotated as non-coding RNAs in ncRNA databases, namely RNA-db [28] and NONCODE [29]. (Y: yes, N: no).

C: Highest ranked hits when performing NCBI BLASTx using all 6 frames in Refseq protein database. Cov: % coverage of RNA transcript, Indet: % sequence identity.

Reinius et al. BMC Genomics 2010 11:614   doi:10.1186/1471-2164-11-614

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