RetrogeneDB ID: | retro_btau_683 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 17:56084032..56084726(-) | ||
| Located in intron of: | ENSBTAG00000003092 | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000048014 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BT.53698 | ||
| Ensembl ID: | ENSBTAG00000007253 | ||
| Aliases: | None | ||
| Description: | tetraspanin-33 [Source:RefSeq peptide;Acc:NP_001029844] |
Retrocopy-Parental alignment summary:
>retro_btau_683
GAGGCAGCGCTGGCCTGCCTGGCCGTGGACCCGGCCATCCTGCTAATCCTGGTGGGCATCCTCAGGTTCCTGCTCACCTT
CTGCAGCTGCATCAGATGATCTCTCTGCGAGAACGTCTGCCTCCTGCAGACGCTCTCCCTCTGTCCCACCATTGTGTTCC
TGCTACAGCTGGCAGCTGGGGTCCTGGGCTTCGTCTTCTCAGACAAGGTGCGGGGCAAAGTGAGTGAGATTATCAATAAT
GCCATTGTGCACTACCGAGATAACTTGGACCTTCAGAATCTCATAGATTTTTGGCCAGAAGGAGTTCAGCTACTGTGGAG
GGATTTCCTATAAGGACTGGTCCCTGAACATGTACTTCAACTGTTCAGAAGACAACCCCAGGCATGAGCACTATTCTGTG
CATTACTCCTGTTGCTTGCCTACCCCTAACCAGGCAGTGATCAACACCATGTGTGGCCAAGGTATGCAGACCTTTGACTA
CTCGGAAGCTAGTCAAGTCATCTACACCCATGGCTGTATTGACAGATTGGTCAACTGGATACACAGCAACCTCTTCATAC
TTGGTGGTGTGGCACTGGGCCTGGCCATCCCGCAGCTCGTGAGAATCCTGCTGTCCATGAACCTTGTGAGTCAGATCAAA
GATCAGATCCAACTATAGCTCTACAACCAGCAGCACCGGGCGGACCCATGGTAC
ORF - retro_btau_683 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.93 % |
| Parental protein coverage: | 81.27 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | EAALACLAVDPAILLIVVGILMFLLTFCGCIG-SLRENICLLQTFSLCLTVVFLLQLAAGVLGFVFSDKV |
| EAALACLAVDPAILLI.VGIL.FLLTFC.CI..SL.EN.CLLQT.SLC.T.VFLLQLAAGVLGFVFSDKV | |
| Retrocopy | EAALACLAVDPAILLILVGILRFLLTFCSCIR*SLCENVCLLQTLSLCPTIVFLLQLAAGVLGFVFSDKV |
| Parental | RGKVSEIINNAIVHYRDDLDLQNLIDF-GQKEFSCCGGISYKDWSLNMYFNCSEDNPSRERCSVPYSCCL |
| RGKVSEIINNAIVHYRD.LDLQNLIDF.GQKEFS.CGGISYKDWSLNMYFNCSEDNP..E..SV.YSCCL | |
| Retrocopy | RGKVSEIINNAIVHYRDNLDLQNLIDF>GQKEFSYCGGISYKDWSLNMYFNCSEDNPRHEHYSVHYSCCL |
| Parental | PTPNQAVINTMCGQGMQALDYLEASKVIYTNGCIDRLVNWIHSNLFVLGGVALGLAIPQLVGILLSMILV |
| PTPNQAVINTMCGQGMQ..DY.EAS.VIYT.GCIDRLVNWIHSNLF.LGGVALGLAIPQLV.ILLSM.LV | |
| Retrocopy | PTPNQAVINTMCGQGMQTFDYSEASQVIYTHGCIDRLVNWIHSNLFILGGVALGLAIPQLVRILLSMNLV |
| Parental | SQIKDQIKLQLYNQQHRADPWY |
| SQIKDQI.L.LYNQQHRADPWY | |
| Retrocopy | SQIKDQIQL*LYNQQHRADPWY |
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 | 5 .70 RPM |
| ERP005899_muscle | 0 .00 RPM | 6 .60 RPM |
| SRP017611_brain | 0 .00 RPM | 80 .12 RPM |
| SRP017611_kidney | 0 .00 RPM | 132 .12 RPM |
| SRP017611_liver | 0 .00 RPM | 4 .23 RPM |
| SRP030211_testis | 0 .08 RPM | 7 .24 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_683 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_683 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_683 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000007253 | 1 retrocopy |
retro_btau_683 ,
|
| Dasypus novemcinctus | ENSDNOG00000007532 | 1 retrocopy |