RetrogeneDB ID: | retro_btau_1829 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | X:79694992..79696162(-) | ||
| Located in intron of: | ENSBTAG00000038434 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BT.87407 | ||
| Ensembl ID: | ENSBTAG00000037935 | ||
| Aliases: | None | ||
| Description: | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 [Source:RefSeq peptide;Acc:NP_001033648] |
Retrocopy-Parental alignment summary:
>retro_btau_1829
AAAAAAACGATGGCTGACAAAATTCTATCTCAAAGGATTCATGAAATGGTACCAGAATCCTAAGCCTATATGGATATCTT
GGCTTTTGAAAGGAAACTGGACCAGACTATTGTGAGCAAACGGCTAGGTATCCAGGAAGCCTTGAAACGTTCCATCAAGC
AAAAACAAAAGCTGTGAATTTTCATTTCTAACACTTTCAATCTGGCTAAGTCAGATGCCAAGGATGGAGAAGGGACAATG
GCTTCCTGGGAGCTTCAGGTAGAAGGACGGCTCCTGGAGGATTCAGCCTTGTCCAAATATGATGCCACCAAACAAAAGAG
GAAGTTCTCTTCTTTTAAGTCCTTGGTAATCAAACTGGACAAAGACTTGTATGGACCAGACAACCATCTGGTAGAATGGC
ACAAGACCACCACTACCCAGGAGATGGATGGCTTCCAGGTGAAATAGCCAGGAGATGTGAATATACGGTGTACTGTCCTG
TTGATACTGAATTACCAGCCTCCTCAGTTTAAATTAGACCTTTGTCTGGCTTGGTTCCTGGGCATCCACACCCAGACCTG
TCCAGTGATCATTCAAGCACTGTGGCAATATATTAAGACACATAAGCTCCAGGACAGACATGAGCGGGAGTTTGTCATCT
CTGACAAGTACCTCCAGCAGATCTTTGATTCTCAATGTATGAAGTTTTCAGAGGTCCCCCAACAGCCCCATGCCTTGCTT
ATGACACCTGAGCCCATCATCATTAATCATGTCATCAGTGTTGACCCGAATGATCAGAAAAAGACAGCTTGTTATGACAC
TGATGTGAAAGTGGATGATACCTTGAAAACCCAGATGAATTCTCTTTTGCTGTCTACTGCTAGCCAGCAGGAGATTGCTA
CTCTAGACAACAAGATCCATGAGACAACAGAAACTATCAGTCTGCTGAAGACCCAGCAAGAGTTCTTGCTGAGCTTTGCC
AAAGACCCTCAAGGTTTCATCAGTGACTTGCTTCAGTCCCAGTGCCGGGACCTCAAGACCATGACTGATATGGTGGGTAA
CCCAGAGGAGGAACACTGAGCAGAATTCTACTTCCAGCCTTGGGCCCAGGAAGCTGTGTGCCGATATTTCTACTCCAAGG
TGCAGCAGAGATGACAAAAATTAGAGCAAGCCCTGGGAATCCAAAATACA
ORF - retro_btau_1829 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.42 % |
| Parental protein coverage: | 75.92 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | KKKMADKILPQRIRELVPESQAYMDLLAFERKLDQTIMRKRLDIQEALKRPIKQKRKLRIFISNTFNPAK |
| KK.MADKIL.QRI.E.VPES.AYMD.LAFERKLDQTI..KRL.IQEALKR.IKQK.KL.IFISNTFN.AK | |
| Retrocopy | KKTMADKILSQRIHEMVPES*AYMDILAFERKLDQTIVSKRLGIQEALKRSIKQKQKL*IFISNTFNLAK |
| Parental | SDAEDGEGTVASWELRVEGRLLEDSALSKYDATKQKRKFSSFFKSLVIELDKDLYGPDNHLVEWHRTATT |
| SDA.DGEGT.ASWEL.VEGRLLEDSALSKYDATKQKRKFSSF.KSLVI.LDKDLYGPDNHLVEWH.T.TT | |
| Retrocopy | SDAKDGEGTMASWELQVEGRLLEDSALSKYDATKQKRKFSSF-KSLVIKLDKDLYGPDNHLVEWHKTTTT |
| Parental | QETDGFQVKRPGDVNVRCTVLLMLDYQPPQFKLDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHER |
| QE.DGFQVK.PGDVN.RCTVLL.L.YQPPQFKLD..LA..LGIHTQT.PVIIQALWQYIKTHKLQD.HER | |
| Retrocopy | QEMDGFQVK*PGDVNIRCTVLLILNYQPPQFKLDLCLAWFLGIHTQTCPVIIQALWQYIKTHKLQDRHER |
| Parental | EFVICDKYLQQIFESQRMKFSEIPQRLHALLMPPEPIIINHVISVDPNDQKKTACYDIDVEVDDTLKTQM |
| EFVI.DKYLQQIF.SQ.MKFSE.PQ..HALLM.PEPIIINHVISVDPNDQKKTACYD.DV.VDDTLKTQM | |
| Retrocopy | EFVISDKYLQQIFDSQCMKFSEVPQQPHALLMTPEPIIINHVISVDPNDQKKTACYDTDVKVDDTLKTQM |
| Parental | NSFLLSTASQQEIATLDNKIHETIETINQLKTQREFMLSFARDPQGFINDWLQSQCRDLKVMTDVVGNSE |
| NS.LLSTASQQEIATLDNKIHET.ETI..LKTQ.EF.LSFA.DPQGFI.D.LQSQCRDLK.MTD.VGN.E | |
| Retrocopy | NSLLLSTASQQEIATLDNKIHETTETISLLKTQQEFLLSFAKDPQGFISDLLQSQCRDLKTMTDMVGNPE |
| Parental | EERRAEFYFQPWAQEAVCRYFYSKVQQRRQELEQALGIRNT |
| EE..AEFYFQPWAQEAVCRYFYSKVQQR.Q.LEQALGI.NT | |
| Retrocopy | EEH*AEFYFQPWAQEAVCRYFYSKVQQR*QKLEQALGIQNT |
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 | 3 .32 RPM |
| ERP005899_muscle | 0 .05 RPM | 10 .77 RPM |
| SRP017611_brain | 0 .00 RPM | 34 .35 RPM |
| SRP017611_kidney | 0 .06 RPM | 16 .95 RPM |
| SRP017611_liver | 0 .00 RPM | 3 .40 RPM |
| SRP030211_testis | 0 .00 RPM | 19 .02 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1829 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1829 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1829 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000037935 | 1 retrocopy |
retro_btau_1829 ,
|
| Tursiops truncatus | ENSTTRG00000001010 | 2 retrocopies |