RetrogeneDB ID: | retro_btau_442 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 11:49070192..49071859(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000039981 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DNAJC11 | ||
| Ensembl ID: | ENSBTAG00000011217 | ||
| Aliases: | None | ||
| Description: | DnaJ homolog subfamily C member 11 [Source:UniProtKB/Swiss-Prot;Acc:Q2NL21] |
Retrocopy-Parental alignment summary:
>retro_btau_442
ATGGCGACGGCCTTGAGCAAGGAGGAGCTGGACAATGAAGACTATTACTCGTTGCTGAACGTGCGCAGGGAGGCCTCTTG
CGAAGAGCCAAAAGCGGCCTACCGGCGGCTGTGCATGCTTTACCACCCCGACAAGCACAGAGACCCAGGGCTCAAATCGC
AGGCCGAGCGGCTGTTTAACCTCATTCACCAGGCTTATGAAGTGTTCAGTGACCCCCAGACCAGGGCCATCTATGACATC
TATGGCAAGAGAGGACTGGAGATGGAAGGCTGGGAGGTTGTGGAAAGGAGGAGAACGCCAGCTGAGATCAGAGAAGAGTT
TGAGCGGCTGCAGCGCGAGAGGGAGGAGAGCAGGCTGCAGCAGCGCACCAACCCCAAGGGGACCATCAGTGTTGGCACTG
ACGCCACTGACCTTTTTGATCGCTATGAGGAGGAGTACGAGGATGTGTCCGGAAGTGGCTTTCCACAGATTGAAGTTAAC
AAGATGCACATATCACAGTCCATTGTGGCACCCCAACAGCTTCAGACACAGCCATCCTCTCTGGAAGCCTCTCAACCCAG
AATGGGAATGGAGGGGGTTCCATTAACTTTGCGCTCAGACGAGTCACTTCTGTGAAGGGCTGGGGAGAGTTAGAATTTGG
AGCTGGGGATCTGCAGGGGCCTTTATTTGGCCTGAAGCTGTTCCGTAATCTCACACCAAGATGCTTTGTGATGACACACT
GTGCCCTGCAGTTTTCATCCCACGGCATCCAGCCGGGCCTCACCACTGTCCTGGCCCGGAACCTGGACAAGAATACGGTG
GGCTACCTGCAGTGGCGCTGGGGCGTCCAGTCAGCCATGAACACCAGCATCGTCCGGGACACCAAGACCAGCCACTTCAC
TGTGGGCCCGCAGCTTGGAATCCCTCACTCCTTCGCACTCATCAGCTATCAGCACGAATTCCAGGATGACGACCAGACCC
GAGTGAAGGGGTCCCTGAAGGCCAGCTTCTTCGGGACGGTGATGGAAGCAGAGAGGAAGATCTCCAGGCACAGTGTCCTC
GGGGCGGCTGTCAGCGTTGGAGTCCCACAGGCCGTTTCCCTCAAAATCAAGTTAAATAGGGCCAGTCAGACCTACTTCTT
CCCTATCTACCTGACAGACCAGCTGCTGCCCAGCGCCGTGTTCTACGCCACCGAGGGGCCGCTCCTGCTGTACTTCGCTC
TGCACCGCCTGGTCATCAGACCCTACCTCAGGGCTCAGAAGGAGAAGGAACTGGAGAAGCAAAGGGAAAGCACAGCCACC
GACATCCTGCAGAAGAAACCAGAGGCAGAAGCTGCCGTTTGGTTGATGCAGGAATCTGTCCGAAGAATAATCGAGGTCGA
AGAGTCCAGAATGGGGCTCATCATCATCAATGCCTGGTATGGAAAATTTGTCAATGACAAGAGCAAGAAGAGCGAGAAGG
TGAAGGTGATCGATGTGACCGTGCCCCTGCAGTGTCTGATGAAGGACTCCAAGCTCATCCTCACCGAGGCCTCCAAGGCT
GGGCTGCCCAGCTTCTACGACCCGTGTGTGGGTGAAGAGAACCTGAAAGTGCTTTACCAGTTCCGCGGGGTCCTTCATCA
GGTGATGGTGCTCGACAGCGAGGCACTCAGGATACCAAAGCAGTCTCACAGAATTGATACTGATGGA
ORF - retro_btau_442 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.75 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MATALSEEELDNEDYYSLLNVRREASCEELKAAYRRLCMLYHPDKHRDPELKSQAERLFNLVHQAYEVLS |
| MATALS.EELDNEDYYSLLNVRREASCEE.KAAYRRLCMLYHPDKHRDP.LKSQAERLFNL.HQAYEV.S | |
| Retrocopy | MATALSKEELDNEDYYSLLNVRREASCEEPKAAYRRLCMLYHPDKHRDPGLKSQAERLFNLIHQAYEVFS |
| Parental | DPQTRAIYDIYGKRGLEMEGWEVVERRRTPAEIREEFERLQREREERRLQQRTNPKGTISVGIDATDLFD |
| DPQTRAIYDIYGKRGLEMEGWEVVERRRTPAEIREEFERLQREREE.RLQQRTNPKGTISVG.DATDLFD | |
| Retrocopy | DPQTRAIYDIYGKRGLEMEGWEVVERRRTPAEIREEFERLQREREESRLQQRTNPKGTISVGTDATDLFD |
| Parental | RYEEEYEDVSGSGFPQIEINKMHISQSIEAPL-TASDTAILSGSLSTQNGNGGGSINFALRRVTSAKGWG |
| RYEEEYEDVSGSGFPQIE.NKMHISQSI.AP..TASDTAILSGSLSTQNGNGGGSINFALRRVTS.KGWG | |
| Retrocopy | RYEEEYEDVSGSGFPQIEVNKMHISQSIVAPQ<TASDTAILSGSLSTQNGNGGGSINFALRRVTSVKGWG |
| Parental | ELEFGAGDLQGPLFGLKLFRNLTPRCFVTTHCALQFSSRGIRPGLTTVLARNLDKNTVGYLQWRWGVQSA |
| ELEFGAGDLQGPLFGLKLFRNLTPRCFV.THCALQFSS.GI.PGLTTVLARNLDKNTVGYLQWRWGVQSA | |
| Retrocopy | ELEFGAGDLQGPLFGLKLFRNLTPRCFVMTHCALQFSSHGIQPGLTTVLARNLDKNTVGYLQWRWGVQSA |
| Parental | MNTSIVRDTKTSHFTVALQLGIPHSFALISYQHKFQDDDQTRVKGSLKAGFFGTVVEYGAERKISRHSVL |
| MNTSIVRDTKTSHFTV..QLGIPHSFALISYQH.FQDDDQTRVKGSLKA.FFGTV.E..AERKISRHSVL | |
| Retrocopy | MNTSIVRDTKTSHFTVGPQLGIPHSFALISYQHEFQDDDQTRVKGSLKASFFGTVME--AERKISRHSVL |
| Parental | GAAVSIGVPQGVSLKIKLNRASQTYFFPIHLTDQLLPSAVFYATAGPLVLYFALHRLVIRPYLRAQKEKE |
| GAAVS.GVPQ.VSLKIKLNRASQTYFFPI.LTDQLLPSAVFYAT.GPL.LYFALHRLVIRPYLRAQKEKE | |
| Retrocopy | GAAVSVGVPQAVSLKIKLNRASQTYFFPIYLTDQLLPSAVFYATEGPLLLYFALHRLVIRPYLRAQKEKE |
| Parental | LEKQRESTATDILQKKQEAEAAVRLMQESVRRIIEAEESRMGLIIVNAWYGKFVNDKSKKSEKVKVIDVT |
| LEKQRESTATDILQKK.EAEAAV.LMQESVRRIIE.EESRMGLII.NAWYGKFVNDKSKKSEKVKVIDVT | |
| Retrocopy | LEKQRESTATDILQKKPEAEAAVWLMQESVRRIIEVEESRMGLIIINAWYGKFVNDKSKKSEKVKVIDVT |
| Parental | VPLQCLVKDSKLILTEASKAGLPGFYDPCVGEEKNLKVLYQFRGVLHQVMALDSEALRIPKQSHRIDTDG |
| VPLQCL.KDSKLILTEASKAGLP.FYDPCVGEE.NLKVLYQFRGVLHQVM.LDSEALRIPKQSHRIDTDG | |
| Retrocopy | VPLQCLMKDSKLILTEASKAGLPSFYDPCVGEE-NLKVLYQFRGVLHQVMVLDSEALRIPKQSHRIDTDG |
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 | 15 .79 RPM |
| ERP005899_muscle | 0 .00 RPM | 63 .35 RPM |
| SRP017611_brain | 0 .14 RPM | 43 .26 RPM |
| SRP017611_kidney | 0 .12 RPM | 66 .44 RPM |
| SRP017611_liver | 0 .00 RPM | 33 .00 RPM |
| SRP030211_testis | 1 .24 RPM | 23 .81 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_442 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_442 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_442 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 | ENSBTAG00000011217 | 1 retrocopy |
retro_btau_442 ,
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