RetrogeneDB ID:

retro_shar_823

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL867591.1:463056..464916(+)
Located in intron of:ENSSHAG00000008766
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PABPC4
Ensembl ID:ENSSHAG00000018139
Aliases:None
Description:poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:HGNC Symbol;Acc:8557]


Retrocopy-Parental alignment summary:






>retro_shar_823
AGCGGATCCTCTGGGGGGCAAATGGCGTCCCTCTATGTAGGTGACCTCCATCACGACGTGACCGAAGCAATGTTATACGA
GAAGTTCAGTCCAGCGGGGCCCATCTTATCTATTCGAGTGTGTAGGGATATGATCACCCGGAGTTCCCTAGGATATGCCT
ACGTTAACTTCCAACAATCGTCAGATGCCCAGCGGGTGTTGGAAACCATGAACCTGGATGTGATCAAGGGCAAGCCGGTT
CGTATTATGTGGTCCCAACGTGACCCTTCACTGCGCAAGAGTGGTGTGGGAAACATTTTTGTTAAAAATCTAGAAAAGTC
CATTGACAACAGGGCCCTATTTGATGCTTTCTCTGGCTTCGGCAATATTCTGTCCTGCAAAGTGGTCAGTGATGAGAACG
GTTCCAAAGGCTACGGCTTTGTTCACTTTGAAACTCAAGAGTCTGCCGAAAAAGCTATAGAAAAGATGAACGGGATAGTT
TTGAAAAGCCTCAAAGTATTTGTCGGTCACTTTAAATCCCGCAAAGAGCGAGAATTGGAACTTGGAGCTAGAGCTAGAGA
GTTCACCAACGTTTACATCAAGAATTTCGGAGAAGACATGGACAATGCTAGACTCGGTGAGATATTTGGAAGATTCGGAC
GGGCTCTGAGTGTAAAAGTAATGACTGACGAAAGGGGGAGGTCTAAAGGTTTTGGATTTGTTAGTTATGCAACACACGAA
GATGCTCAGAGAGCCGTGGATGAAATGAATGGAAAAGAACTCAATGGAAGACGGATTTATGTTGGAAGAGCTCAGAAAAA
GGGAGAGAGGCAGACAGAACTGAAACGCCATTTTGAACAGATTAAACAAGACAGAGTTACCAGGTACCAGGGGGTCAATC
TTTATGTGAAAAATCTTGATGACACCATTGATGACGAGCGGTTGAGAACAGAATTCTCCCCATTTGGTACAATTACAAGT
GCAAAGGTCATGATGGAAGGAGGACACAGCAGAGGCTTTGGATTTGTTTGTTTTTCAGCACCAGATGAAGCTGCCAAGGC
AGTCACAGAAATGAATGGCAAATTAGTAACCAGTAAGCCTCTGTACGTAGCGTTAGCCCAGCGCAAAGAAGAACGCCAAG
CGCACTTGACAAACCAGTATATGCGGAGAATGGCTAACATTCAGACCTTTGCCAATCCGGTGCTCAATCCCTACCACCAG
CCAACATCATCTTCCAGATATATCATGACCACTGTCCCATCGTCTCAGACCCGCACTTCATACTATCCTTATGGCCAAGT
TCCCCAACTCAGAACATCTTCTCACTGGGGCCCTCCAGGTGGAAGACTTCCCCCATTTCCAACTGTCTCCGGTGTCGTCC
GTCCCAAGACTCCTAGACCACCATTCAACCCTATGAGATCTGCTTCGGGCCCGGTTCCGAGAATGATGACCACCCAGCGC
GTTGTCAATCCGCCAAACCAGGTGTTTGGGCCTCCACGTCCACCATTCATTCCCAATCTGCGAGCAGTTCAGCAATACAA
ATACGCCGCCGGTGTCCGCAATCCAAAACGTTTCGAGCTACCGATGCAAATCAACATTCCACAGCCTGCCGTCCATGCTG
CGGCCCAAGAGGTGTTAACCGCTTCCATGTTAGCAGATGCCCTTCCCCAGGAGCAAAAGCAGATGTTAGGAGAACGCCTG
TTTCCACTCATTCAAGTCATGCATCCTGCTCTGGCCGGTAAGATCACAGGCATGCTGCTAGAGATCGACAACTCCGAACT
TCTTCACATGCTTGAGTCTCCCGAATCTCTGCGCTCCAAAGTGGACGAAGCTGTGGCTGTCCTGCAGGCCCACCAGGTGA
AAGAAGCTGCCCGGAGGGAA

ORF - retro_shar_823 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.32 %
Parental protein coverage: 98.41 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalTAASSYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM
...S...MASLYVGDLH.DVTEAMLYEKFSPAGP.LSIRVCRDMITR.SLGYAYVNFQQ..DA.R.L.TM
RetrocopySGSSGGQMASLYVGDLHHDVTEAMLYEKFSPAGPILSIRVCRDMITRSSLGYAYVNFQQSSDAQRVLETM
ParentalNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYAF
N.DVIKGKP.RIMWSQRDPSLRKSGVGN.F.KNL.KSIDN.AL.D.FS.FGNILSCKVV.DENGSKGY.F
RetrocopyNLDVIKGKPVRIMWSQRDPSLRKSGVGNIFVKNLEKSIDNRALFDAFSGFGNILSCKVVSDENGSKGYGF
ParentalVHFETQDAADRAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGDDMDDERLKELFS
VHFETQ..A..AIEKMNG..L...KVFVG.FKSRKERE.ELGA.A.EFTNVYIKNFG.DMD..RL.E.F.
RetrocopyVHFETQESAEKAIEKMNGIVLKSLKVFVGHFKSRKERELELGARAREFTNVYIKNFGEDMDNARLGEIFG
ParentalKYGKTLSVKVMTDSSGKSKGFGFVSFEKHEDANKAVEEMNGKDINGKMVFVGRAQKKVERQAELKRKFEQ
..G..LSVKVMTD..G.SKGFGFVS...HEDA..AV.EMNGK..NG....VGRAQKK.ERQ.ELKR.FEQ
RetrocopyRFGRALSVKVMTDERGRSKGFGFVSYATHEDAQRAVDEMNGKELNGRRIYVGRAQKKGERQTELKRHFEQ
ParentalLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPDEATKAVTE
.KQ.R..RYQGVNLY.KNLDDTIDDE.LR.EFSPFG.ITSAKVM.E.G.S.GFGFVCFS.PDEA.KAVTE
RetrocopyIKQDRVTRYQGVNLYVKNLDDTIDDERLRTEFSPFGTITSAKVMMEGGHSRGFGFVCFSAPDEAAKAVTE
ParentalMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQRIAGMRALPANTIINQF-QPTPGG-YFMPAVPQAQNRP
MNG..V.SKPLYVALAQRKEER.AHLTNQYM.R.A......AN...N...QPT....Y.M..VP..Q.R.
RetrocopyMNGKLVTSKPLYVALAQRKEERQAHLTNQYMRRMANIQTF-ANPVLNPYHQPTSSSRYIMTTVPSSQTRT
ParentalPYYAPNQIAQMRPNPRW-QQGGRPQGFQGVPNAIRQSGPRPTLRHLTPASNTQASRGLPTTPQRVGVPTA
.YY...Q..Q.R....W...GGR...F..V....R...PRP.......AS.........TT...V..P..
RetrocopySYYPYGQVPQLRTSSHWGPPGGRLPPFPTVSGVVRPKTPRPPFNPMRSASGPVPR--MMTTQRVVNPPNQ
ParentalVQNLSPRPSVATPAPRAVPPYKYAANVRSPHPAIQPLQ--TPQPAVHVQGQEPLTASMLAAAPPQEQKQM
V....PRP....P..RAV..YKYAA.VR.P.....P.Q...PQPAVH...QE.LTASMLA.A.PQEQKQM
RetrocopyVFG-PPRPPF-IPNLRAVQQYKYAAGVRNPKRFELPMQINIPQPAVHAAAQEVLTASMLADALPQEQKQM
ParentalLGERLFPLIQTMHNNLAGKITGMLLEIDNSELLHMLESPESLRSKVEEAVAVLQAHHAKKEAAQK
LGERLFPLIQ.MH..LAGKITGMLLEIDNSELLHMLESPESLRSKV.EAVAVLQAH..K..A...
RetrocopyLGERLFPLIQVMHPALAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQVKEAARRE

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






RNA-Seq - click to see more details

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST - click to see more details

Sarcophilus harrisii was not studied using EST data.

TSS - click to see more details

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab - click to see more details

retro_shar_823 was not experimentally validated.

Retrocopy orthology:
Sarcophilus harrisii 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 29 parental genes, and 63 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000115352 retrocopies
retro_amel_107, retro_amel_676,
Bos taurus ENSBTAG000000171253 retrocopies
retro_btau_1492, retro_btau_28, retro_btau_656,
Canis familiaris ENSCAFG000000030812 retrocopies
retro_cfam_45, retro_cfam_837,
Choloepus hoffmanni ENSCHOG000000053273 retrocopies
retro_chof_1150, retro_chof_1182, retro_chof_1274,
Callithrix jacchus ENSCJAG000000025123 retrocopies
retro_cjac_214, retro_cjac_2722, retro_cjac_284,
Cavia porcellus ENSCPOG000000095522 retrocopies
retro_cpor_1330, retro_cpor_77,
Equus caballus ENSECAG000000093962 retrocopies
retro_ecab_2, retro_ecab_502,
Felis catus ENSFCAG000000152542 retrocopies
retro_fcat_116, retro_fcat_545,
Homo sapiens ENSG000000906212 retrocopies
retro_hsap_109, retro_hsap_74,
Gorilla gorilla ENSGGOG000000040023 retrocopies
retro_ggor_2127, retro_ggor_87, retro_ggor_916,
Loxodonta africana ENSLAFG000000001513 retrocopies
retro_lafr_1144, retro_lafr_390, retro_lafr_597,
Microcebus murinus ENSMICG000000166331 retrocopy
retro_mmur_675,
Myotis lucifugus ENSMLUG000000120682 retrocopies
retro_mluc_228, retro_mluc_397,
Macaca mulatta ENSMMUG000000074971 retrocopy
retro_mmul_178,
Monodelphis domestica ENSMODG000000176572 retrocopies
retro_mdom_1090, retro_mdom_1805,
Mustela putorius furoENSMPUG000000144142 retrocopies
retro_mputfur_152, retro_mputfur_546,
Mus musculus ENSMUSG000000112577 retrocopies
retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Nomascus leucogenys ENSNLEG000000119282 retrocopies
retro_nleu_1517, retro_nleu_62,
Oryctolagus cuniculus ENSOCUG000000005622 retrocopies
retro_ocun_153, retro_ocun_792,
Otolemur garnettii ENSOGAG000000040671 retrocopy
retro_ogar_71,
Ochotona princeps ENSOPRG000000119841 retrocopy
retro_opri_1133,
Pongo abelii ENSPPYG000000015062 retrocopies
retro_pabe_190, retro_pabe_2563,
Pan troglodytes ENSPTRG000000005733 retrocopies
retro_ptro_101, retro_ptro_2093, retro_ptro_8,
Rattus norvegicus ENSRNOG000000156422 retrocopies
retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii ENSSHAG000000112671 retrocopy
retro_shar_24,
Sarcophilus harrisii ENSSHAG000000138321 retrocopy
retro_shar_78,
Sarcophilus harrisii ENSSHAG00000018139 1 retrocopy
retro_shar_823 ,
Sus scrofa ENSSSCG000000036603 retrocopies
retro_sscr_1210, retro_sscr_974, retro_sscr_975,
Tursiops truncatus ENSTTRG000000143402 retrocopies
retro_ttru_1117, retro_ttru_246,


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