RetrogeneDB ID:

retro_etel_2058

Retrocopy
location
Organism:Lesser hedgehog tenrec (Echinops telfairi)
Coordinates:scaffold_43788:2013..2856(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DPPA2
Ensembl ID:ENSETEG00000007985
Aliases:None
Description:developmental pluripotency associated 2 [Source:HGNC Symbol;Acc:19197]


Retrocopy-Parental alignment summary:






>retro_etel_2058
GTGGAGTCCTCGACGTACCTCGACATGGAAAAGAATTACTTTGAAAGCGAATTGGACTAGGAGAGTTTCGTCATCACACT
GGTTCCAGTTAAAGAGGAACCCAACGGAGAGCAACCAAGTGAACAAAGAGTTTTTATACCACCAGAATACAAACCGAAGA
AGCCTAGGAAAATAAATAAAGTTCATCTTCCTCAAACAAGCGAACAAGCCAAAGTGCACCGAAAAAGTAGCACAGATATA
AACCTTCCTCTGCCGCATGGTTTGCCTCCAGTTACTGAGGTACATGGGGACACTTTGCGGAAATGGTGCCAGCAAGCCAA
GTTGAGCACCGCTGGGCAGAAAGTGGAAGTTTATCTATGGCTCCAGCAGTTTGTTTACCCTCACCCAAAATAGAACATTC
CTGATACACCACAGGCAGCCAGGATACAATCAATATCGAGGAAACGCAAGATCAAGCAACCCAGACTTGAGGACAAGCAG
ACAGGCGTTCCAGAGACAGAAGTCACCAACGTTGTTGAAGTGGACTCTCCAGCTCCGGAGGCCACGCTGGCATCCTGGGC
AAGGATTTCCTCAAAAGCACTTCAACCTAAGGCTGGGAACTCACGTCACCTTCACTCTGCAATTGAAGCTTTTTTGGCAC
CAGGCTTTGGCAGCAGATGGTGTGTGGTCCATGGCAAAACCCACCCTGCAGAGACAGAGGGCTGGGTCCGCCTGCAGTTC
CACTCCGGTCAAACCTGGGGGCCGAGCATGCCCAGGAGGATGATCTCTCTCTTCCTTTTACCTGGTTACGTTTTCCCACC
CCTGGATGTAGAAGACAATATGTTGTGTCCTGAGTGTGTTAAG

ORF - retro_etel_2058 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.34 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVETSAYVDMEKNYFESELDEESFVITLVPVKEEPNGEQPSEQSVLVPPEVKPKKPRKRNKVHLPQTSEQA
VE.S.Y.DMEKNYFESELD.ESFVITLVPVKEEPNGEQPSEQ.V..PPE.KPKKPRK.NKVHLPQTSEQA
RetrocopyVESSTYLDMEKNYFESELD*ESFVITLVPVKEEPNGEQPSEQRVFIPPEYKPKKPRKINKVHLPQTSEQA
ParentalKVRRRNNTNIDLPLPDVLPPVTEVHRDTLRKWCQQAKLSTDGQKVEVYLRLQKFVYPHQKQDVPDSPRAA
KV.R...T.I.LPLP..LPPVTEVH.DTLRKWCQQAKLST.GQKVEVYL.LQ.FVYPH.K...PD.P.AA
RetrocopyKVHRKSSTDINLPLPHGLPPVTEVHGDTLRKWCQQAKLSTAGQKVEVYLWLQQFVYPHPK*NIPDTPQAA
ParentalKIQSISRKRKIKQPTLEDKDR-PSRAQVANVVEVDSPAPEATLASWARISSKALQPKAVNSRHLHSAIEA
.IQSISRKRKIKQP.LEDK........V.NVVEVDSPAPEATLASWARISSKALQPKA.NSRHLHSAIEA
RetrocopyRIQSISRKRKIKQPRLEDKQTGVPETEVTNVVEVDSPAPEATLASWARISSKALQPKAGNSRHLHSAIEA
ParentalFLAPGFGSRWCVVHGKTLPAETEGWVRLQFHAGQTWVPSTPRRMISLFLLPAYVFPPLDVEDNMLCPECV
FLAPGFGSRWCVVHGKT.PAETEGWVRLQFH.GQTW.PS.PRRMISLFLLP.YVFPPLDVEDNMLCPECV
RetrocopyFLAPGFGSRWCVVHGKTHPAETEGWVRLQFHSGQTWGPSMPRRMISLFLLPGYVFPPLDVEDNMLCPECV
ParentalK
K
RetrocopyK

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






RNA-Seq - click to see more details

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Echinops telfairi was not studied using ChIP-Seq data.

EST - click to see more details

Echinops telfairi was not studied using EST data.

TSS - click to see more details

Echinops telfairi was not studied using FANTOM5 data.

Lab - click to see more details

retro_etel_2058 was not experimentally validated.

Retrocopy orthology:
Echinops telfairi 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 21 parental genes, and 64 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000204602 retrocopies
retro_btau_435, retro_btau_529,
Callithrix jacchus ENSCJAG000000201684 retrocopies
retro_cjac_1378, retro_cjac_1991, retro_cjac_3832, retro_cjac_944,
Dasypus novemcinctus ENSDNOG000000107456 retrocopies
retro_dnov_1248, retro_dnov_1626, retro_dnov_1714, retro_dnov_2462, retro_dnov_2583, retro_dnov_2656,
Erinaceus europaeus ENSEEUG000000089444 retrocopies
retro_eeur_205, retro_eeur_415, retro_eeur_426, retro_eeur_616,
Echinops telfairi ENSETEG000000027221 retrocopy
retro_etel_312,
Echinops telfairi ENSETEG00000007985 4 retrocopies
retro_etel_2051, retro_etel_2058 , retro_etel_506, retro_etel_918,
Homo sapiens ENSG000001635303 retrocopies
retro_hsap_1642, retro_hsap_2903, retro_hsap_357,
Microcebus murinus ENSMICG000000137446 retrocopies
retro_mmur_1171, retro_mmur_156, retro_mmur_1634, retro_mmur_213, retro_mmur_598, retro_mmur_955,
Myotis lucifugus ENSMLUG000000074441 retrocopy
retro_mluc_1706,
Macaca mulatta ENSMMUG000000221123 retrocopies
retro_mmul_1550, retro_mmul_342, retro_mmul_475,
Monodelphis domestica ENSMODG000000180833 retrocopies
retro_mdom_1057, retro_mdom_1478, retro_mdom_999,
Mus musculus ENSMUSG000000724197 retrocopies
retro_mmus_1303, retro_mmus_1832, retro_mmus_1847, retro_mmus_2391, retro_mmus_2935, retro_mmus_3699, retro_mmus_394,
Nomascus leucogenys ENSNLEG000000040202 retrocopies
retro_nleu_1329, retro_nleu_633,
Oryctolagus cuniculus ENSOCUG000000031751 retrocopy
retro_ocun_61,
Otolemur garnettii ENSOGAG000000312287 retrocopies
retro_ogar_1678, retro_ogar_1722, retro_ogar_1953, retro_ogar_2404, retro_ogar_2567, retro_ogar_2900, retro_ogar_586,
Ochotona princeps ENSOPRG000000050591 retrocopy
retro_opri_433,
Pongo abelii ENSPPYG000000135663 retrocopies
retro_pabe_1360, retro_pabe_2401, retro_pabe_346,
Pan troglodytes ENSPTRG000000151993 retrocopies
retro_ptro_1113, retro_ptro_1962, retro_ptro_281,
Sarcophilus harrisii ENSSHAG000000173981 retrocopy
retro_shar_542,
Tupaia belangeri ENSTBEG000000062121 retrocopy
retro_tbel_3864,
Tursiops truncatus ENSTTRG000000095001 retrocopy
retro_ttru_1524,


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