RetrogeneDB ID: | retro_btau_1271 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 3:43241180..43242539(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ARID3A | ||
| Ensembl ID: | ENSBTAG00000008607 | ||
| Aliases: | None | ||
| Description: | AT-rich interactive domain-containing protein 3A [Source:RefSeq peptide;Acc:NP_001192624] |
Retrocopy-Parental alignment summary:
>retro_btau_1271
GAGGAGGAGGAGCTGGAGGAAGACCTGAGGGACGACAAAGAGGACGAGGAGGATGAGGACTATGAGGATGAGGAGGGGCT
TGGGCCCCGGGGCACCGCCAGCCTGGGCCCCTCAGCCCTGTTCCCCCACAAGGCTCAGCTGCTCCAAGCCTTCCGCCCGG
ACAGTGGATCCCGGCACTGGGTGGCCAGGAGCACCCGGGAACTGGCCCGGCTGTCCCCGGAGGGGTTGCCCGTCCTGCAC
CTCAGCTGCAGCCACCAGACCACGGGGACTGGACATATGAGGAGCAGTTCAAGCAGCTGTATAAACTGGACGCAAACCAC
AAGAGGAAGGAGTTCCTGGATGACTTGTTCAGTTTCATGCAGAAGCGAGGGACACCTGTGAACCGCATCCCATCGTGGCA
AAGCAGGTGCTCGACCTGTTCATGTTGTATGTGCCGGTGATGGAGAAGGGCAACCTGGTGGAGGTCATCAACAAGAAGCC
GTGGCGGGAGATTACCAAAGGACTGAACCTGCCCACATCCATCACCAGTGCTGCCTTCATGCTGCGAACCCAGTATATGA
AGTACCTGTACCCCTAGGAGTGTGAGAAGAGTGGCCTCAGCAACCCCAACCAGCTCCAGGCAGCCATCGGCAGCAATCGG
AGGGAGGGCCAGCACCAGAGCTTTGGGGGCTCCCTCTTTGCCTACTTGCCGGCCGGGGCCCACAGCATGCGGTCCTCGCC
CAAGCTGCCTGTGTCCTCCCTGGGCCTGGCCACCAGCACCAATGGCAGCTCCATCACCCCAGCCCCCAAGGTCAAGAAAG
AGGAGGATGTGGCCATCCCCATCACAGTCCCCAGCTGCCTGCCAGTCTCCCTGGTCACCCAGTGGTGGTGGCCCAGGCAG
CAGCAGCCCAAGCGGCCGTAGCAGCACAGGTGGCTGCCTTGGAGCAGCTTCAGGAGAAACTGGAGTATGGGGAACCTCCT
GAGAAGAAAATGGCCCTAGTGGCAGAGGAGCAGCAGCAGCTGATGCAGCAGGCACTTCAGCAGAACTTCCTGGCCATGAC
GGCACAGCTGCCCATGAGCGTCCATGAGATCAACAGCCAAGCCTCTGAGAGCAACCAGGACTCAGCTACGAACCTGACCA
GCACCAACGACAGCAAGAGTATTGACATGTCAGGAGAGATTAACGGAATCATGTACACAGGAGTGCTGTTCGACCAGCTG
CCGGCCTCCACGCCACGCTCCGCTCCCAGCAAAGGTGGAGGCGGCAGCAGCCGGGGAGGAAACAGCGGGACCCACAGCAG
CAGCAGCCGTGCAGGCAGCTAGGCAGGGCCAGCAGGGATGTCTGCACTCCCGACAGCCACCTCAAACACTCTCCATCCT
ORF - retro_btau_1271 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.7 % |
| Parental protein coverage: | 77.12 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | EEEELEEDLGDDEEDEEDEDYEDEEGLGPPGAASLGPAALFPRKAQPLQAFRGDSGSR-ALGGQERPGTG |
| EEEELEEDL.DD.............GLGP.G.ASLGP.ALFP.KAQ.LQAFR.DSGSR.ALGGQE.PGTG | |
| Retrocopy | EEEELEEDLRDDKXXXXXXXXXXXXGLGPRGTASLGPSALFPHKAQLLQAFRPDSGSR<ALGGQEHPGTG |
| Parental | PAVPGGAAHAAPQLQPPDHGDWTYEEQFKQLYELDADPKRKEFLDDLFSFMQKRGTPVNRIP-IMAKQVL |
| PAVPGG.A..APQLQPPDHGDWTYEEQFKQLY.LDA..KRKEFLDDLFSFMQKRGTPVNRIP.I.AKQVL | |
| Retrocopy | PAVPGGVARPAPQLQPPDHGDWTYEEQFKQLYKLDANHKRKEFLDDLFSFMQKRGTPVNRIP<IVAKQVL |
| Parental | DLFMLYVLVTEKGGLVEVINKKLWREITKGLNLPTSITSAAFTLRTQYMKYLYPYECEKRGLSNPNELQA |
| DLFMLYV.V.EKG.LVEVINKK.WREITKGLNLPTSITSAAF.LRTQYMKYLYP.ECEK.GLSNPN.LQA | |
| Retrocopy | DLFMLYVPVMEKGNLVEVINKKPWREITKGLNLPTSITSAAFMLRTQYMKYLYP*ECEKSGLSNPNQLQA |
| Parental | AIDSNRREGRRQSFGGSLFAYSPGGAHSMLSSPKLPVSSLGLAASTNGSSITPAPKIKKEEDAAIPITVP |
| AI.SNRREG..QSFGGSLFAY.P.GAHSM.SSPKLPVSSLGLA.STNGSSITPAPK.KKEED.AIPITVP | |
| Retrocopy | AIGSNRREGQHQSFGGSLFAYLPAGAHSMRSSPKLPVSSLGLATSTNGSSITPAPKVKKEEDVAIPITVP |
| Parental | GRLPVSLAGH-PVVAAQAVAAQAAVAAQAAALEQLREKLESGEPPEKKMALVAEEQQRLMQRALQQNFLA |
| ..LPVSL.....VVA.QA.AAQAAVAAQ.AALEQL.EKLE.GEPPEKKMALVAEEQQ.LMQ.ALQQNFLA | |
| Retrocopy | SCLPVSLVTQ<VVVA-QAAAAQAAVAAQVAALEQLQEKLEYGEPPEKKMALVAEEQQQLMQQALQQNFLA |
| Parental | MTAQLPMSI-RINSQASESRQDSAANLTSTNGSNSISMSVEINGIMYTGVLFAQPPAPTPPSAPSKGGGS |
| MTAQLPMS...INSQASES.QDSA.NLTSTN.S.SI.MS.EINGIMYTGVLF.Q.PA.TP.SAPSKGGG. | |
| Retrocopy | MTAQLPMSVHEINSQASESNQDSATNLTSTNDSKSIDMSGEINGIMYTGVLFDQLPASTPRSAPSKGGGG |
| Parental | SSRGGNSGTNSSSSSSAGSQAGPAGMSAPPTSTSNNSLP |
| SSRGGNSGT..SSSS.AGS.AGPAGMSA.PT.TSN...P | |
| Retrocopy | SSRGGNSGTH-SSSSRAGS*AGPAGMSALPTATSNTLHP |
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 .07 RPM | 0 .14 RPM |
| ERP005899_muscle | 0 .00 RPM | 8 .60 RPM |
| SRP017611_brain | 0 .00 RPM | 2 .06 RPM |
| SRP017611_kidney | 0 .18 RPM | 4 .09 RPM |
| SRP017611_liver | 0 .00 RPM | 8 .23 RPM |
| SRP030211_testis | 5 .53 RPM | 69 .87 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1271 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1271 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1271 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000008607 | 1 retrocopy |
retro_btau_1271 ,
|