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Table 2 Coding/non-coding property of female-biased X-linked genes

From: Female-biased expression of long non-coding RNAs in domains that escape X-inactivation in mouse

   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
  1. A: Coding potential calculation (CPC) and coding/non-coding classification based on sequence composition [27].
  2. B: Genes that are annotated as non-coding RNAs in ncRNA databases, namely RNA-db [28] and NONCODE [29]. (Y: yes, N: no).
  3. C: Highest ranked hits when performing NCBI BLASTx using all 6 frames in Refseq protein database. Cov: % coverage of RNA transcript, Indet: % sequence identity.