RetrogeneDB ID:

retro_dord_80

Retrocopy
location
Organism:Kangaroo rat (Dipodomys ordii)
Coordinates:GeneScaffold_2323:36162..36503(-)
Located in intron of:ENSDORG00000010955
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSDORG00000001065
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_dord_80
ATGGCAGCAGAGAAAAAAATGGTAAAAATTAGATCTGAAACACTACAGACCAAGAAGAGACCTGAACAGTTCAATATACC
TGTGGTCTTGGAGAGTAAGAAAGGTGCTTAGGCAGATAGGTTTGGAATTTCTTCTGTTTCAACAAAAGACCTGTCATCTG
ACAACAAGCCTGTGGTTAAAATGGGCCAGCTAAAGGAAAGAGTACAATGATTTGGTTTGTCTCTTCTATCCCTAGAAAGT
CTAAAGATGATTAGAAATTGAAAAAGAGCAAGGAACAATTTGGGATTGTCTCAAGTTCTGCTGGAACTGGAACCATAGAA
GATACAAAGACAAAGTAAAGG

ORF - retro_dord_80 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.66 %
Parental protein coverage: 56.19 %
Number of stop codons detected: 4
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalVAAEKKVVKITSEISQTERMQKRAERFNVPVSLESKKAARAARFGISSVPTKGLSSDNKTMVNLDKLKER
.AAEKK.VKI.SE..QT....KR.E.FN.PV.LESKK.A.A.RFGISSV.TK.LSSDNK..V....LKER
RetrocopyMAAEKKMVKIRSETLQTK---KRPEQFNIPVVLESKKGA*ADRFGISSVSTKDLSSDNKPVVKMGQLKER
ParentalAQRFGLNVSSIS-RKSEDDEKLKKRKERFGIVTSSAGTGTTEDTEAKKR
.Q.FGL...S.......D....K..KE.FGIV.SSAGTGT.EDT..K.R
RetrocopyVQ*FGLSLLSLE<KSKDD*KLKKS-KEQFGIVSSSAGTGTIEDTKTK*R

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






RNA-Seq - click to see more details

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Dipodomys ordii was not studied using ChIP-Seq data.

EST - click to see more details

Dipodomys ordii was not studied using EST data.

TSS - click to see more details

Dipodomys ordii was not studied using FANTOM5 data.

Lab - click to see more details

retro_dord_80 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 18 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000117692 retrocopies
retro_amel_1602, retro_amel_347,
Bos taurus ENSBTAG000000206621 retrocopy
retro_btau_202,
Callithrix jacchus ENSCJAG000000078538 retrocopies
retro_cjac_1070, retro_cjac_1487, retro_cjac_1801, retro_cjac_2439, retro_cjac_2560, retro_cjac_389, retro_cjac_4139, retro_cjac_731,
Cavia porcellus ENSCPOG000000117551 retrocopy
retro_cpor_1313,
Dipodomys ordii ENSDORG00000001065 1 retrocopy
retro_dord_80 ,
Erinaceus europaeus ENSEEUG000000151761 retrocopy
retro_eeur_549,
Homo sapiens ENSG000002053231 retrocopy
retro_hsap_3882,
Gorilla gorilla ENSGGOG000000132172 retrocopies
retro_ggor_2613, retro_ggor_2753,
Loxodonta africana ENSLAFG000000150531 retrocopy
retro_lafr_1024,
Microcebus murinus ENSMICG000000109021 retrocopy
retro_mmur_358,
Monodelphis domestica ENSMODG000000289491 retrocopy
retro_mdom_1909,
Mustela putorius furoENSMPUG000000008851 retrocopy
retro_mputfur_617,
Mus musculus ENSMUSG000000784271 retrocopy
retro_mmus_54,
Nomascus leucogenys ENSNLEG000000175992 retrocopies
retro_nleu_2779, retro_nleu_569,
Procavia capensis ENSPCAG000000094772 retrocopies
retro_pcap_262, retro_pcap_45,
Pongo abelii ENSPPYG000000046302 retrocopies
retro_pabe_3116, retro_pabe_3358,
Pan troglodytes ENSPTRG000000297472 retrocopies
retro_ptro_2644, retro_ptro_2782,
Rattus norvegicus ENSRNOG000000305202 retrocopies
retro_rnor_1326, retro_rnor_471,


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