RetrogeneDB ID: | retro_btau_849 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 2:2319072..2319443(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ARPC4 | ||
| Ensembl ID: | ENSBTAG00000007964 | ||
| Aliases: | None | ||
| Description: | Actin-related protein 2/3 complex subunit 4 [Source:UniProtKB/Swiss-Prot;Acc:Q148J6] |
Retrocopy-Parental alignment summary:
>retro_btau_849
AAAGAGCTCATTCTACAACCCATGACCATCAGCAGGACTGAGAAGGAAAAGATTCTGATGAAATGCTCCATCAACTCTGT
CAGGGTCAGCATTGCTGCGAAACAGGCTGATAAAACAGAGTCGATTCTAGGTCACAAGTTCAGGCACCTCATCATGATGC
GAGCAGAGAGCTTCTTTATCCTCTGAAGGAAACCAGTGGAGGGGATGACATCAGCTTTCTGTTCACCAACTTCCACACAG
AGCAGATGTATAAACACAAGTTTGTGGACTTTGTGATCCCCTTCATGGAAGAAATTGACAAGGAGATCAATGAGATAAAG
CCGTTGGTCAATGCCTGTGAGCGCTTTGTGGTGGAGGAGTTCCTCAAGAAT
ORF - retro_btau_849 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.2 % |
| Parental protein coverage: | 73.81 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | KELLLQPVTISRNEKEKVLIEGSINSVRVSIAVKQADEIEKILCHKFMRFMMMRAENFFILRRKPVEGY- |
| KEL.LQP.TISR.EKEK.L...SINSVRVSIA.KQAD..E.IL.HKF....MMRAE.FFIL.RKPVEG.. | |
| Retrocopy | KELILQPMTISRTEKEKILMKCSINSVRVSIAAKQADKTESILGHKFRHLIMMRAESFFIL*RKPVEGM< |
| Parental | DISFLITNFHTEQMYKHKLVDFVIHFMEEIDKEISEMKLSVNARARIVAEEFLKN |
| DISFL.TNFHTEQMYKHK.VDFVI.FMEEIDKEI.E.K..VNA..R.V.EEFLKN | |
| Retrocopy | DISFLFTNFHTEQMYKHKFVDFVIPFMEEIDKEINEIKPLVNACERFVVEEFLKN |
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 | 15 .72 RPM |
| ERP005899_muscle | 0 .00 RPM | 67 .25 RPM |
| SRP017611_brain | 0 .00 RPM | 36 .63 RPM |
| SRP017611_kidney | 0 .00 RPM | 49 .91 RPM |
| SRP017611_liver | 0 .00 RPM | 18 .73 RPM |
| SRP030211_testis | 0 .00 RPM | 27 .68 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_849 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_849 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_849 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000007964 | 2 retrocopies |
retro_btau_680, retro_btau_849 ,
|
| Callithrix jacchus | ENSCJAG00000016175 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000025088 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000005136 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000026074 | 2 retrocopies |