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.