RetrogeneDB ID: | retro_itri_1788 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393785.1:100504..102798(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CARD11 | ||
| Ensembl ID: | ENSSTOG00000007608 | ||
| Aliases: | None | ||
| Description: | caspase recruitment domain family, member 11 [Source:HGNC Symbol;Acc:16393] |
Retrocopy-Parental alignment summary:
>retro_itri_1788
GGAGGCTGGCCGGGGATGGATGACGACATGGAGACCCTCAAGGACGAGGAGGATGCCCTGTGGGAGAACGTGGAGTGTAA
CAGGCACATGCTGAGTCGCTACATCAACCCGGCCAAGCTCACCCCCTACCTGCACCAGTGCAAGGTCATCAATGAGCAAG
ACAAAGATGAAGCGCTTAACGCGCCCATGCTGCCGTCCAAGATCAACCCGGCAGGCCGACTGTTGGGCATTCTACACACC
AAAGGGCAAAGAGGCTATGTGGTCTTCTTAGAGAGCTTGGAGTTTTACTACCCAGAACTGTACAAGCTGGTGAGGGGGAA
GGAGCCCACCCGTAGGTTCTCCACTATCGTGGTGGAGGAGGGCCACAAGGGCCTCACGCACTTCTTGATGAATGAGGTCA
TCAAGCTGCAGCAGCAGATGAAGGCCAAGGACCTCCAGCGCTGCGAGCTGCTGGCCAAGGCTCGGCAGCTGGAGGACGAG
AAGAAGCAGCTGACGCTGACCCGGGTGGAGCTGCTGACCTTCCAGGAGCGGTACTACAAGATGAAGGAAGAGCCGGATGG
CTACAACGAGGAGCTGGTCAAGGTCAAGGACAACTACACCTTGGCCATGCACTATGCCCAGCTCAGAGAAGAGAAAAACA
TGGCCGTGATGAGAAGCTGGGACCTCCAACTCAAGATCAATCAACTCAAGCACTGATTGAACAAGATGGAGGAGGAATGT
AAGCTGGAGAGAAATCAGCCGCTGAAACTGAAGAATGACATCGAGAATCGGCCCAAGAAGGAGCAGGTCCTGGAATTGGA
GCGGGAGAATGAGATGCTCAAGACCAAGACCCAGGAGCTGCAGTCCATCATCCAGGCCGGCAAATGCAGCCAGCCAGACT
CAGACAAGGCCATCGTGGACATCCTGGAGCATGACAGGAAAGAGGCACTGGAGGACCGGCAGGAGCTCGTCAACAAAATC
TACAACTTGCAGGAGGAGGTCCGCCAGGCAGAGGAGCTTCGAGACAAGTACTTGGTGGAAAAGGAAGACCTGGAGCTTAG
GTGCTCGACCCTGGGGAAAGACTGTGAAATGTACAAGCACCGTATGAACACGGTCATGCTGCAACTGGAGGAGGTGGAGC
AGGAGCAGGACCAGGCCTTCCATTTCTGAGACGAAGCGCAGACTCAGTACTCGCAGTGCTTGATCCAGAAAGACAAGTAC
CGGAAACAGATCCGGGAGCTGGAGAAGAAAGAGGAGATGAGGATCGAGATGGTGTGGCGGGAAGCCTGCATCGTCAACCT
GGAGAGCAAGCTCCGGCGCCTCTCCAAAGACAATGGCAGCCTCGACCAGAGTCTGCCCAGGAACCTGCCAGCCACCATCA
TCTCACAGAACTTTGGGGACGCCAGCCCCAGGGTTAACGGGCAAGAGGCTGACTTCCACCTCGGAGGAGTCACCTGAAGA
CAACAAGTACTTCCTGCCCTACCACCCGCCCCGGCGCAGGATGAACCTGAAGGGCATCCAGCTGCAGAGAGCCAAATCCC
CCATCAGCCTGAAGCAAGCGTCGATTTTCAAGGCAAGGGACATGAAGACAAGGATGCCAGCCCCAGCTCCTCCCACTCTC
TGCCCATCACCAGCTCCTTCTCCAAGATGCAGCCCCATCGAAGCCGCAGCAGTATCATGTCCATCACTGCCGAGCCCCCG
GGAAACGACTCCATGTCAGGCGCTGTAAGGAGGATGCCCCGCTCCGCAGCACAGTCGAAGAAGACAACGACAGTGGTGGG
TTCGACGCTTTGGACCTGGACGACGACAGTCACGAGCGCAGCTCCTTTGGTCCACCGTCCATCCACTCCTCCTCCTCGTC
CCACCAGTCTGAAGGCCTAGATGCCTACGACCTGGAGCAGGTCAACCTCATGTTTAGGAAATTCTCACTTGAAAGACCCT
TCCCGCCCTCGGTCACATCCGTGGGGCACGTGCGAGGCCCTGGACCCTCAGTGCAGCACACAACGCTGAATGGCGACAGC
CTCATCACCCAGCTCACCCTGCTGGGTGGCAACGCCCGCGGCAGCTTCATCTACTCAGTCAAGCCGGGCTCCCTGGCTGA
GAAGGCAGGACTCCACCAGGGCCACCAGCTGCTGCTGCTGGAAGGCTGCATCAAAGGCGAGAGGCAGAGTGTCCCCTTGG
ACGCGTGCACAACGGAGGAGGCCCACTGGACCATCCAGAAGTGCAGTGGCCCGGTCACCCTGCACTACAAGGTCAACCAA
GAAGGGTACCGGAAGCTACTGAGAGACATGGAGGAGGGTCTGATCCTCGGGGGA
ORF - retro_itri_1788 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.62 % |
| Parental protein coverage: | 66.87 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | GGWPGMDDDMETLKDEEDALWENVECNRHMLSRYINPAKLTPYLRQCKVIDEQDEDEVLNAPMLPSKINR |
| GGWPGMDDDMETLKDEEDALWENVECNRHMLSRYINPAKLTPYL.QCKVI.EQD.DE.LNAPMLPSKIN. | |
| Retrocopy | GGWPGMDDDMETLKDEEDALWENVECNRHMLSRYINPAKLTPYLHQCKVINEQDKDEALNAPMLPSKINP |
| Parental | AGRLLDILHTKGQRGYVVFLESLEFYYPELYKLVTGKEPTRRFSTIVVEEGHEGLTHFLMNEVIKLQQQM |
| AGRLL.ILHTKGQRGYVVFLESLEFYYPELYKLV.GKEPTRRFSTIVVEEGH.GLTHFLMNEVIKLQQQM | |
| Retrocopy | AGRLLGILHTKGQRGYVVFLESLEFYYPELYKLVRGKEPTRRFSTIVVEEGHKGLTHFLMNEVIKLQQQM |
| Parental | KAKDLQRCELLAKARQLEDEKKQLTLTRVELLTFQERYYKMKEERDGYNEELVKVKDDNYTLAMRYAQLS |
| KAKDLQRCELLAKARQLEDEKKQLTLTRVELLTFQERYYKMKEE.DGYNEELVKVKD.NYTLAM.YAQL. | |
| Retrocopy | KAKDLQRCELLAKARQLEDEKKQLTLTRVELLTFQERYYKMKEEPDGYNEELVKVKD-NYTLAMHYAQLR |
| Parental | EEKNMAVMRSRDLQLEIDQLKHRLNKMEEECKLERNQSLKLKNDIENRPKKEQVLELERENEMLKTKIQE |
| EEKNMAVMRS.DLQL.I.QLKH.LNKMEEECKLERNQ.LKLKNDIENRPKKEQVLELERENEMLKTK.QE | |
| Retrocopy | EEKNMAVMRSWDLQLKINQLKH*LNKMEEECKLERNQPLKLKNDIENRPKKEQVLELERENEMLKTKTQE |
| Parental | LQSIIQAGKRSLPDSDKAILDILEHDRKEALEDRQELVNKIYNLQEEVRQAEELRDKYLEEKEDLELRCS |
| LQSIIQAGK.S.PDSDKAI.DILEHDRKEALEDRQELVNKIYNLQEEVRQAEELRDKYL.EKEDLELRCS | |
| Retrocopy | LQSIIQAGKCSQPDSDKAIVDILEHDRKEALEDRQELVNKIYNLQEEVRQAEELRDKYLVEKEDLELRCS |
| Parental | TLGKDCEMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMRIEMV |
| TLGKDCEMYKHRMNTVMLQLEEVE.E.DQAFH..DEAQTQYSQCLI.KDKYRKQIRELE.K..EMRIEMV | |
| Retrocopy | TLGKDCEMYKHRMNTVMLQLEEVEQEQDQAFHF*DEAQTQYSQCLIQKDKYRKQIRELEKK-EEMRIEMV |
| Parental | RREACIVNLESKLRRLSKDNGSLDQSLPRNLPATIISQNFGDAS-PRVNGQEADDSSTSEESPEDSKYFL |
| .REACIVNLESKLRRLSKDNGSLDQSLPRNLPATIISQNFGDAS.P...G......STSEESPED.KYFL | |
| Retrocopy | WREACIVNLESKLRRLSKDNGSLDQSLPRNLPATIISQNFGDAS>PGLTGKRL--TSTSEESPEDNKYFL |
| Parental | PYHPPRRRMNLKGIQLQRAKSPISLKRAS-DFQGKGHEDRDASPSSSHSLPITSSFSKMQPHRSRSSIMS |
| PYHPPRRRMNLKGIQLQRAKSPISLK.AS.DFQGKGHED.DASPSSSHSLPITSSFSKMQPHRSRSSIMS | |
| Retrocopy | PYHPPRRRMNLKGIQLQRAKSPISLKQAS<DFQGKGHEDKDASPSSSHSLPITSSFSKMQPHRSRSSIMS |
| Parental | ITAEPPGNDSI-VRRCKEDAPLRSTVEEDNDSGGFDALDLDDDSHERSSFGPPSIHSSSSSHQSEGLDAY |
| ITAEPPGNDS..VRRCKEDAPLRSTVEEDNDSGGFDALDLDDDSHERSSFGPPSIHSSSSSHQSEGLDAY | |
| Retrocopy | ITAEPPGNDSM<VRRCKEDAPLRSTVEEDNDSGGFDALDLDDDSHERSSFGPPSIHSSSSSHQSEGLDAY |
| Parental | DLEQVNLMFRKFSLERPFRPSVTSVGHVRGPGPSVQHTTLNGDSLITQLTLLGGNARGSFIHSVKPGSLA |
| DLEQVNLMFRKFSLERPF.PSVTSVGHVRGPGPSVQHTTLNGDSLITQLTLLGGNARGSFI.SVKPGSLA | |
| Retrocopy | DLEQVNLMFRKFSLERPFPPSVTSVGHVRGPGPSVQHTTLNGDSLITQLTLLGGNARGSFIYSVKPGSLA |
| Parental | EKAGLREGHQLLLLEGCIKGERQSVPLDSCTKEEARWTIQRCSGPVTLHYKVNQEGYRKLLRDMEEGLIT |
| EKAGL..GHQLLLLEGCIKGERQSVPLD.CT.EEA.WTIQ.CSGPVTLHYKVNQEGYRKLLRDMEEGLI. | |
| Retrocopy | EKAGLHQGHQLLLLEGCIKGERQSVPLDACTTEEAHWTIQKCSGPVTLHYKVNQEGYRKLLRDMEEGLIL |
| Parental | SG |
| .G | |
| Retrocopy | GG |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.
Ictidomys tridecemlineatus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_itri_1788 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1788 was not experimentally validated.
Retrocopy orthology:
Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ictidomys tridecemlineatus | ENSSTOG00000007608 | 1 retrocopy |
retro_itri_1788 ,
|