RetrogeneDB ID:

retro_dord_117

Retrocopy
location
Organism:Kangaroo rat (Dipodomys ordii)
Coordinates:GeneScaffold_3546:95..780(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Gnb2l1
Ensembl ID:ENSDORG00000010735
Aliases:None
Description:guanine nucleotide binding protein (G protein), beta polypeptide 2 like 1 [Source:MGI Symbol;Acc:MGI:101849]


Retrocopy-Parental alignment summary:






>retro_dord_117
CTGCGCCTGTGGGATCTCACCATGGGCACCACCACAAGACGATTCGTAGGTCATACCAAGGATGTGCTGAGCGTGGCCTT
CTCCTCTGACAACCGGCAGATTGTCTCTGGATCCCAAGACAAAACTATCAAGTTATGGAATACTCTGGGTGTCTGCAAGT
ACACAGTCCAGGATGAGAGCACTCTGTGTGGGTTTCCTGTGTCCAGTTTTCACCCAACAGCAGCAACCCTATCATCATCT
TGTGTGGCTGGGACAAGCTGGGGAAGGTATGGAATTTGGCTAATTGTAAGCTGAAAACCAATCGCATTGGCCACATGGGC
TATCTGAACACTGTGACTGTCTTTCCAGATGGTTCTCTCTGTGCTTCAGGAGACAAGGATGGCCAGGCCATGTTGTGGGA
TCTCAATGAAGGCAAGCACCTTTATATGCTAGGTGGTGGGGCATCATCACTGCCCTTGTGCTTCAGCCCCACCACTACTG
GCTGTGTGCTGCCACCGGCCCCAGCATCAAGATCTGGGACTTAGAAGGCAAGATCATTGTAGATGAACTTAAACAAGAAG
TTATCAGTACCAGCAGCAAGGCAGAGCCACCCCAGTGCACCTCATTGGCCTGGTCGGGTAATGGGCAGACTCTGTTTGCT
GAATACACTGACAACCTGGTGTGGGTATGGCAGGTGACCATCGGT

ORF - retro_dord_117 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.74 %
Parental protein coverage: 69.82 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLRLWDLTTGTTTRRFVGHTKDVLSVAFSSDNRQIVSGSRDKTIKLWNTLGVCKYTVQDES-HSEWVSCVR
LRLWDLT.GTTTRRFVGHTKDVLSVAFSSDNRQIVSGS.DKTIKLWNTLGVCKYTVQDES.HS.WVSCV.
RetrocopyLRLWDLTMGTTTRRFVGHTKDVLSVAFSSDNRQIVSGSQDKTIKLWNTLGVCKYTVQDES<HSVWVSCVQ
ParentalFSPNSSNPIIVSCGWDKLVKVWNLANCKLKTNHIGHTGYLNTVTVSPDGSLCASGGKDGQAMLWDLNEGK
FSPNSSNPII..CGWDKL.KVWNLANCKLKTN.IGH.GYLNTVTV.PDGSLCASG.KDGQAMLWDLNEGK
RetrocopyFSPNSSNPIIILCGWDKLGKVWNLANCKLKTNRIGHMGYLNTVTVFPDGSLCASGDKDGQAMLWDLNEGK
ParentalHLYTLDGG-DIINALCFSPNRYWLCAATGPSIKIWDLEGKIIVDELKQEVISTSSKAEPPQCTSLAWSAD
HLY.L.GG..II.AL...P..YWLCAATGPSIKIWDLEGKIIVDELKQEVISTSSKAEPPQCTSLAWS..
RetrocopyHLYMLGGG<GIITALVLQPHHYWLCAATGPSIKIWDLEGKIIVDELKQEVISTSSKAEPPQCTSLAWSGN
ParentalGQTLFAGYTDNLVRVWQVTIG
GQTLFA.YTDNLV.VWQVTIG
RetrocopyGQTLFAEYTDNLVWVWQVTIG

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_117 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 26 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000120081 retrocopy
retro_acar_185,
Ailuropoda melanoleuca ENSAMEG000000000041 retrocopy
retro_amel_1627,
Bos taurus ENSBTAG000000196481 retrocopy
retro_btau_1461,
Canis familiaris ENSCAFG000000248181 retrocopy
retro_cfam_1824,
Callithrix jacchus ENSCJAG000000187521 retrocopy
retro_cjac_2876,
Cavia porcellus ENSCPOG000000087241 retrocopy
retro_cpor_687,
Dipodomys ordii ENSDORG00000010735 1 retrocopy
retro_dord_117 ,
Equus caballus ENSECAG000000225673 retrocopies
retro_ecab_172, retro_ecab_218, retro_ecab_986,
Erinaceus europaeus ENSEEUG000000087291 retrocopy
retro_eeur_368,
Echinops telfairi ENSETEG000000160243 retrocopies
retro_etel_1135, retro_etel_114, retro_etel_2086,
Homo sapiens ENSG000002046281 retrocopy
retro_hsap_3226,
Gorilla gorilla ENSGGOG000000253671 retrocopy
retro_ggor_2194,
Macropus eugenii ENSMEUG000000110553 retrocopies
retro_meug_1095, retro_meug_1109, retro_meug_1532,
Myotis lucifugus ENSMLUG000000155071 retrocopy
retro_mluc_811,
Macaca mulatta ENSMMUG000000036041 retrocopy
retro_mmul_1956,
Monodelphis domestica ENSMODG000000040911 retrocopy
retro_mdom_1426,
Mustela putorius furoENSMPUG000000011482 retrocopies
retro_mputfur_1103, retro_mputfur_1111,
Mus musculus ENSMUSG000000203721 retrocopy
retro_mmus_3282,
Nomascus leucogenys ENSNLEG000000026041 retrocopy
retro_nleu_729,
Ornithorhynchus anatinus ENSOANG000000026001 retrocopy
retro_oana_127,
Otolemur garnettii ENSOGAG000000149242 retrocopies
retro_ogar_1257, retro_ogar_1591,
Pongo abelii ENSPPYG000000199391 retrocopy
retro_pabe_149,
Pan troglodytes ENSPTRG000000227341 retrocopy
retro_ptro_2178,
Rattus norvegicus ENSRNOG000000023903 retrocopies
retro_rnor_1831, retro_rnor_2130, retro_rnor_895,
Ictidomys tridecemlineatus ENSSTOG000000070631 retrocopy
retro_itri_1752,
Tupaia belangeri ENSTBEG000000146612 retrocopies
retro_tbel_3897, retro_tbel_3899,


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