RetrogeneDB ID: | retro_btau_662 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 17:39208175..39208772(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ASF1B | ||
| Ensembl ID: | ENSBTAG00000004085 | ||
| Aliases: | None | ||
| Description: | Histone chaperone ASF1B [Source:UniProtKB/Swiss-Prot;Acc:Q17QJ0] |
Retrocopy-Parental alignment summary:
>retro_btau_662
ATGGCTAAGGTGTCAGTATTGAACATGGCGGTGCTGGAAAATCTGAGCCTTTTCCACAGCCCTTTCTGGTTGAGACATCA
GCTTCGAGTGCAATGAGGCCCTGGCAGACTACCTGGAGTGGAAGAACGTTTATATTGGCTCAGCTGAGAGTGAATTTGAT
CAAATCCTAGACTCTGCTGGTTGGCCCTGTCCTGGCAGGGAGACACATGTTCATCTTTCAGGCAGATTCCCCCAACCCAT
CCCTCATCCTCGAGTCTGATAGCCTGGGAGTGACCATGGTCCTCATCACCTGCAGCTACCACAGACAGGAGTTCATCCGA
GTCAGCTACAGCGTCGACAGTGGGTACCTTAGCAGCTAGCTGTGCGAGAACCCACCCCTGAAGTCACACTTCTCTCAGCT
CCAGTGGAACATCTTGGCCTCAGATCCCCTGGTGAACTGCTTCCACATCAACTGGGACAACAACACAGACAGGTTGGAAG
CCATAGAGAACCAGGACCCTGCCCTGGGCTGCTGTCTCCCCCTCAGCTGCACAGGTACCCTTGGGTCTCCCTGGCTGCGT
AATGGGCCTCCTCCCTCAGAATTCCATGGACTTCATC
ORF - retro_btau_662 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 72.2 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MAKVSVLNVAVLENPSPFHSPFRF-EISFECNEALADDLEWKIIYVGSAESEEFDQILDSVLVGPVP-AG |
| MAKVSVLN.AVLEN.S.FHSPF....ISFECNEALAD.LEWK..Y.GSAES.EFDQILDS....P.P.AG | |
| Retrocopy | MAKVSVLNMAVLENLSLFHSPFWL>DISFECNEALADYLEWKNVYIGSAES-EFDQILDSA-GWPCP>AG |
| Parental | RHMFVFQADAPNPSLIPETDAVGVTVVLITCTYHGQEFIRVGYYVNNEYLSPELRENPPLKPDFSQLQRN |
| RHMF.FQAD.PNPSLI.E.D..GVT.VLITC.YH.QEFIRV.Y.V...YLS..L.ENPPLK..FSQLQ.N | |
| Retrocopy | RHMFIFQADSPNPSLILESDSLGVTMVLITCSYHRQEFIRVSYSVDSGYLSS*LCENPPLKSHFSQLQWN |
| Parental | ILASNPRVTRFHINWDNNMDRLEAIENQDSSLGCGLPLSCTPIKGLGLP-SCIPGLLPENSMDCI |
| ILAS.P.V..FHINWDNN.DRLEAIENQD..LGC.LPLSCT....LG.P..C..GLLP.NSMD.I | |
| Retrocopy | ILASDPLVNCFHINWDNNTDRLEAIENQDPALGCCLPLSCTGT--LGSP>GCVMGLLPQNSMDFI |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| ERP005899_liver | 0 .00 RPM | 0 .87 RPM |
| ERP005899_muscle | 0 .00 RPM | 9 .08 RPM |
| SRP017611_brain | 0 .00 RPM | 1 .51 RPM |
| SRP017611_kidney | 0 .00 RPM | 1 .30 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .60 RPM |
| SRP030211_testis | 0 .00 RPM | 59 .31 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_662 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_662 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_662 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 6 parental genes, and 12 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000004085 | 1 retrocopy |
retro_btau_662 ,
|
| Canis familiaris | ENSCAFG00000016482 | 1 retrocopy | |
| Echinops telfairi | ENSETEG00000013713 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000000537 | 4 retrocopies | |
| Monodelphis domestica | ENSMODG00000012099 | 4 retrocopies | |
| Sorex araneus | ENSSARG00000000534 | 1 retrocopy |