RetrogeneDB ID:

retro_dord_716

Retrocopy
location
Organism:Kangaroo rat (Dipodomys ordii)
Coordinates:scaffold_6035:19661..20021(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Vti1b
Ensembl ID:ENSDORG00000015939
Aliases:None
Description:vesicle transport through interaction with t-SNAREs 1B [Source:MGI Symbol;Acc:MGI:1855688]


Retrocopy-Parental alignment summary:






>retro_dord_716
ATGGCCATCTCTGCCGCCTCCTGGAGCACTTGGAGAGCTGCACGAGCTCTTCCATGGCCTCCATGAAGACCTACAAGCAG
TGCCCTAGCAGCTGCTGGGGACGGCGGGGACAGAAGAGAAGGTAATCAGAGGTTTTGATGAAAAGCAACAGGAATGAATG
AAACGCTGGCAGCGATGGGGCAGAACTTTGACAGGCACCCCAGTCTTTCCGTAACCCCACGATGCCTAAGCTACGGAAAC
TACCTGAAGGACCTTGCCAAACTCTATCGGGAATTTAGGATCAGGCCTTTGACAGCCACACCTAGGGGCCGAGGAGACAT
GAAGTATGGCACATGTGCCTTAGAAAATGAACATATGGAT

ORF - retro_dord_716 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.88 %
Parental protein coverage: 53.02 %
Number of stop codons detected: 2
Number of frameshifts detected: 5


Retrocopy - Parental Gene Alignment:

ParentalMATSAAS-SEHFE-KLHEIFRGLHEDLRAVPERLLGTAGTEEKKKLIRDFDEKQQE-ANETLAEMEE-EL
MA.SAAS..EH.E..LHE.F.GLHEDL.AVP..LLGTAGTEEK...IR.FDEKQQE..NETLA.M...EL
RetrocopyMAISAAS<LEHLE<ELHELFHGLHEDLQAVP*QLLGTAGTEEK--VIRGFDEKQQE<MNETLAAMGQ<EL
ParentalRYAPLSFRNPMMSKLR-NYRKDLAKLHREVRTTPLTATPGGRGDIKYGTYALENEHMN
..AP.SFRNP.M.KLR.NY.KDLAKL.RE.R..PLTATP.GRGD.KYGT.ALENEHM.
Retrocopy*QAPQSFRNPTMPKLR>NYLKDLAKLYREFRIRPLTATPRGRGDMKYGTCALENEHMD

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_716 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 38 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000152631 retrocopy
retro_cjac_1439,
Dasypus novemcinctus ENSDNOG000000036432 retrocopies
retro_dnov_1503, retro_dnov_2031,
Dipodomys ordii ENSDORG00000015939 2 retrocopies
retro_dord_52, retro_dord_716 ,
Echinops telfairi ENSETEG000000061011 retrocopy
retro_etel_783,
Felis catus ENSFCAG000000140901 retrocopy
retro_fcat_1855,
Homo sapiens ENSG000001005683 retrocopies
retro_hsap_1002, retro_hsap_2682, retro_hsap_3013,
Gorilla gorilla ENSGGOG000000056202 retrocopies
retro_ggor_1871, retro_ggor_797,
Macropus eugenii ENSMEUG000000049102 retrocopies
retro_meug_499, retro_meug_697,
Microcebus murinus ENSMICG000000108431 retrocopy
retro_mmur_849,
Myotis lucifugus ENSMLUG000000111843 retrocopies
retro_mluc_1299, retro_mluc_2393, retro_mluc_781,
Macaca mulatta ENSMMUG000000158661 retrocopy
retro_mmul_1420,
Mustela putorius furoENSMPUG000000071301 retrocopy
retro_mputfur_1516,
Nomascus leucogenys ENSNLEG000000007804 retrocopies
retro_nleu_1184, retro_nleu_2241, retro_nleu_231, retro_nleu_83,
Pongo abelii ENSPPYG000000059275 retrocopies
retro_pabe_2298, retro_pabe_2498, retro_pabe_2602, retro_pabe_845, retro_pabe_974,
Pan troglodytes ENSPTRG000000064683 retrocopies
retro_ptro_1808, retro_ptro_2037, retro_ptro_751,
Pteropus vampyrus ENSPVAG000000116713 retrocopies
retro_pvam_132, retro_pvam_592, retro_pvam_797,
Tupaia belangeri ENSTBEG000000030491 retrocopy
retro_tbel_3432,
Tarsius syrichta ENSTSYG000000076882 retrocopies
retro_tsyr_1662, retro_tsyr_94,


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