RetrogeneDB ID: | retro_btau_748 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 19:3972274..3973002(+) | ||
| Located in intron of: | ENSBTAG00000036115 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSBTAG00000036115 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_btau_748
TTACAAACCTACTATAAATCAAATTCCAAACAGGCCATCCCCAACTTTTAGTAAGAATGCAAAGAAGACTTGGAATTAAT
AATGTGTCTCTAATATCTTCATTAGTTCAAGATAACAAGACGTATGTTAAAGCAAGGGTCAACAAAGATGATCATAACTC
TGACTTTCTTTGAGAAACGAGTGGAGAGAGTGCATTTTCAGCCTCCAGAACTTTAAATGTGCCATACATACCAAAGCCTC
ATAGCAGCCAGATATTTGCTAATACAAGCGCTGTAAGTCCATGTGACTTACCTTCCCCATCACCAATATCACTTAGACAA
ACAGACCAGATTGTAGTAGATCAACCTGCTGTTTTTAAAACACTGAGCATTTTTAATTGGCACTCACAAAGCAGCTACAC
TCAGGTAAATGGCCACGTTGAGGACTTCGCTACTACAACTACATCTACTTCTCAGAACCACATTGTGTCTCCATTACAAA
TCAGTTATTCCAGACTGATGGTGGAATCTTCTAAATTTCCAGTCACATATAGCAATATGTCAGCACATGACAGCCCTTTT
CCTATCCTGCAAGAGACAGGCAACTCATGGTCCTCAATGTCAATGATCGCTTATACATCTGCCTCCTCTCTTTCAAGTCA
ACTGATCAACAATCATCATCAGATGAAAACTATGCTAATTAAAACTGACCTATCAAATAAGTGTCAGATTATGGAGCCTA
AAGAAGAT
ORF - retro_btau_748 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.34 % |
| Parental protein coverage: | 59.18 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LQTYYKSNSKQ-GHPQLLVRMQRRLGINNVSLISSLVQDNKTYVKARVNKDDHNSDFLRETSGESAFSAS |
| LQTYYKSNSKQ.GHPQLLVRMQRRLGINNVSLISSLVQDNKTYVKARVNKDDHNSDFL.ETSGESAFSAS | |
| Retrocopy | LQTYYKSNSKQ<GHPQLLVRMQRRLGINNVSLISSLVQDNKTYVKARVNKDDHNSDFL*ETSGESAFSAS |
| Parental | RTLNVPYIPKPHSSQIFDNTSAVSPCDLPSPSPISLRQTDQIVVDQPAVFKTLSIFNWHSHSSYTQVNGH |
| RTLNVPYIPKPHSSQIF.NTSAVSPCDLPSPSPISLRQTDQIVVDQPAVFKTLSIFNWHS.SSYTQVNGH | |
| Retrocopy | RTLNVPYIPKPHSSQIFANTSAVSPCDLPSPSPISLRQTDQIVVDQPAVFKTLSIFNWHSQSSYTQVNGH |
| Parental | VEDFATTTTSTSQNHIVSPLQSSYSGLMVESSKFPVTYSNINMSAHDSPFPILQETGNSWSSMSMIAYTS |
| VEDFATTTTSTSQNHIVSPLQ.SYS.LMVESSKFPVTYS..NMSAHDSPFPILQETGNSWSSMSMIAYTS | |
| Retrocopy | VEDFATTTTSTSQNHIVSPLQISYSRLMVESSKFPVTYS--NMSAHDSPFPILQETGNSWSSMSMIAYTS |
| Parental | ASSLSSQLINNHHQMKAMLIKTDLSNKCQIMEPKED |
| ASSLSSQLINNHHQMK.MLIKTDLSNKCQIMEPKED | |
| Retrocopy | ASSLSSQLINNHHQMKTMLIKTDLSNKCQIMEPKED |
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 .00 RPM |
| ERP005899_muscle | 0 .00 RPM | 0 .00 RPM |
| SRP017611_brain | 0 .00 RPM | 0 .00 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .00 RPM |
| SRP030211_testis | 0 .04 RPM | 0 .08 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_748 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_748 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_748 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000036115 | 3 retrocopies |
retro_btau_549, retro_btau_681, retro_btau_748 ,
|