RetrogeneDB ID: | retro_btau_875 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 2:72589722..72590563(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000019464 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BT.53009 | ||
| Ensembl ID: | ENSBTAG00000020338 | ||
| Aliases: | None | ||
| Description: | T-complex protein 1 subunit zeta-2 [Source:RefSeq peptide;Acc:NP_001029814] |
Retrocopy-Parental alignment summary:
>retro_btau_875
AAGAGTACAAAGGAGAGAGAGAAATTAGTGAAAGCTGAAAGGAAATTCATCGAAGACAGAGTTAAAAAAATAATCGACCT
GAAAAAGAAAGTCTGTGTTGATTCAGATAAAGGATTTGTTGTTATTAGTCAAAAGGGAATTGATCCCTTTTCCTTAGATG
CTCTTGCCAAAGAAGGCATAATAGCTCTGCGCAGAGCTAAAAGGAGAAACATGGAAAGGCTGACTCTTGCTTGTGGCGGG
ATAGCCCTAAATTCTCTTAATGACCTAAATCCTGATTGTTTGGGACATGCAGGACTTGTCTATGAATATACATTGGGAGA
AGAGAAGTTCACCTTTATTGAGAGATGTAACAATCCTCGCTCTGTCACATTATTGATCAAAGGACCAAATGAGCACACGT
TTACTCAAATCGAAGATGTCATAAGAGATGGCTTGAGGGCTGTTTAAAATGCTACTGATGATGGCTGTTAGTCCCAGGTG
CTGGCGCAGTGGACGTGCAATGGCAGAAGCCCTGGTTAAATACATGCCCAGTGTAAAGGGCAGGGCCCAGCTTGGAGTTC
AAGCATTTGCTGATGCATTGCTCATTATTCCCAAGGTTCTCGCTCAGAACTCTGGTTTTGACCTTCAGGAAACACTAGTT
AAAATTCAAGCAGAACATTCAGAATCCAGTCAGCTTGTGGGTGTGGACTTGAACACTGATGAACCAATGGTAGCAGCAGA
AGCAGGCATATGGGATAAGTACTGTGTAAAGAAACAGCTTCTTCACTCCTGCACTGTGATTGCCACCAACATTCTCCTGG
TTGATGAGATCATGAGAGCTGGAATGTCTTCTCTAAAAGGT
ORF - retro_btau_875 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.92 % |
| Parental protein coverage: | 52.92 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | KTAEEKEKLVKAERKFIEDRVQKIIDLKDKVCAQSNKGFVVINQKGIDPFSLDALAKHGILALRRAKRRN |
| K...E.EKLVKAERKFIEDRV.KIIDLK.KVC..S.KGFVVI.QKGIDPFSLDALAK.GI.ALRRAKRRN | |
| Retrocopy | KSTKEREKLVKAERKFIEDRVKKIIDLKKKVCVDSDKGFVVISQKGIDPFSLDALAKEGIIALRRAKRRN |
| Parental | MERLSLACGGVAVNSVEDLSVDCLGHAGLVYEYTLGEEKYTFIEDCINPRSVTLLVKGPNKHTLTQIKDA |
| MERL.LACGG.A.NS..DL..DCLGHAGLVYEYTLGEEK.TFIE.C.NPRSVTLL.KGPN.HT.TQI.D. | |
| Retrocopy | MERLTLACGGIALNSLNDLNPDCLGHAGLVYEYTLGEEKFTFIERCNNPRSVTLLIKGPNEHTFTQIEDV |
| Parental | VRDGLRAIKNAIEDGC-VVPGAGAVEV-AIAEALVTYKHTIQGRARLGVQAFADALLIIPKVLAQNSGYD |
| .RDGLRA..NA..DGC..VPGAGAV.V.A.AEALV.Y.....GRA.LGVQAFADALLIIPKVLAQNSG.D | |
| Retrocopy | IRDGLRAV*NATDDGC<LVPGAGAVDV<AMAEALVKYMPSVKGRAQLGVQAFADALLIIPKVLAQNSGFD |
| Parental | LQETLVKVQAEHSNSKQPVGIDLNTGEPMVAADAGVWDNYCVKKQLLHSCTVIATNILLVDEIMRAGMSS |
| LQETLVK.QAEHS.S.Q.VG.DLNT.EPMVAA.AG.WD.YCVKKQLLHSCTVIATNILLVDEIMRAGMSS | |
| Retrocopy | LQETLVKIQAEHSESSQLVGVDLNTDEPMVAAEAGIWDKYCVKKQLLHSCTVIATNILLVDEIMRAGMSS |
| Parental | LKG |
| LKG | |
| Retrocopy | LKG |
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 .50 RPM | 2 .16 RPM |
| ERP005899_muscle | 2 .38 RPM | 0 .69 RPM |
| SRP017611_brain | 3 .20 RPM | 1 .19 RPM |
| SRP017611_kidney | 3 .67 RPM | 1 .84 RPM |
| SRP017611_liver | 2 .64 RPM | 0 .38 RPM |
| SRP030211_testis | 2 .70 RPM | 143 .87 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_875 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_875 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_875 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 | ENSBTAG00000020338 | 1 retrocopy |
retro_btau_875 ,
|
| Canis familiaris | ENSCAFG00000018298 | 1 retrocopy |