RetrogeneDB ID: | retro_btau_1023 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 23:27835638..27836363(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RRAGC | ||
| Ensembl ID: | ENSBTAG00000009368 | ||
| Aliases: | None | ||
| Description: | ras-related GTP-binding protein C [Source:RefSeq peptide;Acc:NP_001069924] |
Retrocopy-Parental alignment summary:
>retro_btau_1023
AACTTTACCATTTCTAAAGCCTACAAAGTTAACATAGACATGAATTTTGAGGTTTTTATTCACAAAGTTGATGGTCTGTC
TGATGATTACAAAATATAAACACAGAGGGACATTCATCAATGGGCCAATGATGACCTTGCAGATGCTGGGCTAGAAAAAC
TCCATCTTAGCTTTTATTTTACTAGTATTTATGACCATTCAACATTTGCAGCCTTTAGTAAGGTGCTGCAGAAACTATCC
CACAGCTACTGGCCTTGGAATACCTATTAAATACCTTTATATCAAATTCAGGTATTGAAAAAGCTTTTCTCTTTGATGTT
GTCAGCAAAATCTACATTACAACAGATAGTTCTCCTGTAGATATGCAGTCACAGGAACTTTGCTGTGACATGATTGATAT
TGTAATTGATGTGTGTTGTATGTTTGGGTTAAAGGAAAATAGAAGTGGAAGTGCTTACCACAAAGAGTCCAAGGCCATCA
TCAAGCTGAATAACACAACTGTCCTGTATTTAAAGGAGGTAACTAAATTTTTGGCACTGGTTTGCATCCATAGGGAAGAA
AGTTTTGAATGAAAAAGTTTAATAGACTATAACTTCCATTGTTTCCGAAAAGCTATTCATGAGGTTTTTGAGGTGGGTGT
GACTTCTCACAGAAGCTGTGGTCACCAGACCAGTGTCCCCAACCTGAAAGCTTTGACACGCAATTGCACACCATGAAACG
TCATC
ORF - retro_btau_1023 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.19 % |
| Parental protein coverage: | 60.65 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | HITVSKAYKVNPDMNFEVFIHKVDGLSDDHKIETQRDIHQRANDDLADAGLEKLHLSFYLTSIYDHSIFE |
| ..T.SKAYKVN.DMNFEVFIHKVDGLSDD.KI.TQRDIHQ.ANDDLADAGLEKLHLSFY.TSIYDHS.F. | |
| Retrocopy | NFTISKAYKVNIDMNFEVFIHKVDGLSDDYKI*TQRDIHQWANDDLADAGLEKLHLSFYFTSIYDHSTFA |
| Parental | AFSKVVQKL-IPQLPTLENLLNIFISNSGIEKAFLFDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDVS |
| AFSKV.QKL.IPQL..LE.LLN.FISNSGIEKAFLFDVVSKIYI.TDSSPVDMQS.ELCCDMID.VIDV. | |
| Retrocopy | AFSKVLQKL<IPQLLALEYLLNTFISNSGIEKAFLFDVVSKIYITTDSSPVDMQSQELCCDMIDIVIDVC |
| Parental | CIYGLKEDGSGSAYDKESMAIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYNFHCFRKAIHEV |
| C..GLKE..SGSAY.KES.AIIKLNNTTVLYLKEVTKFLALVCI.REESFE.K.LIDYNFHCFRKAIHEV | |
| Retrocopy | CMFGLKENRSGSAYHKESKAIIKLNNTTVLYLKEVTKFLALVCIHREESFE*KSLIDYNFHCFRKAIHEV |
| Parental | FEVGVTSHRSCSHQTSAPSLKALTHNGTPRNAI |
| FEVGVTSHRSC.HQTS.P.LKALT.N.TP.N.I | |
| Retrocopy | FEVGVTSHRSCGHQTSVPNLKALTRNCTP*NVI |
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 | 10 .45 RPM |
| ERP005899_muscle | 0 .00 RPM | 19 .27 RPM |
| SRP017611_brain | 0 .00 RPM | 19 .28 RPM |
| SRP017611_kidney | 0 .00 RPM | 29 .52 RPM |
| SRP017611_liver | 0 .00 RPM | 6 .42 RPM |
| SRP030211_testis | 0 .01 RPM | 22 .26 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1023 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1023 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1023 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000009368 | 2 retrocopies |
retro_btau_1023 , retro_btau_851,
|
| Bos taurus | ENSBTAG00000018438 | 1 retrocopy | |
| Microcebus murinus | ENSMICG00000006241 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000017710 | 1 retrocopy |