RetrogeneDB ID: | retro_btau_1608 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 8:42534257..42535907(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DLGAP1 | ||
| Ensembl ID: | ENSBTAG00000005372 | ||
| Aliases: | None | ||
| Description: | disks large-associated protein 1 [Source:RefSeq peptide;Acc:NP_001179558] |
Retrocopy-Parental alignment summary:
>retro_btau_1608
ATGAAAGGGTTATCGGGCAGCCGCAGCCATCACCACGGAGTCACCTGCGATTCAGCCTGTGACTCGCTGTCGCGCCACGC
GGACCGCAAGCCATACCTGCTGAGCCTGGTGGAGCACCATCCGGCCGACCACCCCTACTACACTCAGCGGACCTCCTTCC
AGGCCGAGTGTGTGGGCCCCTTAAGCGACCCGCTGGCCAGCAGCACCTTCCCGCGGTGGCACTACACCTCGCAGCAGGAG
CTGAAGGACGAGTGTGCCCTGGTGCCCCGCACCCTGGCCACCAAGGCCAACCGCATCCCCGCCAACCTCCTGGACCAGTT
TGAGAGGCAGCTACCTCTCAGCCGGGATGGCTACCACACTTTGCAGTACAAGCGCACGGCCGTGGAGCACCGCAGCGACG
GCCCCGGCTGCATCCGCCACCTGGTCCACTCGGTCCAGAAGCTCTTCACCAAATCGCACTCCCTGGAGGGACCGTCCAAG
GGCAGCGTCAACGGAGGCAAGGCCAGCCCGGACGAGACGCAGACCGTGAGGTACGGCAAGCGCAGCAAAAGCAAGGAGCG
GCGCCCGGAGCCCAAGCCGCGCAACAACACATCCCCTGGCTGGTGGAGTTCTGACGACAACCTCGACAGCGACATGTGTA
TCTACCACTCCCCCTCGGGTGTGATGACCATGGGCAGGTGACCCGACCGCTCAGCCTCTCAGTACTTTATGGAGGCCTAC
AACACCATCAGCGAGCAGGCAGTGAAGGCCTCCCGGAGTAACAACGACGTCAAGTGCTCCACTTGCACCAACCTGCCCGT
CACCCTAGACGCACCGCTGCTCAAGAAGAGTGCCTGGTCCTCCACGCTGACCGTGAGTCGAGCCCGAGAGGTTTACCAGA
AAGCCTCGGTCAACATGGACCAAGCCATGGTGAAGTCAGAGTCGTGTCAACAAGAACGTTCCTGCCAGTACCTTCAGGTC
CCTCAGGATGAATGGACAGGGTACACCCCTAGAGGTAAAGATGATGAAATCCCCTGCCGAAGAATGCGGAGCAGCAGCTA
CATCAAGGGAGATGAAGACAGCGGTGACTCGGACACCAGCCCCAAGCCTTTTCCCAAAGTGGCTGCGCGAAGGGAAAGCT
ATCTCAAGGCGACTCAGCCATCCCTCACAGAACTCACCACTCTCAAGATTTCCAATGAGCACTCCCCCAAACTCCAGATC
CGGAGTCACAGTTACCTGAGGGCGGTCAGTGAGGTCTCCATCAACCGAAGCCTCGACAGCCTTGACCCTGCGGGGCTGCT
CACGTCTCCGAAGTTCCGCTCCAGGAACGACAGCTGCATGCGTGCCATGAGCACCATCAGCCAGGTGAGTGAGATGGAGG
TGAACGGGCAGTTCGAGTCGGTGTGCGAGTCGGTGTTCAGCGAGCTGGAGTCGCAGGTGGTGGAGGCCCTGGACCTGCCG
ATGCCTGGCTGCTTCCGCATGCGGAGCCACAGCTACGTGCGAGCCATCGAGAACGGCTGTTCGCAGGACGACGAGTGCGT
GTCGCTGCGGTCCTCCTCCCCGCCGCCCACCACCACCACCGTGAGGACCATCCAAAGCAGCACGGGTGAGTGTGCAGAGC
CAGCCCCGCGCACCACCCCCCGCCGCCCGGGCAGCGCCTCAACTGTCCCC
ORF - retro_btau_1608 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.67 % |
| Parental protein coverage: | 56.6 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MKGLSGSRSHHHGVTCDSACDSLSHHADRKPYLLSPVEHHPADHPYYTQRTSFQAECVGPFSDPLASSTF |
| MKGLSGSRSHHHGVTCDSACDSLS.HADRKPYLLS.VEHHPADHPYYTQRTSFQAECVGP.SDPLASSTF | |
| Retrocopy | MKGLSGSRSHHHGVTCDSACDSLSRHADRKPYLLSLVEHHPADHPYYTQRTSFQAECVGPLSDPLASSTF |
| Parental | PRRHYTSQQELKDECALVPRTLATKANRIPANLLDQFERQLPLSRDGYHTLQYKRTAVEHRSDSPGRIRH |
| PR.HYTSQQELKDECALVPRTLATKANRIPANLLDQFERQLPLSRDGYHTLQYKRTAVEHRSD.PG.IRH | |
| Retrocopy | PRWHYTSQQELKDECALVPRTLATKANRIPANLLDQFERQLPLSRDGYHTLQYKRTAVEHRSDGPGCIRH |
| Parental | LVHSVQKLFTKSHSLEGPSKGSVNGGKASPDETQTVRYGKRSKSKERRPEPKPRNNTSPGWWSSDDNLDG |
| LVHSVQKLFTKSHSLEGPSKGSVNGGKASPDETQTVRYGKRSKSKERRPEPKPRNNTSPGWWSSDDNLD. | |
| Retrocopy | LVHSVQKLFTKSHSLEGPSKGSVNGGKASPDETQTVRYGKRSKSKERRPEPKPRNNTSPGWWSSDDNLDS |
| Parental | DMCIYHSPSGVMTMGRCPDRSASQYFMEAYNTISEQAVKASRSNNDVKCSTCANLPVTLDAPLLKKSAWS |
| DMCIYHSPSGVMTMGR.PDRSASQYFMEAYNTISEQAVKASRSNNDVKCSTC.NLPVTLDAPLLKKSAWS | |
| Retrocopy | DMCIYHSPSGVMTMGR*PDRSASQYFMEAYNTISEQAVKASRSNNDVKCSTCTNLPVTLDAPLLKKSAWS |
| Parental | STLTVSRAREVYQKASVNMDQAMVKSESCQQERSCQYLQVPQDEWTGYTPRGKDDEIPCRRMRSGSYIKA |
| STLTVSRAREVYQKASVNMDQAMVKSESCQQERSCQYLQVPQDEWTGYTPRGKDDEIPCRRMRS.SYIK. | |
| Retrocopy | STLTVSRAREVYQKASVNMDQAMVKSESCQQERSCQYLQVPQDEWTGYTPRGKDDEIPCRRMRSSSYIK- |
| Parental | MGDEDSGDSDTSPKPSPKVAARRESYLKATQPSLTELTTLKISNEHSPKLQIRSHSYLRAVSEVSINRSL |
| .GDEDSGDSDTSPKP.PKVAARRESYLKATQPSLTELTTLKISNEHSPKLQIRSHSYLRAVSEVSINRSL | |
| Retrocopy | -GDEDSGDSDTSPKPFPKVAARRESYLKATQPSLTELTTLKISNEHSPKLQIRSHSYLRAVSEVSINRSL |
| Parental | DSLDPAGLLTSPKFRSRNESYMRAMSTISQVSEMEVNGQFESVCESVFSELESQAVEALDLPMPGCFRMR |
| DSLDPAGLLTSPKFRSRN.S.MRAMSTISQVSEMEVNGQFESVCESVFSELESQ.VEALDLPMPGCFRMR | |
| Retrocopy | DSLDPAGLLTSPKFRSRNDSCMRAMSTISQVSEMEVNGQFESVCESVFSELESQVVEALDLPMPGCFRMR |
| Parental | SHSYVRAIEKGCSQDDECVSLRSSSPPRTTTTVRTIQSSTVSSCITTYKKTPPPVPPRTTTKP |
| SHSYVRAIE.GCSQDDECVSLRSSSPP.TTTTVRTIQSST...C......T.P..P....T.P | |
| Retrocopy | SHSYVRAIENGCSQDDECVSLRSSSPPPTTTTVRTIQSST-GECAEPAPRTTPRRPGSASTVP |
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 .29 RPM |
| ERP005899_muscle | 0 .00 RPM | 0 .58 RPM |
| SRP017611_brain | 0 .41 RPM | 46 .23 RPM |
| SRP017611_kidney | 0 .00 RPM | 2 .19 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .00 RPM |
| SRP030211_testis | 7 .20 RPM | 23 .67 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1608 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1608 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1608 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 | ENSBTAG00000005372 | 1 retrocopy |
retro_btau_1608 ,
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