RetrogeneDB ID: | retro_btau_1404 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 5:107214851..107215352(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TMEM220 | ||
| Ensembl ID: | ENSBTAG00000003958 | ||
| Aliases: | None | ||
| Description: | transmembrane protein 220 [Source:RefSeq peptide;Acc:NP_001178972] |
Retrocopy-Parental alignment summary:
>retro_btau_1404
ATGACGCCGGGGGCGGGGCGCAGGGCGCGGGGCCTATGGCGCGCCTGCGCCTGGCTCGTGGGCGCCTTCTTCGCGCTGGC
GGTCTTTGTGCAGGTGAACGATCCGGATGCAGAACTGTGGGTGGTTGTGTATACGATTCCTGCCACTCTGACCCTGCGTG
TTGGACTTAACCCTCTTGTCACAGGTAACTTTATTTGGAAGAGTGTGTCTGCAATACACATATTCCTTTGTGTCCTGTGG
GCTATCAGCTTGGCATACAACCTCTTGCTTCATAAGAAACAGAACCTCTTGCATGAGGAGGAAGGCAGGAAGCTGTTTGG
TCCCGTGATCATCACAGCATGGCTGGGCCTGTGCCACAGCTCTTCAAAGGCTCCAGGTGGTGGAAGAGTTCAGCTGGCCA
ATGCTACCACAGTCGCTCTTCTCCCGTTTATCTCCTAGGTCTACATATACATACACAAGGAGATGTGCTCCCCCTGGCCA
ACTCATTGCAAGACGGTGATT
ORF - retro_btau_1404 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.22 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAPAAGRGARGLWRACNWLMGAFFALAAFVQVNDPDAELWVVMYTIPATLTLLVGLNPLVTGNFIWKSVS |
| M.P.AGR.ARGLWRAC.WL.GAFFALA.FVQVNDPDAELWVV.YTIPATLTL.VGLNPLVTGNFIWKSVS | |
| Retrocopy | MTPGAGRRARGLWRACAWLVGAFFALAVFVQVNDPDAELWVVVYTIPATLTLRVGLNPLVTGNFIWKSVS |
| Parental | AIHIFLCVLWAISLAYNLLLHKKQNLLHEEEGRELFGLVIITAWLGLCHSSSKAPGGGRIQLAIATTVAF |
| AIHIFLCVLWAISLAYNLLLHKKQNLLHEEEGR.LFG.VIITAWLGLCHSSSKAPGGGR.QLA.ATTVA. | |
| Retrocopy | AIHIFLCVLWAISLAYNLLLHKKQNLLHEEEGRKLFGPVIITAWLGLCHSSSKAPGGGRVQLANATTVAL |
| Parental | LPFISWVYIYINKEMRSSWPDHCKTVI |
| LPFIS.VYIYI.KEM.S.WP.HCKTVI | |
| Retrocopy | LPFIS*VYIYIHKEMCSPWPTHCKTVI |
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 | 139 .65 RPM |
| ERP005899_muscle | 0 .05 RPM | 24 .39 RPM |
| SRP017611_brain | 0 .00 RPM | 5 .07 RPM |
| SRP017611_kidney | 0 .41 RPM | 43 .27 RPM |
| SRP017611_liver | 0 .00 RPM | 33 .22 RPM |
| SRP030211_testis | 0 .03 RPM | 3 .70 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1404 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1404 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1404 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000003958 | 1 retrocopy |
retro_btau_1404 ,
|
| Echinops telfairi | ENSETEG00000015072 | 1 retrocopy |