RetrogeneDB ID:

retro_shar_567

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL849974.1:192392..193313(+)
Located in intron of:ENSSHAG00000005377
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CNN3
Ensembl ID:ENSSHAG00000002670
Aliases:None
Description:calponin 3, acidic [Source:HGNC Symbol;Acc:2157]


Retrocopy-Parental alignment summary:






>retro_shar_567
AAGAACAAGTATGCCTCCAAATATGACCATCAGGCAGAGGAAGACCTTCGCAAATGGATAGAAGAAGTTACAGGCTTTAG
TATTGGGACAAACTTTCAATGGAGTTTAAAAAACGGCATCATCCTCTGCGAACTTATAAACAAGCTAGAGCCAGGTTCAG
TGAAGACAGTCAATGTATCTTTATTACACTGGCCTCAGTTGGAGAATATTAGTAACTTTATTAAAGCCGTTCAAGCTTAT
GGTGTGAAGCCGCCTGATGTCTTTGAAGAAAATGATCTTTATGATAATGAAAACATGACTCGAGTTCGGTCTACACTGTT
AGCTTTAGCAGATCTGGCTAAAACAAAAGGATTCCATACGACAATTGAGGATAGCATCAAACATTCAGAAAACCAAGCAA
GGTCTTTTGATGAAGAGCCAAGAAATGAAGAAAATGTAATTGACTCACAGAAGGAAACCAACAGACCTGATGGCCAGGTA
GGAATGACTGCCTTTGGGACTAGGGAGTATCTTTATGATTCTCTCTGGACAAACTTGGACAAACTTTTTGATATGACAAC
AATTGAGCTGGAGATGGATACTAACAAAGGAACCAGACTGGCTGGAAAGTTAGCACAAGGTACTGGAAGAGACATCTATG
ATTAGAAGCTAACATTAGGACCAATGGACAGCTCAGTTTTCACTACAAATGGGTAACTACAAAGTCGATTCCCAGAAAGG
AATGAGTCTTGGGGGACAAGTATATGATCCTAAATATTTTGCTGCACCAACAGAATCTGTAATACATAATTCAAGCTAAG
GAACAGGAACAAATGGGTCTGAAATCAGTGATAGTGATTATCAGGCAAAATTTCCAGATGAATAATATGCGAGTACCAAG
ACGGCTATCCAAGATATTACCAACATAGTGACCAGGCACTG

ORF - retro_shar_567 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.52 %
Parental protein coverage: 99.36 %
Number of stop codons detected: 3
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalKNKIASKYDHQAEEDLRNWIEEVTGLSIGTNFQLGLKDGIILCELINKLQPGSVKKVNESSLNWPQLENI
KNK.ASKYDHQAEEDLR.WIEEVTG.SIGTNFQ..LK.GIILCELINKL.PGSVK.VN.S.L.WPQLENI
RetrocopyKNKYASKYDHQAEEDLRKWIEEVTGFSIGTNFQWSLKNGIILCELINKLEPGSVKTVNVSLLHWPQLENI
ParentalGNFIKAIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAKTKGFHTTIDIGVKYAEKQARRFDEGK
.NFIKA.QAYG.KP.D.FE.NDL..N.NMT.V..TL.ALA.LAKTKGFHTTI....K..E.QAR.FDE..
RetrocopySNFIKAVQAYGVKPPDVFEENDLYDNENMTRVRSTLLALADLAKTKGFHTTIEDSIKHSENQARSFDE-E
ParentalLKAGQSVIGLQMGTNKCASQAGMTAYGTRRHLYDPKMQT-DKPFDQTTISLQMGTNKGASQAGMLAPGTR
......VI..Q..TN....Q.GMTA.GTR..LYD......DK.FD.TTI.L.M.TNKG...AG.LA.GT.
RetrocopyPRNEENVIDSQKETNRPDGQVGMTAFGTREYLYDSLWTNLDKLFDMTTIELEMDTNKGTRLAGKLAQGTG
ParentalRDIYDQKLTLQPVDNSTI-SLQMGTNKVASQKGMSVYGLGRQVYDPKYCAAPTEPVIHNGSQGTGTNGSE
RDIYD.KLTL.P.D.S...SLQMG..KV.SQKGMS...LG.QVYDPKY.AAPTE.VIHN.S.GTGTNGSE
RetrocopyRDIYD*KLTLGPMD-SSV>SLQMGNYKVDSQKGMS---LGGQVYDPKYFAAPTESVIHNSS*GTGTNGSE
ParentalISDNDYQAEYPDEYHV-EYQDDCPRDYEYSDQGI
ISD.DYQA..PDE....EYQD..PR.Y..SDQ..
RetrocopyISDSDYQAKFPDE*YA<EYQDGYPRYYQHSDQAL

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_567 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 18 parental genes, and 44 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000167071 retrocopy
retro_amel_1412,
Bos taurus ENSBTAG000000203451 retrocopy
retro_btau_1211,
Callithrix jacchus ENSCJAG000000181283 retrocopies
retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Dasypus novemcinctus ENSDNOG000000128833 retrocopies
retro_dnov_223, retro_dnov_403, retro_dnov_815,
Equus caballus ENSECAG000000201881 retrocopy
retro_ecab_655,
Echinops telfairi ENSETEG000000100951 retrocopy
retro_etel_638,
Homo sapiens ENSG000001175191 retrocopy
retro_hsap_3419,
Gorilla gorilla ENSGGOG000000138701 retrocopy
retro_ggor_2312,
Macropus eugenii ENSMEUG000000029212 retrocopies
retro_meug_2020, retro_meug_42,
Macaca mulatta ENSMMUG000000016901 retrocopy
retro_mmul_1747,
Monodelphis domestica ENSMODG000000043261 retrocopy
retro_mdom_442,
Mustela putorius furoENSMPUG000000033321 retrocopy
retro_mputfur_896,
Mus musculus ENSMUSG000000539312 retrocopies
retro_mmus_1052, retro_mmus_2544,
Nomascus leucogenys ENSNLEG000000112075 retrocopies
retro_nleu_122, retro_nleu_1342, retro_nleu_2698, retro_nleu_480, retro_nleu_668,
Pan troglodytes ENSPTRG0000000097915 retrocopies
retro_ptro_1061, retro_ptro_1149, retro_ptro_1247, retro_ptro_1447, retro_ptro_1505, retro_ptro_1554, retro_ptro_1871, retro_ptro_215, retro_ptro_2323, retro_ptro_2377, retro_ptro_2831, retro_ptro_2894, retro_ptro_3007, retro_ptro_483, retro_ptro_653,
Sarcophilus harrisii ENSSHAG00000002670 1 retrocopy
retro_shar_567 ,
Tarsius syrichta ENSTSYG000000107492 retrocopies
retro_tsyr_1458, retro_tsyr_1907,
Vicugna pacos ENSVPAG000000048892 retrocopies
retro_vpac_190, retro_vpac_449,


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