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:

ParentalGGWPGMDDDMETLKDEEDALWENVECNRHMLSRYINPAKLTPYLRQCKVIDEQDEDEVLNAPMLPSKINR
GGWPGMDDDMETLKDEEDALWENVECNRHMLSRYINPAKLTPYL.QCKVI.EQD.DE.LNAPMLPSKIN.
RetrocopyGGWPGMDDDMETLKDEEDALWENVECNRHMLSRYINPAKLTPYLHQCKVINEQDKDEALNAPMLPSKINP
ParentalAGRLLDILHTKGQRGYVVFLESLEFYYPELYKLVTGKEPTRRFSTIVVEEGHEGLTHFLMNEVIKLQQQM
AGRLL.ILHTKGQRGYVVFLESLEFYYPELYKLV.GKEPTRRFSTIVVEEGH.GLTHFLMNEVIKLQQQM
RetrocopyAGRLLGILHTKGQRGYVVFLESLEFYYPELYKLVRGKEPTRRFSTIVVEEGHKGLTHFLMNEVIKLQQQM
ParentalKAKDLQRCELLAKARQLEDEKKQLTLTRVELLTFQERYYKMKEERDGYNEELVKVKDDNYTLAMRYAQLS
KAKDLQRCELLAKARQLEDEKKQLTLTRVELLTFQERYYKMKEE.DGYNEELVKVKD.NYTLAM.YAQL.
RetrocopyKAKDLQRCELLAKARQLEDEKKQLTLTRVELLTFQERYYKMKEEPDGYNEELVKVKD-NYTLAMHYAQLR
ParentalEEKNMAVMRSRDLQLEIDQLKHRLNKMEEECKLERNQSLKLKNDIENRPKKEQVLELERENEMLKTKIQE
EEKNMAVMRS.DLQL.I.QLKH.LNKMEEECKLERNQ.LKLKNDIENRPKKEQVLELERENEMLKTK.QE
RetrocopyEEKNMAVMRSWDLQLKINQLKH*LNKMEEECKLERNQPLKLKNDIENRPKKEQVLELERENEMLKTKTQE
ParentalLQSIIQAGKRSLPDSDKAILDILEHDRKEALEDRQELVNKIYNLQEEVRQAEELRDKYLEEKEDLELRCS
LQSIIQAGK.S.PDSDKAI.DILEHDRKEALEDRQELVNKIYNLQEEVRQAEELRDKYL.EKEDLELRCS
RetrocopyLQSIIQAGKCSQPDSDKAIVDILEHDRKEALEDRQELVNKIYNLQEEVRQAEELRDKYLVEKEDLELRCS
ParentalTLGKDCEMYKHRMNTVMLQLEEVERERDQAFHSRDEAQTQYSQCLIEKDKYRKQIRELEEKNDEMRIEMV
TLGKDCEMYKHRMNTVMLQLEEVE.E.DQAFH..DEAQTQYSQCLI.KDKYRKQIRELE.K..EMRIEMV
RetrocopyTLGKDCEMYKHRMNTVMLQLEEVEQEQDQAFHF*DEAQTQYSQCLIQKDKYRKQIRELEKK-EEMRIEMV
ParentalRREACIVNLESKLRRLSKDNGSLDQSLPRNLPATIISQNFGDAS-PRVNGQEADDSSTSEESPEDSKYFL
.REACIVNLESKLRRLSKDNGSLDQSLPRNLPATIISQNFGDAS.P...G......STSEESPED.KYFL
RetrocopyWREACIVNLESKLRRLSKDNGSLDQSLPRNLPATIISQNFGDAS>PGLTGKRL--TSTSEESPEDNKYFL
ParentalPYHPPRRRMNLKGIQLQRAKSPISLKRAS-DFQGKGHEDRDASPSSSHSLPITSSFSKMQPHRSRSSIMS
PYHPPRRRMNLKGIQLQRAKSPISLK.AS.DFQGKGHED.DASPSSSHSLPITSSFSKMQPHRSRSSIMS
RetrocopyPYHPPRRRMNLKGIQLQRAKSPISLKQAS<DFQGKGHEDKDASPSSSHSLPITSSFSKMQPHRSRSSIMS
ParentalITAEPPGNDSI-VRRCKEDAPLRSTVEEDNDSGGFDALDLDDDSHERSSFGPPSIHSSSSSHQSEGLDAY
ITAEPPGNDS..VRRCKEDAPLRSTVEEDNDSGGFDALDLDDDSHERSSFGPPSIHSSSSSHQSEGLDAY
RetrocopyITAEPPGNDSM<VRRCKEDAPLRSTVEEDNDSGGFDALDLDDDSHERSSFGPPSIHSSSSSHQSEGLDAY
ParentalDLEQVNLMFRKFSLERPFRPSVTSVGHVRGPGPSVQHTTLNGDSLITQLTLLGGNARGSFIHSVKPGSLA
DLEQVNLMFRKFSLERPF.PSVTSVGHVRGPGPSVQHTTLNGDSLITQLTLLGGNARGSFI.SVKPGSLA
RetrocopyDLEQVNLMFRKFSLERPFPPSVTSVGHVRGPGPSVQHTTLNGDSLITQLTLLGGNARGSFIYSVKPGSLA
ParentalEKAGLREGHQLLLLEGCIKGERQSVPLDSCTKEEARWTIQRCSGPVTLHYKVNQEGYRKLLRDMEEGLIT
EKAGL..GHQLLLLEGCIKGERQSVPLD.CT.EEA.WTIQ.CSGPVTLHYKVNQEGYRKLLRDMEEGLI.
RetrocopyEKAGLHQGHQLLLLEGCIKGERQSVPLDACTTEEAHWTIQKCSGPVTLHYKVNQEGYRKLLRDMEEGLIL
ParentalSG
.G
RetrocopyGG

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_1788 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

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 ,


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