RetrogeneDB ID:

retro_dord_27

Retrocopy
location
Organism:Kangaroo rat (Dipodomys ordii)
Coordinates:scaffold_9938:12930..14031(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSDORG00000000075
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Tram1
Ensembl ID:ENSDORG00000001901
Aliases:None
Description:translocating chain-associating membrane protein 1 [Source:MGI Symbol;Acc:MGI:1919515]


Retrocopy-Parental alignment summary:






>retro_dord_27
ATGGGACTCCGTAAGAAGAGCGCCAAGAACCCCCCGATGCTGAGCCAGGAATTCATCCTGCAGAACCACGCGGACCTCGT
CTCGTGCGTGGGCATGTTCTTCGTGCTGGGGCTGATGTTCGAGGGCACGGCCGACGTGTCCATCGTGTTTCTGACGCTGC
AGCACGGCGTGGTGGTCCCCGCAGACGAGGAGCCGGAGGGCACCAAGACCCTCTATCATTATGGGGTGAAGGATCTGGCC
ACGGTGTTCTTCTACATGCTGGTGACCATCATCCTGCATGCCACCATCCAGGAGTACGTGCTGGATAAGATCAGCCGGAG
GATGCAGTTCACCAAGGCCAAGCAGAACAAGTGCAACGAATCCGGCCAGTTCAGCGCCTTCTACTTGGTGTCTTGCATCT
GGGGGACCTTCATCCTCATCTCGGAAGACTGCCTGTCGGACCCGGCTCTCCTGTGGAGAGCTCAGGGCCACAACATGATG
ACGTTCCAGATGAAGTTCTTCTACATCTCGCAGCTGGCTTATTGGTTCCACGGGTTTCCAGAACTCTACTTCCAGAAAAT
CAAGAAGCAGGACATCCCCAGCCAGCTGATCTACATCGGGGTGCACCTGTTCCACATCGCCGGCGCTTACCTTCTGTACC
TCAACCACCTGGGGCTCCTTCTCTTGGTGCTGCATTATCTGGTGGAGTTGCTCTCCCATCTGTGCGCCCTGGTGTATTTC
AGCGATGAGAAGTATCAGAAAGGGGTGTCTCTGTGGACTTTTGTATTTATCCTGGGGAGACTGGTGACGTTGATCGTGTC
TGTGGTCACCGTGGGCCTTCACCTGGCCGGATCCCCGGGTCGGAGCACCGACGCCATCAGCGGGAATGTCAATGTGTTGG
CCGCTAAGATCGCGGTCCTGTCGTCCAGCTGTTCCATCCAGGCGTACATCACGTGGACCTTGATTACCGTGCGTCTGCAG
AGGTGGGTGGAGGATGCGAACCTGCAGGCCTCCTGTGTGAAGAAGCGACGGTCCAGGTCTTCGAGAAAAGGCACCGAAAA
TGGAGTGGAAGCTACCCAGAGGGCTGACGCTCTCCCAAAGAGGAAAGAGAAATCTTCCTAG

ORF - retro_dord_27 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.31 %
Parental protein coverage: 83.16 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalEQATESASLYYYGIKDLATVFFYMLVAIIIHAIIQEYVLDKINRRMHFSKTKHSKFNESGQLSAFYLFAC
E.......LY.YG.KDLATVFFYMLV.II.HA.IQEYVLDKI.RRM.F.K.K..K.NESGQ.SAFYL..C
RetrocopyEEPEGTKTLYHYGVKDLATVFFYMLVTIILHATIQEYVLDKISRRMQFTKAKQNKCNESGQFSAFYLVSC
ParentalVWGTFILISENYISDPTILWRAYPHNLMTFQMKFFYISQLAYWLHAFPELYFQKTKKEDIPRQLVYIGLY
.WGTFILISE...SDP..LWRA..HN.MTFQMKFFYISQLAYW.H.FPELYFQK.KK.DIP.QL.YIG..
RetrocopyIWGTFILISEDCLSDPALLWRAQGHNMMTFQMKFFYISQLAYWFHGFPELYFQKIKKQDIPSQLIYIGVH
ParentalLFHIAGAYLLNLNHLGLVLLVLHYFVEFLFHISRLFYFSDEKYQKGFSLWAVLFVLGRLLTLILSVLTVG
LFHIAGAYLL.LNHLGL.LLVLHY.VE.L.H...L.YFSDEKYQKG.SLW...F.LGRL.TLI.SV.TVG
RetrocopyLFHIAGAYLLYLNHLGLLLLVLHYLVELLSHLCALVYFSDEKYQKGVSLWTFVFILGRLVTLIVSVVTVG
ParentalFGLARAENQKLDFSTGNFNVLAVRIAVLASICITQAFMMWKFINFQLRRWREHSTFQAPPVKKKPAVTKG
..LA.......D...GN.NVLA..IAVL.S.C..QA...W..I...L.RW.E....QA..VKK.......
RetrocopyLHLAGSPGRSTDAISGNVNVLAAKIAVLSSSCSIQAYITWTLITVRLQRWVEDANLQASCVKKR----RS
ParentalRSSRKGAKNGVNGTVTSNGADSPRNRKEKSS
RSSRKG..NGV..T.....AD....RKEKSS
RetrocopyRSSRKGTENGVEAT---QRADALPKRKEKSS

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_27 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 25 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000063251 retrocopy
retro_amel_78,
Bos taurus ENSBTAG000000075621 retrocopy
retro_btau_24,
Canis familiaris ENSCAFG000000078661 retrocopy
retro_cfam_15,
Callithrix jacchus ENSCJAG000000078931 retrocopy
retro_cjac_168,
Dasypus novemcinctus ENSDNOG000000092962 retrocopies
retro_dnov_27, retro_dnov_906,
Dipodomys ordii ENSDORG00000001901 1 retrocopy
retro_dord_27 ,
Equus caballus ENSECAG000000183781 retrocopy
retro_ecab_506,
Echinops telfairi ENSETEG000000184471 retrocopy
retro_etel_674,
Felis catus ENSFCAG000000287751 retrocopy
retro_fcat_136,
Homo sapiens ENSG000000671671 retrocopy
retro_hsap_51,
Loxodonta africana ENSLAFG000000116251 retrocopy
retro_lafr_9,
Macaca mulatta ENSMMUG000000015161 retrocopy
retro_mmul_235,
Monodelphis domestica ENSMODG000000073161 retrocopy
retro_mdom_308,
Mustela putorius furoENSMPUG000000106161 retrocopy
retro_mputfur_558,
Mus musculus ENSMUSG000000259351 retrocopy
retro_mmus_117,
Nomascus leucogenys ENSNLEG000000113761 retrocopy
retro_nleu_73,
Oryctolagus cuniculus ENSOCUG000000087341 retrocopy
retro_ocun_52,
Otolemur garnettii ENSOGAG000000063791 retrocopy
retro_ogar_2932,
Pongo abelii ENSPPYG000000186601 retrocopy
retro_pabe_169,
Pan troglodytes ENSPTRG000000203341 retrocopy
retro_ptro_2081,
Rattus norvegicus ENSRNOG000000078921 retrocopy
retro_rnor_287,
Sus scrofa ENSSSCG000000061931 retrocopy
retro_sscr_980,
Ictidomys tridecemlineatus ENSSTOG000000055371 retrocopy
retro_itri_38,
Tarsius syrichta ENSTSYG000000138871 retrocopy
retro_tsyr_24,
Tursiops truncatus ENSTTRG000000003281 retrocopy
retro_ttru_24,


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