RetrogeneDB ID: | retro_btau_1479 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 6:12264615..12266077(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BT.68997 | ||
| Ensembl ID: | ENSBTAG00000020308 | ||
| Aliases: | None | ||
| Description: | eukaryotic translation initiation factor 4 gamma 2 [Source:RefSeq peptide;Acc:NP_001093329] |
Retrocopy-Parental alignment summary:
>retro_btau_1479
GTGGAGAATGCGATCGCAGAAGTGGGTGCTTCTCGTTTCAGCGCTTCTTCGGGCGGAGGAGGAAGTAGGGGTGCACCTCA
GCACTATCCCAAGACTGCTGGTAACAGCGAGTTCCCAGGGGAAACCCCAGGGCAAAACGCTCAGAAATGGATTCCTGCAC
GAAGCCCTAGACGAGATGACAACTCCGCAGCAAACAACTCCGCAAATGAAAAAGAACGACATGATGCAATCTTCAGGAAA
GTAAGGGCATATTAAACAAGCTTACTCCTGAGAAGTTTGACAAGCTATGCCTTGAGCTCCTCAGTGTGGGTGTAGAGTCT
AAACTCATCCTTAAAGGGGTCATACAGCTGATTGTGGACAAAGCCCTAGAAGAGCCAAAGTATAGCTCACTGTATGCTCA
GCTATGTCTGCGATTGGCAGAAGATGCACCAAAAAACTTTGATGGCCCAGCAGCAGAGGGTCAACCAGGACAGAAGCAAA
GCACAACATTCAGATGCCTCCTAATTTCCAAATTACAAGATGAATTTGAAAACCAAACCAGAAATGTTGATGTCTATGAT
AAGCGTGAAAATCCCCTCCTCCCTGAGGAGGAGGAACAGAGAGCTATTGCCAACATCAAGATGTTGGGGAACATCATATT
CATTGGAGAACTTGGAAAGCTTGATCTTATTCATGAATCTATCCTTCATAAGTGCATCAAAACACTTTTGGAAAAAAAGA
AGAGAGTCCAACTCAAAGATATGGGAGAGGATTTGGAGTGCCTCTGTCAGATAATGAGGACAGTGGGGCCTAGATTAGAC
CATGAACGAGCCAAGCCCTTAATGGATCAGTACTTTGCCCGAATGTGCTCCTTGATGTTAAGTAAGGAACTGCTGGTGAG
GATTCGTTCCCTGCTGCAGAATGCTGTAGAGTTGCGAGAATACCATTGGGCTCCTTGCAAAGCTTTTCTTGACAATGGAC
CAAAGACGATCAATCAAATCCGTCAAGATGCAGGAAAAGATCTAGGAGTATTTATTCCTGCTCCTATGGCTCAAGGGATG
AGAAGTGACTTCTTCTGGAGGGACTGTTTATGCCACCCAGGATGAAAATAGATAGGGACCCACTTGGAGGACTTGCTGAT
ATGTTTGGACAAATGCCAGGAAGCGGAATTGGTATTGGTCCAGGAGTTATCCAGGATAGATTTTCACCCACCATGGGGCG
CCATCGTTCAAATCAGCTCTTCAGTGGCCATGGGGGACACATCATGCCTCCCACACAGTCGCAGTTTGGGGAGATGGGAG
GCAAGTTTATGAAAAGCCAGGGGCTAAGCCAGCTCTACCATAACCAGAGTCAGGGACTCTTATCCCAGCTGCAAGGACAG
TCGAAGAATATGCCACCTCGGTTTTTTAAGAAAGGACAGCTTAATGCAGATGAGGTTAGCTTGAGGCCTGCTCAGTCTTT
CCTAATGAATAAAAATCAAGTC
ORF - retro_btau_1479 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.67 % |
| Parental protein coverage: | 53.69 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | VESAIAEGGASRFSASSGGGGSRGAPQHYPKTAGNSEFLGKTPGQNAQKWIPARSTRRDDNSAANNSANE |
| VE.AIAE.GASRFSASSGGGGSRGAPQHYPKTAGNSEF.G.TPGQNAQKWIPARS.RRDDNSAANNSANE | |
| Retrocopy | VENAIAEVGASRFSASSGGGGSRGAPQHYPKTAGNSEFPGETPGQNAQKWIPARSPRRDDNSAANNSANE |
| Parental | KERHDAIFRKVR-GILNKLTPEKFDKLCLELLNVGVESKLILKGVILLIVDKALEEPKYSSLYAQLCLRL |
| KERHDAIFRKVR.GILNKLTPEKFDKLCLELL.VGVESKLILKGVI.LIVDKALEEPKYSSLYAQLCLRL | |
| Retrocopy | KERHDAIFRKVR<GILNKLTPEKFDKLCLELLSVGVESKLILKGVIQLIVDKALEEPKYSSLYAQLCLRL |
| Parental | AEDAP-NFDGPAAEGQPGQKQSTTFRRLLISKLQDEFENRTRNVDVYDKRENPLLPEEEEQRAIAKIKML |
| AEDAP.NFDGPAAEGQPGQKQSTTFR.LLISKLQDEFEN.TRNVDVYDKRENPLLPEEEEQRAIA.IKML | |
| Retrocopy | AEDAPKNFDGPAAEGQPGQKQSTTFRCLLISKLQDEFENQTRNVDVYDKRENPLLPEEEEQRAIANIKML |
| Parental | GNIKFIGELGKLDLIHESILHKCIKTLLEKKKRVQLKDMGEDLECLCQIMRTVGPRLDHERAKSLMDQYF |
| GNI.FIGELGKLDLIHESILHKCIKTLLEKKKRVQLKDMGEDLECLCQIMRTVGPRLDHERAK.LMDQYF | |
| Retrocopy | GNIIFIGELGKLDLIHESILHKCIKTLLEKKKRVQLKDMGEDLECLCQIMRTVGPRLDHERAKPLMDQYF |
| Parental | ARMCSLMLSKELPARIRFLLQDTVELREHHWVPRKAFLDNGPKTINQIRQDAVKDLGVFIPAPMAQGMRS |
| ARMCSLMLSKEL..RIR.LLQ..VELRE.HW.P.KAFLDNGPKTINQIRQDA.KDLGVFIPAPMAQGMRS | |
| Retrocopy | ARMCSLMLSKELLVRIRSLLQNAVELREYHWAPCKAFLDNGPKTINQIRQDAGKDLGVFIPAPMAQGMRS |
| Parental | DFF-LEGPFMPPRMKMDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFSPTMGRHRSNQLFNGHGGHIMPP |
| DFF.LEG.FMPPRMK.DRDPLGGLADMFGQMPGSGIG.GPGVIQDRFSPTMGRHRSNQLF.GHGGHIMPP | |
| Retrocopy | DFF<LEGLFMPPRMKIDRDPLGGLADMFGQMPGSGIGIGPGVIQDRFSPTMGRHRSNQLFSGHGGHIMPP |
| Parental | TQSQFGEMGGKFMKSQGLSQLYHNQSQGLLSQLQGQSKDMPPRFSKKGQLNADEISLRPAQSFLMNKNQV |
| TQSQFGEMGGKFMKSQGLSQLYHNQSQGLLSQLQGQSK.MPPRF.KKGQLNADE.SLRPAQSFLMNKNQV | |
| Retrocopy | TQSQFGEMGGKFMKSQGLSQLYHNQSQGLLSQLQGQSKNMPPRFFKKGQLNADEVSLRPAQSFLMNKNQV |
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 | 370 .65 RPM |
| ERP005899_muscle | 3 .17 RPM | 684 .20 RPM |
| SRP017611_brain | 2 .60 RPM | 579 .26 RPM |
| SRP017611_kidney | 2 .13 RPM | 739 .18 RPM |
| SRP017611_liver | 1 .66 RPM | 373 .99 RPM |
| SRP030211_testis | 2 .13 RPM | 568 .55 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1479 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1479 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1479 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 | ENSBTAG00000020308 | 1 retrocopy |
retro_btau_1479 ,
|
| Rattus norvegicus | ENSRNOG00000017158 | 2 retrocopies |