RetrogeneDB ID:

retro_etel_2048

Retrocopy
location
Organism:Lesser hedgehog tenrec (Echinops telfairi)
Coordinates:scaffold_41305:2800..3517(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF3E
Ensembl ID:ENSETEG00000013105
Aliases:None
Description:eukaryotic translation initiation factor 3, subunit E [Source:HGNC Symbol;Acc:3277]


Retrocopy-Parental alignment summary:






>retro_etel_2048
ATGGCGGAGTACGACCTGACTACTCGTATCGCACATTTCTTGGCTCGGCATCTCGTCTTCCCGCTGCTGGAGTTCCTCTC
CGTGAAGGAGATATATAATGAAAAGGAATTATTACAGGGAAACTGGATCTTCTTAGTGATACCAACATGGTAGGCTTTGC
CATGGACGTAGATAAAAACCTTTATTCCGATGATATCCCTCCTGCTCTGCAAGAAGAAAGAACCACAGTTGTTGCACAAC
GGAAACAACTCCAGGCAGAAACAGAACCAATTGTGAAAATGTTTGAAGATCCAGAAGCCACAAGGCAGATGCAATCAACT
AGGGATGGTCGGATGTCATTTGACTACCTGGCAGATAAGCATGGTGTTAGGCAGGGATATTTAGACACTCTCTACAGATA
TGCAAAATTCCAGTATAAATGTGGGAATTACTCAGGAGCAGCAGAATATCTTTATTTTTTTAGAGGGCTGGTTCCAGCAA
CTGATAGGAATGCTCTGAGTTCCCTTTGGGGGAAACTGGCCTCTGAAATCTGAATGCAGAATTGGGATGCAGCCATGGAA
GACCTTACAAGGTTGAAAGAGACCATTGATAATAATTCTGTGAGTTCTCCCCTCCAGTCTCTTCAGCAGCGAACATGGCT
CATTCACTGCTCTCTGTTTGTTTTCTTCAACCACCCCAGGCTGGGATAACATTATTGATCTCTTCCTTTACCAACCA

ORF - retro_etel_2048 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.77 %
Parental protein coverage: 54.18 %
Number of stop codons detected: 1
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalMAEYDLTTRIAHFLDRHLVFPLLEFLSVKEIYNEKELLQG-KLDLLSDTNMVDFAMDVYKNLYSDDIPHA
MAEYDLTTRIAHFL.RHLVFPLLEFLSVKEIYNEKELLQG.KLDLLSDTNMV.FAMDV.KNLYSDDIP.A
RetrocopyMAEYDLTTRIAHFLARHLVFPLLEFLSVKEIYNEKELLQG<KLDLLSDTNMVGFAMDVDKNLYSDDIPPA
ParentalLREKRTTVVAQLKQLQAETEPIVKMFEDPETTRQMQSTXXXXXXXXXXXXXXXFRQEYLDTLYRYAKFQY
L.E.RTTVVAQ.KQLQAETEPIVKMFEDPE.TRQMQST................RQ.YLDTLYRYAKFQY
RetrocopyLQEERTTVVAQRKQLQAETEPIVKMFEDPEATRQMQSTRDGRMSFDYLADKHGVRQGYLDTLYRYAKFQY
ParentalECGNYSGAAEYLYFFRVLVPATDRNALSSLWGKLASEILMQNWDAAMEDLTRLKETIDNNSVSSPLQSLQ
.CGNYSGAAEYLYFFR.LVPATDRNALSSLWGKLASEI.MQNWDAAMEDLTRLKETIDNNSVSSPLQSLQ
RetrocopyKCGNYSGAAEYLYFFRGLVPATDRNALSSLWGKLASEI*MQNWDAAMEDLTRLKETIDNNSVSSPLQSLQ
ParentalQRTWLIHWSLFV-FFNHPK-GRDNIIDLFLYQP
QRTWLIH.SLFV.F...P..G.DNIIDLFLYQP
RetrocopyQRTWLIHCSLFV<FLQPPQ<GWDNIIDLFLYQP

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_2048 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 18 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000067021 retrocopy
retro_btau_291,
Canis familiaris ENSCAFG000000007021 retrocopy
retro_cfam_1127,
Callithrix jacchus ENSCJAG000000064583 retrocopies
retro_cjac_2333, retro_cjac_2686, retro_cjac_701,
Equus caballus ENSECAG000000002361 retrocopy
retro_ecab_860,
Echinops telfairi ENSETEG00000013105 1 retrocopy
retro_etel_2048 ,
Felis catus ENSFCAG000000036651 retrocopy
retro_fcat_231,
Homo sapiens ENSG000001044081 retrocopy
retro_hsap_3489,
Gorilla gorilla ENSGGOG000000229552 retrocopies
retro_ggor_2354, retro_ggor_2355,
Myotis lucifugus ENSMLUG000000072691 retrocopy
retro_mluc_1796,
Macaca mulatta ENSMMUG000000113591 retrocopy
retro_mmul_2585,
Mustela putorius furoENSMPUG000000059242 retrocopies
retro_mputfur_193, retro_mputfur_736,
Mus musculus ENSMUSG000000223362 retrocopies
retro_mmus_1801, retro_mmus_2807,
Nomascus leucogenys ENSNLEG000000041201 retrocopy
retro_nleu_333,
Oryctolagus cuniculus ENSOCUG000000080501 retrocopy
retro_ocun_1399,
Pan troglodytes ENSPTRG000000205051 retrocopy
retro_ptro_2362,
Rattus norvegicus ENSRNOG000000276904 retrocopies
retro_rnor_1133, retro_rnor_2879, retro_rnor_583, retro_rnor_584,
Ictidomys tridecemlineatus ENSSTOG000000089761 retrocopy
retro_itri_545,
Tursiops truncatus ENSTTRG000000110252 retrocopies
retro_ttru_1602, retro_ttru_1794,


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