RetrogeneDB ID:

retro_itri_610

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393306.1:903868..905083(+)
Located in intron of:ENSSTOG00000021179
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF4A1
Ensembl ID:ENSSTOG00000024814
Aliases:None
Description:eukaryotic translation initiation factor 4A1 [Source:HGNC Symbol;Acc:3282]


Retrocopy-Parental alignment summary:






>retro_itri_610
ATATCTGCAAGTCAGGATTCCCGATCCAGAGACAATGGCCCTGATGGAATGGAGCCTGAAGTCGTCATGGAAAGTAACTG
AAATGAGATTGTTGATAGCTTTGATGACATGAATCTCTCCGAGTCCCTCCTCCATGGCATCTATGCCTATGGTTTTGAGA
AGTCCTCTGCCATCCAGCAGTGAGCCATTCTTCCTTGTATCAAGGGTTATGATGTGATTGCTAAGGCCCAATCTGGGACT
GGGAAACAGCTACATTTGCCATATCAATTCTCCAGCAGACTGAATTAGATCTAAAGGCCACCCAAGCCTTGGTACTGGCA
CCCATTCAAGAATTGGCTCAGCAGATACAAAAGGTGGTCATGGCACTAGGAGATTACATTGGTGCCTCCAGTCATGCATG
CACTGGGGGCACCAATGTACGTGCTGAGGTGCAAAAGTTGCAGATGGAAATTCCCCATATCATTGAGGGTACCCCTGGCT
GCGTGTCTGATATGCTCAACCAGAGATATCTGTCTCCCAAATGCATTAAGATGTTTGTATTAATTGAAGCTGATGAAATG
GTAAGCCGTTGATTCAAGGAACAGATCTACGACATATTCCAGAAGCGTAATAGCAATACCCAGGTGGTTTTGTTTCAGCA
ACAATGCCTTCCGATGTGCTTGAGGTGACCAAGAAGTTCATGAGGGACCCCATTCGAATTCTTGTCAAGAAGGAAGAATT
GACTCTGGAGAGTATCCGCCAGTTCTACATCAATGTTGAATGAGAGAAGGGGAAGCTGAACACACTGTGTGACTTGTATG
AAACCCTGACCATTACCTAGGCAGTGATCTTCATCAACACCCGAAGGAAGGTTAATTGGCTCACTGAGAAAATGCATGCC
TGAGATTTTACTGTCTCTGCCATGCATAGAGACATGGACCAAAAGGAAAGAGATGTGATCATGAGGAGTTCTGATCTGGC
TCTAGCAGAGTATTCATTACCACTGACTTACTGGCCAGAGGCATTGATATACAGCAAGTTTCTTTAGTCATCAACTATGA
CCTTCCTACCAACAGGGAAAACTATATCCATAGAATTAGTGGAGGTGAGCATTTTGGCCATAAGGGTGTGGTTATTAACA
TGGTGACAGAAGAAGACAAGAGGATGCTCCAAGACATCGTGACCTTCTACACCACCTCCATTGAAGAGATGCACCTTAAT
GTTGCTGACCTCATC

ORF - retro_itri_610 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.29 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 7
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalMSASQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGY
.SASQDSRSRDNGPDGMEPE.V.ESN.NEIVDSFDDMNLSESLL.GIYAYGFEK.SAIQQ.AILPCIKGY
RetrocopyISASQDSRSRDNGPDGMEPEVVMESN*NEIVDSFDDMNLSESLLHGIYAYGFEKSSAIQQ*AILPCIKGY
ParentalDVIAQAQSGTGK-TATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTN
DVIA.AQSGTGK.TATFAISILQQ.ELDLKATQALVLAP..ELAQQIQKVVMALGDY.GAS.HAC.GGTN
RetrocopyDVIAKAQSGTGK<TATFAISILQQTELDLKATQALVLAPIQELAQQIQKVVMALGDYIGASSHACTGGTN
ParentalVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQV
VRAEVQKLQME.PHII.GTPG.V.DMLN.RYLSPK.IKMFVL.EADEM.SR.FK.QIYDIFQK.NSNTQV
RetrocopyVRAEVQKLQMEIPHIIEGTPGCVSDMLNQRYLSPKCIKMFVLIEADEMVSR*FKEQIYDIFQKRNSNTQV
ParentalVL-LSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIF
VL..SATMPSDVLEVTKKFMRDPIRILVKKEELTLE.IRQFYINVE.E..KL.TLCDLYETLTIT.AVIF
RetrocopyVL<VSATMPSDVLEVTKKFMRDPIRILVKKEELTLESIRQFYINVE*EKGKLNTLCDLYETLTIT*AVIF
ParentalINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMR-EFRSGSSRVLITTDLLARGIDVQQVSLVINY
INTRRKV.WLTEKMHA.DFTVSAMH.DMDQKERDVIMR.EF.SGSSRV.ITTDLLARGID.QQVSLVINY
RetrocopyINTRRKVNWLTEKMHA*DFTVSAMHRDMDQKERDVIMR<EF*SGSSRVFITTDLLARGIDIQQVSLVINY
ParentalDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI
DLPTNRENYIHRI..G..FG.KGV.INMVTEEDKR.L.DI.TFY.TSIEEM.LNVADLI
RetrocopyDLPTNRENYIHRISGGEHFGHKGVVINMVTEEDKRMLQDIVTFYTTSIEEMHLNVADLI

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_610 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_610 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 16 parental genes, and 66 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000049001 retrocopy
retro_cpor_1088,
Erinaceus europaeus ENSEEUG000000035811 retrocopy
retro_eeur_610,
Felis catus ENSFCAG000000248971 retrocopy
retro_fcat_370,
Homo sapiens ENSG0000016196010 retrocopies
retro_hsap_1004, retro_hsap_1182, retro_hsap_1252, retro_hsap_1270, retro_hsap_1796, retro_hsap_2520, retro_hsap_4836, retro_hsap_4873, retro_hsap_4931, retro_hsap_610,
Gorilla gorilla ENSGGOG000000247028 retrocopies
retro_ggor_1321, retro_ggor_1572, retro_ggor_3015, retro_ggor_537, retro_ggor_798, retro_ggor_920, retro_ggor_983, retro_ggor_998,
Macropus eugenii ENSMEUG000000107802 retrocopies
retro_meug_158, retro_meug_179,
Myotis lucifugus ENSMLUG000000034153 retrocopies
retro_mluc_1047, retro_mluc_1229, retro_mluc_1805,
Macaca mulatta ENSMMUG000000134991 retrocopy
retro_mmul_1280,
Monodelphis domestica ENSMODG000000070903 retrocopies
retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Mus musculus ENSMUSG000000597967 retrocopies
retro_mmus_1810, retro_mmus_1853, retro_mmus_2320, retro_mmus_2473, retro_mmus_3122, retro_mmus_325, retro_mmus_527,
Nomascus leucogenys ENSNLEG000000095477 retrocopies
retro_nleu_2109, retro_nleu_2117, retro_nleu_230, retro_nleu_2470, retro_nleu_2769, retro_nleu_440, retro_nleu_701,
Pan troglodytes ENSPTRG0000000869410 retrocopies
retro_ptro_1201, retro_ptro_1465, retro_ptro_2954, retro_ptro_3112, retro_ptro_3247, retro_ptro_450, retro_ptro_750, retro_ptro_810, retro_ptro_862, retro_ptro_870,
Rattus norvegicus ENSRNOG000000306283 retrocopies
retro_rnor_1059, retro_rnor_2213, retro_rnor_2306,
Sorex araneus ENSSARG000000060177 retrocopies
retro_sara_224, retro_sara_383, retro_sara_461, retro_sara_567, retro_sara_6, retro_sara_605, retro_sara_89,
Ictidomys tridecemlineatus ENSSTOG000000126011 retrocopy
retro_itri_858,
Ictidomys tridecemlineatus ENSSTOG00000024814 1 retrocopy
retro_itri_610 ,


Copyright © RetrogeneDB 2014-2017