RetrogeneDB ID:

retro_mdom_242

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:2:180369276..180371283(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000014874
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:KIF2A
Ensembl ID:ENSMODG00000019605
Aliases:None
Description:kinesin heavy chain member 2A [Source:HGNC Symbol;Acc:6318]


Retrocopy-Parental alignment summary:






>retro_mdom_242
ACGGCCAGCCAGTTGTCTCGCCACATTTTATCTGATTCCACCTCCCTGAAACGCATGAGTCCACACTTTGGAGCGATTCA
AATAGGCGTCTCCCTGAATATCAGGAGAAGTGACGGAAGAATCCACCCCGCAGTGGTCGCTTCGATCAACAAGAACAACA
ACAGCGTGACGGTAGAGTGGCTCGAGAAGGGTGCCAACAAGGGCAAGAAAGTTGATCTAGCCACAGTGCTCCTGCTCAAT
CCAGGACTGTCCGCTCCAGGGTATCTCCAGTCTTCTAGAGTCCCAACCCCGCTGCCGTTGACTGCCCTCTATTCCGCCAA
GGGCGACAAAGCCTCCACGAACCAATGGGTGGTGCACCCTCAGAAGAATGAGACGGCTTCGGGGGACAGCCTGGTGACCT
TCAGCGAGCCGGTCTTAGTGAAGCAGAGAAAGTCACACTGCCTGCTGGAGATTGAAAAACTACAGAAGCAGCGGCAAAAG
AGGAGGCAGCAGCTGCTGGAATTTCAGGCCAAGAGAGCCCAAAATGTCAATGTGGTTAGACCTAACTATGAGATCATGTG
TATGATTCAGGAGTTCCGAAGGAAGATAGACTACTCCAAGATGCTCAGCCCTGACCCCACAGACGACCATCGAATCTGTG
TCTGTGTACGCAAAAGGCCACTCAATGAGCAAGAGACCCTGGTGAAAGATTTGGACATCATCACAGTCCCCACCAGGAAT
GTGGTCATGGTGCATGAATCCAAGCAAAAGGTGGATCTGACCCGCTACCTTGAACACCACACCTTCCGCTTTGACCATGC
CTTTGATGACACTGCTTCCAACGAATTTGTGTACCGATTCACTGCCCAACCACTGGTGGAGAACATCTTCCACAAGGGTA
TGGCCACTTGCTTTGCCTATGGTCAGACGGGCAGTGGGAAAACACACACAATGGGAGGGGATCTTTTCGGGAGAAGCCAA
AATTGCTCTAAAGGCATCTATGCCCTCGTGGCTGAGGATGTCTTCTTAATGCTCAAGAAGCCCACTTATGAGAAGTTGGA
CCTGAAGGTCTATGGGACATTTTTTGAGATTTATGGGGGCAAAGTGTATGATTTACTGAACTGGAAGACGAAACTCAGGG
TCCTTGAGGATGCCAAGCAACAAATCCAGGTTTTGGGACTACAGGAACAGGAAGTGTGCTGTGTAGAAGACGTGCTGAAC
CTCATTGAGCTAGGCAGCAGCTACCGGACTTCTGGTCAGACATCTGTCAATGCCCACTCTTCTCGAAGTCATGCTGTATT
TCAGATCATACTGAAGAGGAAAGGGAAGTTGCATGGAAAGTTTTCCCTCATTGACCTAGCTGGAAATGAGAGGGGAGCAG
ACACCTGCAGAACCAGCAGACAGAGGCAATTAGAAGGAGCAGAAATAAACAAAAGTCTCCTGGCACTCAAAGAATGCATA
AGGGCACTGGGACAAAATAAGCCTCATACCCCATTCAGAGCCAGCAAACTGACACAGGTGCTTAGGGATTCATTCATAGG
CAAGAACGCTTGCACCTGTATGATTGCTACAATCTCTCCAGGACTGAGTTCATGTGAAAACACACTCAATACTTTAAGGT
ATGCAAACAGAGTAAAGGAATTAACTCTGGATTCTAGTCTTTTAAATTATCTCCATCCACATGTGCATCAGGAGTCAAAG
CTACTAGATAAACAAATTGTGACTCCAACAGGAAAACAGGAGAAGCGTGATTATAAAATATTTTTACAAAGTGAAGATGT
GGATGAGGCAGATGAAGAGGAAGTGACATCTACAAAATTAGACAAAAAAAAATCAGCGTCCTGCAAAGAATCCAGTCAGT
GGCTCAGAGCATTTTTAGAGATGGCAGATGGAATAAACTATGATGTAGATTTCTGTGCTGCCCAGTTAGAGTCCATCTTG
GAGCAGAAAATTGTTACTCTGAAAGAAATCCAAGGAAAGGTGAAATTATTCCGGGAAAATCTCCAGAAGGAAAAGCCAGG
CAATTGA

ORF - retro_mdom_242 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.54 %
Parental protein coverage: 54.44 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRRKSNCVKEVEKLQEKREKRRLQQQELREKRAQDVDATNPNYEIMCMIRDFRGSLDYRPLTTADPIDEHR
.RKS.C..E.EKLQ..R.KRR.Q..E...KRAQ.V....PNYEIMCMI..FR...DY......DP.D.HR
RetrocopyQRKSHCLLEIEKLQKQRQKRRQQLLEFQAKRAQNVNVVRPNYEIMCMIQEFRRKIDYSKMLSPDPTDDHR
ParentalICVCVRKRPLNKKETVMKDLDVITIPSKDVVMVHEPKQKVDLTRYLENQTFRFDYAFDDSAPNEMVYRFT
ICVCVRKRPLN..ET..KDLD.IT.P...VVMVHE.KQKVDLTRYLE..TFRFD.AFDD.A.NE.VYRFT
RetrocopyICVCVRKRPLNEQETLVKDLDIITVPTRNVVMVHESKQKVDLTRYLEHHTFRFDHAFDDTASNEFVYRFT
ParentalARPLVETIFERGMATCFAYGQTGSGKTHTMGGDFSGKNQDCSKGIYALAARDVFLMLKKPNYKKLELQVY
A.PLVE.IF..GMATCFAYGQTGSGKTHTMGGD..G..Q.CSKGIYAL.A.DVFLMLKKP.Y.KL.L.VY
RetrocopyAQPLVENIFHKGMATCFAYGQTGSGKTHTMGGDLFGRSQNCSKGIYALVAEDVFLMLKKPTYEKLDLKVY
ParentalATFFEIYSGKVFDLLNRKTKLRVLEDGKQQVQVVGLQEREVKCVEDVLKLIEIGNSCRTSGQTSANAHSS
.TFFEIY.GKV.DLLN.KTKLRVLED.KQQ.QV.GLQE.EV.CVEDVL.LIE.G.S.RTSGQTS.NAHSS
RetrocopyGTFFEIYGGKVYDLLNWKTKLRVLEDAKQQIQVLGLQEQEVCCVEDVLNLIELGSSYRTSGQTSVNAHSS
ParentalRSHAVFQIILRRKGKLHGKFSLIDLAGNERGADTSSADRQTRLEGAEINKSLLALKECIRALGRNKPHTP
RSHAVFQIIL.RKGKLHGKFSLIDLAGNERGADT....RQ..LEGAEINKSLLALKECIRALG.NKPHTP
RetrocopyRSHAVFQIILKRKGKLHGKFSLIDLAGNERGADTCRTSRQRQLEGAEINKSLLALKECIRALGQNKPHTP
ParentalFRASKLTQVLRDSFIGENSRTCMIATISPGMASCENTLNTLRYANRVKEFGISPS
FRASKLTQVLRDSFIG.N..TCMIATISPG..SCENTLNTLRYANRVKE.....S
RetrocopyFRASKLTQVLRDSFIGKNACTCMIATISPGLSSCENTLNTLRYANRVKELTLDSS

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






RNA-Seq - click to see more details

(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
SRP007412_brain 0 .00 RPM 0 .00 RPM
SRP007412_cerebellum 0 .00 RPM 0 .00 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .00 RPM
SRP007412_liver 0 .00 RPM 0 .00 RPM
SRP007412_testis 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

Monodelphis domestica was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mdom_242 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_242 was not experimentally validated.

Retrocopy orthology:
Monodelphis domestica 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 24 parental genes, and 30 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 ENSMODG00000019605 1 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 ENSSTOG000000127101 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,


Copyright © RetrogeneDB 2014-2017