RetrogeneDB ID:

retro_dord_544

Retrocopy
location
Organism:Kangaroo rat (Dipodomys ordii)
Coordinates:scaffold_29583:132..851(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Vps37a
Ensembl ID:ENSDORG00000014879
Aliases:None
Description:vacuolar protein sorting 37A (yeast) [Source:MGI Symbol;Acc:MGI:1261835]


Retrocopy-Parental alignment summary:






>retro_dord_544
GGTTTTCCATTTCTTCCAGCATATCCTCCTCAAGAAGTTAACAGAACATCACTTCTTTGTTACTGACACTGTTTCTTCTT
CAACAAGTTATACAACAGCCAAGTCTGCTGCTCCTACATTTGGTGTCCTTTCAAGTCTGCCATTGCCTGTTCCCACAATG
GAAACTTCAACACCGATAAGCCAAAATGGTTTTGGGTACAAGATGCCAGATGTCCCTGATGCATTTCCAGAACTCTCAGG
ATTGTGTCACAACTCACAGATATGAATGAACAAGAGGAAGTATTACTAGAACAGTTTCTGAGTTTACCTCAACTAAAACA
AATTATTAATGACAAGGGTGATTTAGTAAAAAGTATTGAGGAATTAGCAAGAAAACTCTCCTCTTGGAGCCCAGTTTGGA
AGCCAAAAGGCAAACTGTTTTAGATAAGTATGAGTTACTTACACAAATGAAATCTACGTTTGAAAAGAAAATGCAGAGAC
AACATGAACTGAGTGAGAGTTGTAGTGCAAGTGCCCTACAGGCAAGATGGAAAGTCGCTGCACATGAAGCTGAGGAAGAA
TCTGATAATATTGCTGAAGATTTCTCGGAGGGAAAAACTGAAATAGATGATTTTCTCAGTAGCTTCATGGAAAAAAGAAC
AGTTTGCCACTGTAGAAGAGCCAAGGAAGAGAAACTTAAACAAGTGATAGCAATGCACAGCCAACTTCATGGTCCATTA

ORF - retro_dord_544 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.04 %
Parental protein coverage: 62.4 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalGFPFLPAYPPQEANRNITSLS-VADTVSSSTTSYTTAKPAAPTFAVLSSLPLPVPTMETSTPISQNGFGY
GFPFLPAYPPQE.NR..TSL..V.DTVSSST.SYTTAK.AAPTF.VLSSLPLPVPTMETSTPISQNGFGY
RetrocopyGFPFLPAYPPQEVNR--TSLL>VTDTVSSST-SYTTAKSAAPTFGVLSSLPLPVPTMETSTPISQNGFGY
ParentalKMPDVPDAFPELSELSVSQLTDMN-EQEEVLLEQFLSLPQLKQIINDKDDLVKSIEELAR-KNLLLEPSL
KMPDVPDAFPELS.L.......MN...E..L.EQFLSLPQLKQIINDK.DLVKSIEELAR.K.LLLEPSL
RetrocopyKMPDVPDAFPELSGLCHNSQI*MN<QEEVLL-EQFLSLPQLKQIINDKGDLVKSIEELAR<KTLLLEPSL
ParentalEAKRQTVLDKYELLTQMKSTFEKKMQRQHELSESCSASALQARLKVAAHEAEEESDNIAEDFLEGKTEID
EAKRQTVLDKYELLTQMKSTFEKKMQRQHELSESCSASALQAR.KVAAHEAEEESDNIAEDF.EGKTEID
RetrocopyEAKRQTVLDKYELLTQMKSTFEKKMQRQHELSESCSASALQARWKVAAHEAEEESDNIAEDFSEGKTEID
ParentalDFLSSFMEKRTICHCRRAKEEKLQQVIAMHSQFHAPL
DFLSSFMEKRT.CHCRRAKEEKL.QVIAMHSQ.H.PL
RetrocopyDFLSSFMEKRTVCHCRRAKEEKLKQVIAMHSQLHGPL

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






Dipodomys ordii was not studied using RNA-Seq expression data.
Dipodomys ordii was not studied using ChIP-Seq data.
Dipodomys ordii was not studied using EST data.
Dipodomys ordii was not studied using FANTOM5 data.
retro_dord_544 was not experimentally validated.

Retrocopy orthology:
Dipodomys ordii 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 8 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000006822 retrocopies
Callithrix jacchus ENSCJAG000000117691 retrocopy
Dipodomys ordii ENSDORG00000014879 9 retrocopies
Homo sapiens ENSG000001559751 retrocopy
Gorilla gorilla ENSGGOG000000116501 retrocopy
Nomascus leucogenys ENSNLEG000000025581 retrocopy
Pongo abelii ENSPPYG000000183862 retrocopies
Pan troglodytes ENSPTRG000000200191 retrocopy



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