RetrogeneDB ID: | retro_btau_1398 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 5:95726013..95727669(+) | ||
| Located in intron of: | ENSBTAG00000015562 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BT.63577 | ||
| Ensembl ID: | ENSBTAG00000019892 | ||
| Aliases: | None | ||
| Description: | hyaluronan synthase 2 [Source:RefSeq peptide;Acc:NP_776504] |
Retrocopy-Parental alignment summary:
>retro_btau_1398
ATGCACTGTGGGAGGTTACTATGTATCCTGAGAATAATTGGAACCACACTTTTTGGAGTTTCTCTCCTCTTTGGAATCAC
AGCTGCTTATATTGTTGGCTACCAATTTTTCCAAACGGATAATTACTATTTCTCTTTTGGGCTATACGGTGCAGTTTTAG
TATCACACCTCGTCATCCAAAGCCTGTTTGCCTTTTTGGAGCACCAGAAAATGAAAAAATCTCTAGAAACCCCCGTTAAG
TTGAACAAAACTGTTGCTCTTTGCATTGCCGCATATCAAGAAGATCCAGGCTACTTACGGAAATGTTTGCAATCTGTGAA
AAGGCTAACCTACCCCAGCATTAAAGTTGTCATGGTCATAGATGGAAACTCAGAAGATGACCTTTACATGATGGACATCT
TCAGTGAAGTCATGGGCAGGGACATGTCAGCCACGTATATCTGGAAGAGCAACTTCCACATGAAGGGTCCTGGTGAGAGA
AATGAGTCACATAAAGAGAGCTCACAACATGTCACCCAGTTGGTCTTGTCCAGCAAGAATATCTGCATCATGCAAAAATG
GGGTGGTAAAAGAGAAGTCATGTACACGGCTTTCAGAGCACTGGGACGGAGTGTGGATTATGTACAGGTCTGTGATTCAG
ACACCATACTTGACCCTGCCTCATCGGTGGAGATGGTAAAGGTTTTAGAAGAAGATCCCATGGTTGGAGGTGTTGGAGGA
GATGTCCAGATTTTAAACAAGTATGATTCCTGGATATCTTTCCTCAGCAGTGTGAGATACTGGATGGCTTTTAACATAGA
AAGAGCCTGTCAGTCTTATTTTGGCTGTGTCCAGTGCATTAGCGGACCCCTAGGAATGTACCGAAACTCCTTACTGCAGG
AATTTGTGGAAGACTGGTACAATCAAGAATTTATGGGCAGCCATTGTAGTTTCGGAGATGACAGGCACCTAACGAACCGA
GTGCTGAGTCTGGGCTATGCAACGAAATACACAGCTCGATCCAAGTGCCTTACTGAAACACCTAAGGAATATCTCAGATG
GTTAAACCAGCAGACCCGTTGGAGCAAGTCCTACTTCCGAGAGTGGCTGTACAATGCGATGTGGTTCCACAAACATCACC
TGTGGATGACCTATGAAGCCGTCATCACTGGGTTCTTCCCTTTCTTTCTCATTGCCACAGTAATCCAGCTCTTCTACAGG
GGTAAAACTTGGAACATACTCCTCTTCCTCTTAACTGTCCAGTTAGTGGGTCTCATAAAATCATCTTTTGCCAGCTGCCT
TAGAGGAAACACCATCATGGTCTTCATGTCCCTCTACTCCATGTTATACATGTCAAGTTTACTTCCCGCCAAGATGTTTG
CAATTGCAACGATTAACAAAGCTGGGTGGGGTACTTCTGGAAGGAAGACCATTGTTGTTAATTTAATAGGACTCATCCCT
GTAACAATTTGGTTCACAATCCTCCTGGGTGGTGTGGTTTTCACCATTTATATGGAATCTAAAAAGCCATTCTCAGAATC
GAAACAGACAGTTGTAATTGTAGGAACATTGCTGTATGTATGCTACTGGGTCCTGTTTTTGACACTGTATGTGGTTGTCA
TCAAGAAGTGTGGCAGGCAGAGGAAGGGACCACAGTACAGCGTGGCGCTTGATGTA
ORF - retro_btau_1398 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.03 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MHCERFLCILRIIGTTLFGVSLLLGITAAYIVGYQFIQTDNYYFSFGLYGAFLASHLIIQSLFAFLEHRK |
| MHC.R.LCILRIIGTTLFGVSLL.GITAAYIVGYQF.QTDNYYFSFGLYGA.L.SHL.IQSLFAFLEH.K | |
| Retrocopy | MHCGRLLCILRIIGTTLFGVSLLFGITAAYIVGYQFFQTDNYYFSFGLYGAVLVSHLVIQSLFAFLEHQK |
| Parental | MKKSLETPIKLNKTVALCIAAYQEDPDYLRKCLQSVKRLTYPGIKVVMVIDGNSEDDLYMMDIFSEVMGR |
| MKKSLETP.KLNKTVALCIAAYQEDP.YLRKCLQSVKRLTYP.IKVVMVIDGNSEDDLYMMDIFSEVMGR | |
| Retrocopy | MKKSLETPVKLNKTVALCIAAYQEDPGYLRKCLQSVKRLTYPSIKVVMVIDGNSEDDLYMMDIFSEVMGR |
| Parental | DKSATYIWKNNYHVKGPGETDESHKESSQHVTQLVLSNKSICIMQKWGGKREVMYTAFRALGRSVDYVQV |
| D.SATYIWK.N.H.KGPGE..ESHKESSQHVTQLVLS.K.ICIMQKWGGKREVMYTAFRALGRSVDYVQV | |
| Retrocopy | DMSATYIWKSNFHMKGPGERNESHKESSQHVTQLVLSSKNICIMQKWGGKREVMYTAFRALGRSVDYVQV |
| Parental | CDSDTMLDPASSVEMVKVLEEDPMVGGVGGDVQILNKYDSWISFLSSVRYWMAFNIERACQSYFGCVQCI |
| CDSDT.LDPASSVEMVKVLEEDPMVGGVGGDVQILNKYDSWISFLSSVRYWMAFNIERACQSYFGCVQCI | |
| Retrocopy | CDSDTILDPASSVEMVKVLEEDPMVGGVGGDVQILNKYDSWISFLSSVRYWMAFNIERACQSYFGCVQCI |
| Parental | SGPLGMYRNSLLHEFVEDWYNQEFMGSQCSFGDDRHLTNRVLSLGYATKYTARSKCLTETPIEYLRWLNQ |
| SGPLGMYRNSLL.EFVEDWYNQEFMGS.CSFGDDRHLTNRVLSLGYATKYTARSKCLTETP.EYLRWLNQ | |
| Retrocopy | SGPLGMYRNSLLQEFVEDWYNQEFMGSHCSFGDDRHLTNRVLSLGYATKYTARSKCLTETPKEYLRWLNQ |
| Parental | QTRWSKSYFREWLYNAMWFHKHHLWMTYEAVITGFFPFFLIATVIQLFYRGKIWNILLFLLTVQLVGLIK |
| QTRWSKSYFREWLYNAMWFHKHHLWMTYEAVITGFFPFFLIATVIQLFYRGK.WNILLFLLTVQLVGLIK | |
| Retrocopy | QTRWSKSYFREWLYNAMWFHKHHLWMTYEAVITGFFPFFLIATVIQLFYRGKTWNILLFLLTVQLVGLIK |
| Parental | SSFASCLRGNIVMVFMSLYSVLYMSSLLPAKMFAIATINKAGWGTSGRKTIVVNFIGLIPVSVWFTILLG |
| SSFASCLRGN..MVFMSLYS.LYMSSLLPAKMFAIATINKAGWGTSGRKTIVVN.IGLIPV..WFTILLG | |
| Retrocopy | SSFASCLRGNTIMVFMSLYSMLYMSSLLPAKMFAIATINKAGWGTSGRKTIVVNLIGLIPVTIWFTILLG |
| Parental | GVIFTIYKESKKPFSESKQTVLIVGTLLYACYWVMLLTLYVVLINKCGRRKKGQQYDMVLDV |
| GV.FTIY.ESKKPFSESKQTV.IVGTLLY.CYWV..LTLYVV.I.KCGR..KG.QY...LDV | |
| Retrocopy | GVVFTIYMESKKPFSESKQTVVIVGTLLYVCYWVLFLTLYVVVIKKCGRQRKGPQYSVALDV |
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 .16 RPM | 2 .48 RPM |
| SRP017611_brain | 0 .00 RPM | 0 .82 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .77 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .00 RPM |
| SRP030211_testis | 0 .10 RPM | 0 .41 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1398 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1398 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1398 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 | ENSBTAG00000019892 | 1 retrocopy |
retro_btau_1398 ,
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