RetrogeneDB ID:

retro_itri_40

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393300.1:8409097..8411119(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSTOG00000011516
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:KIF2A
Ensembl ID:ENSSTOG00000012710
Aliases:None
Description:kinesin heavy chain member 2A [Source:HGNC Symbol;Acc:6318]


Retrocopy-Parental alignment summary:






>retro_itri_40
ATGGCAAGCCAGTTCTGCCTCCCTCTTGCCCCACGACTTTCACCCCTGAAAGCCTTGAAGTCGCACTTCAGAGACATCCA
AGTGGGCATCTGCCTGGCGATCCAGCGCAGCGACAAGAGGATCCATCTTGCTGTAGTCACAGAGATCAACAGAGAAAAAT
CTTGGGTCACAGTTGAGTGGATTGAGAAAGGAGTCAAGAAAGGCAAGAAGATCGATCTAGAGTCCATATTCCTGCTGAAT
CCAGCTCTGGCCTCTGCAGAACATAGCACCACGTTGCCTAGGCCCTTGCCCTCATTGTCCCTAGTACCCTCCAAGGCCAT
TGGAGATCAGCGTACATCCCCAAGGTGGATTGTGGTTGCCCCCCAGAAAAATGAAACACCCTCAGGGGACAGCTCGGTCC
TGGGGGTCCCCGCCAGCCCTTGTCTGATGAAGCGGAAAAAGTCTCCTTGCCTTCGGGAAATCGAGAAATTGCAAAAGCAG
AGGGAGAAGCGCAGGCGCCTGCAGTTGGAGATCCGAGCCAGACGCGCCCTCAACGTCAACACGGGAAACCCAAACTTCGA
GATCATGCGCATGATCGAAGAGTGCCGCAGACACCTGGACAAAAGCAAGATGTCCATCATGGAGCCCCTGGAAGATCACC
GGATCTGTGTCTGCGTGAGGAAGAGGCCTCTTAATCAGCGAGAGACCACCATGAAGGACCTGGATATCATCACCATCCCC
TCTGACAATGTAGTCATGGTGCACGAGTCCAAGCAGAAGGTGGACCTCACCCGCTACCTGGAGAACCAGACCTTCTGTTT
CGACCATGCTTTTGATGACAAGGCCTCCAATGAGTTAGTGTACCAGTTCACTGCCCAGCCATTGGTGGAGTCTATCTTCC
GCAAGGGCATGGCCACCTGCTTTGCCTATGGACAAACGGGCAGTGGGAAAACGCACACCATGGGCGGAGCCTTTTCTGGA
ACGTCTCAAGATTGCTCTAAAGGTATTTACGCCTTGGTAGCGCAAGACGTCTTTCTCTTGCTCAAAAACTCCACTTACGA
GAATCTGGACCTCAAAGTCTATGGGACCTTTTTTGAGATTTATGGTGGCAAAGTGTATGACTTGTTGAACTGGAAGAGGA
AGCTCCAAGTCCTCGAGGATGGCAATCAGCAAATGCAAGTTGTCGGGCTGCAGGAGAAAGAGGTGGGCTCCGTGGAGGAC
GTGCTGAACCTGGTGGAACTGGGAAACGGCTGTCGGACTTCGGGACAAACGTCTGTCAATGCCCACTCATCCCGGAGCCA
CGCGGTTTTCCAGATCATCTTGAAGTCAAGAGGGAAACTGCACGGCAAGTTCTCTCTGGTTGATTTAGCTGGGAACGAGA
GGGGAGCAGACACCGCCAAGGCCAACCGCAAGAGGCAGCTGGAAGGGGCGGAGATTAACAAGAGTCTCCTGGCCCTCAAA
GAATGCATCAGGGCTTTGGGTCAGAACAAACCTCACACCCCTTTCAGAGCCAGCAAACTCACGCAGGTGCTCCGGGACTC
CTTCATAGGCCAGAACTCTTCCACTTGCATGATCGCTACCATCTCACCAGGGATGACCTCTTGTGAAAACACCCTCAACA
CTTTAAGATATGCAAACAGAGTGAAAGAGTTAGCCCTGGATGTGAGGCCTTACCACCAATGCCTGACTCCCATTAAACAC
GAGACACCGCCCATGTTTGAAAAGCACATTAAAAATTCAGAAATAGCCCTTCAGAGGGAAGAGCTTGTTAAAATATCGTG
TCTACAGAGTGAGGAGGAGAAACGGAGTGAAGCGATTGCCACACTAGCCACGCCCTTAATAAGGGAGGCCGTGACTACCT
GGAAGGATTCTAGTTCGTGGTGGGAGAGCATCCAGGAGACAGCTAATGGCGTGAACTATGATGTTGACTTTTGCATTGCC
CAGTCATTGTCCATTTTGGAGGAGAAAATTGGTATTCTGACCGAGATCCAAACGAAACTGAAATTATTAAGAGTTGACCT
CCAAAACCAAGAGCAAGGTAGA

ORF - retro_itri_40 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.12 %
Parental protein coverage: 55.6 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalRRKSNCVKEVEKLQEKREKRRLQQQELREKRAQDVDATNPNYEIMCMIRDFRGSLDYRPLTTADPIDEHR
R.KS.C..E.EKLQ..REKRR..Q.E.R..RA..V...NPN.EIM.MI...R..LD........P...HR
RetrocopyRKKSPCLREIEKLQKQREKRRRLQLEIRARRALNVNTGNPNFEIMRMIEECRRHLDKSKMSIMEPLEDHR
ParentalICVCVRKRPLNKKETQMKDLDVITIPSKDVVMVHEPKQKVDLTRYLENQTFRFDYAFDDSAPNEMVYRFT
ICVCVRKRPLN..ET.MKDLD.ITIPS..VVMVHE.KQKVDLTRYLENQTF.FD.AFDD.A.NE.VY.FT
RetrocopyICVCVRKRPLNQRETTMKDLDIITIPSDNVVMVHESKQKVDLTRYLENQTFCFDHAFDDKASNELVYQFT
ParentalARPLVETIFERGMATCFAYGQTGSGKTHTMGGDFSGKNQDCSKGIYALAARDVFLMLKKPNYKKLELQVY
A.PLVE.IF..GMATCFAYGQTGSGKTHTMGG.FSG..QDCSKGIYAL.A.DVFL.LK...Y..L.L.VY
RetrocopyAQPLVESIFRKGMATCFAYGQTGSGKTHTMGGAFSGTSQDCSKGIYALVAQDVFLLLKNSTYENLDLKVY
ParentalATFFEIYSGKVFDLLNRKTKLRVLEDGKQQVQVVGLQEREVKCVEDVLKLIDIGNSCRTSGQTSANAHSS
.TFFEIY.GKV.DLLN.K.KL.VLEDG.QQ.QVVGLQE.EV..VEDVL.L...GN.CRTSGQTS.NAHSS
RetrocopyGTFFEIYGGKVYDLLNWKRKLQVLEDGNQQMQVVGLQEKEVGSVEDVLNLVELGNGCRTSGQTSVNAHSS
ParentalRSHAVFQIILRRKGKLHGKFSLIDLAGNERGADTSSADRQTRLEGAEINKSLLALKECIRALGRNKPHTP
RSHAVFQIIL...GKLHGKFSL.DLAGNERGADT..A.R...LEGAEINKSLLALKECIRALG.NKPHTP
RetrocopyRSHAVFQIILKSRGKLHGKFSLVDLAGNERGADTAKANRKRQLEGAEINKSLLALKECIRALGQNKPHTP
ParentalFRASKLTQVLRDSFIGENSRTCMIATISPGMASCENTLNTLRYANRVKEFGI
FRASKLTQVLRDSFIG.NS.TCMIATISPGM.SCENTLNTLRYANRVKE...
RetrocopyFRASKLTQVLRDSFIGQNSSTCMIATISPGMTSCENTLNTLRYANRVKELAL

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_40 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_40 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 25 parental genes, and 31 retrocopies.

Species Parental gene accession Retrocopies number
Anas platyrhynchos ENSAPLG000000095191 retrocopy
retro_apla_3,
Bos taurus ENSBTAG000000150221 retrocopy
retro_btau_180,
Choloepus hoffmanni ENSCHOG000000078881 retrocopy
retro_chof_1348,
Cavia porcellus ENSCPOG000000093931 retrocopy
retro_cpor_72,
Dipodomys ordii ENSDORG000000063351 retrocopy
retro_dord_763,
Equus caballus ENSECAG000000198101 retrocopy
retro_ecab_32,
Homo sapiens ENSG000000687961 retrocopy
retro_hsap_69,
Gorilla gorilla ENSGGOG000000047741 retrocopy
retro_ggor_68,
Macaca mulatta ENSMMUG000000003991 retrocopy
retro_mmul_145,
Monodelphis domestica ENSMODG000000196051 retrocopy
retro_mdom_242,
Mus musculus ENSMUSG000000216931 retrocopy
retro_mmus_68,
Nomascus leucogenys ENSNLEG000000028651 retrocopy
retro_nleu_2329,
Oryctolagus cuniculus ENSOCUG000000104661 retrocopy
retro_ocun_156,
Otolemur garnettii ENSOGAG000000005275 retrocopies
retro_ogar_126, retro_ogar_3166, retro_ogar_3498, retro_ogar_3501, retro_ogar_672,
Ochotona princeps ENSOPRG000000117681 retrocopy
retro_opri_815,
Procavia capensis ENSPCAG000000050891 retrocopy
retro_pcap_22,
Rattus norvegicus ENSRNOG000000140002 retrocopies
retro_rnor_1284, retro_rnor_47,
Sorex araneus ENSSARG000000077681 retrocopy
retro_sara_457,
Sarcophilus harrisii ENSSHAG000000019501 retrocopy
retro_shar_30,
Ictidomys tridecemlineatus ENSSTOG000000075531 retrocopy
retro_itri_1104,
Ictidomys tridecemlineatus ENSSTOG00000012710 1 retrocopy
retro_itri_40 ,
Tupaia belangeri ENSTBEG000000093961 retrocopy
retro_tbel_761,
Tarsius syrichta ENSTSYG000000021151 retrocopy
retro_tsyr_1791,
Vicugna pacos ENSVPAG000000088641 retrocopy
retro_vpac_572,
Drosophila melanogaster FBgn00302682 retrocopies
retro_dmel_1, retro_dmel_2,


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