RetrogeneDB ID:

retro_etel_1174

Retrocopy
location
Organism:Lesser hedgehog tenrec (Echinops telfairi)
Coordinates:scaffold_222632:3611..4424(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSETEG00000011434
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF4A2
Ensembl ID:ENSETEG00000018565
Aliases:None
Description:eukaryotic translation initiation factor 4A2 [Source:HGNC Symbol;Acc:3284]


Retrocopy-Parental alignment summary:






>retro_etel_1174
GTCTCTTTCTTGGGGTATCTATGCATGTGTTTTTGAGAAACCTTCAGCTATTCTGCAGAGAGCTATCATTCCTTACATTT
AAAGATCCAAAAGGTAATCTCGGCACTTGGAGACTATCTGGGAGCAACTTGCCATGCATGTAATGGAGGAACCAATGTTC
AAAATGAAAAGCACAAAGTGCAGGCTGAAGCACTACACGTGTGGTTGTACTCCCAGGAGAGTATTTGTTGTGTTGAATAG
ACAATGTCTTTCTACACAATGAATCAAAATGTTTGTTTAGAGTGAAGCAGATGAAATGTTGAACTGAGGTTCTGAGGATC
AACTTCATGAGATTTTTCAAAAATTAAGTACAAGCATTCAGGTGGTGTTGCTTTCTGACACAATGCCGATAGATGTGTTG
GAAGTGACTAAAAATTCATGAGGGATTCAATGTGAGTTCTAGCGAAGAAGGAAGAAATGACCCCTGAAGGAATCAAACAG
TTTTATATTGATGTTAAAAGAGAGGAATAGAAGTTGGAGTCACTTTATGACTTGTGGGAGACCCTGACGATTACACAGGC
TTTTATTTTCCTCAGTACTAGGCTCTGGGTGGACTGGTGCACTGACAAAATGCATCCTGGGGACTTAGAAGTTTCTGCGT
AGCATAGTGATATGGACCAGAAGGAGAGAGATGTGATCATGAGGAAATTCTGATCAGGCTCAAGCCGTGCTATGATCACT
ACTTCTTTGTGACTTGTGGGCTTGTGGCATTGTTGTACAAGAAGTATCTTTGGTTATAAATTATGACCTACTTACCAATC
ATGAAAAATACAT

ORF - retro_etel_1174 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.82 %
Parental protein coverage: 66.58 %
Number of stop codons detected: 11
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHI-VV
.S.L..L...F.ET..........L...IQKVI.ALGDY.GATCHAC.GGTNV.NE..K.QAEA.H..VV
RetrocopyVSFLGYLCMCF*ETFSYSAESYHSLHLKIQKVISALGDYLGATCHACNGGTNVQNEKHKVQAEALHV<VV
ParentalGTPG-RVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTK
..PG.RVF..LNR..LS...IKMFV..EADEML..G..DQ..EIFQKL.TSIQVVLLS.TMP.DVLEVTK
RetrocopyVLPG<RVFVVLNRQCLSTQ*IKMFV*SEADEMLN*GSEDQLHEIFQKLSTSIQVVLLSDTMPIDVLEVTK
Parental-KFMRDPIRILVKKEELTLEGIKQFYINVEREEWKLDTLCDLYETLTITQAVIFLNTRRKVDWLTEKMHA
.KFMRD....L.KKEE.T.EGIKQFYI.V.REE.KL..L.DL.ETLTITQA.IFL.TR..VDW.T.KMH.
Retrocopy<KFMRDSM*VLAKKEEMTPEGIKQFYIDVKREE*KLESLYDLWETLTITQAFIFLSTRLWVDWCTDKMHP
ParentalRDFTVSALHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL-PTNRENYIH
.D..VSA.H.DMDQKERDVIMR.F.SGSSR..ITT.L...G...........Y.L.PT.....IH
RetrocopyGDLEVSA*HSDMDQKERDVIMRKF*SGSSRAMITTSL*LVGLWHCCTRSIFGYKL*PTYQS*KIH

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_1174 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 49 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000147242 retrocopies
retro_btau_258, retro_btau_522,
Canis familiaris ENSCAFG000000136591 retrocopy
retro_cfam_378,
Cavia porcellus ENSCPOG000000111831 retrocopy
retro_cpor_639,
Dasypus novemcinctus ENSDNOG000000115025 retrocopies
retro_dnov_1264, retro_dnov_2018, retro_dnov_2066, retro_dnov_648, retro_dnov_869,
Echinops telfairi ENSETEG00000018565 3 retrocopies
retro_etel_1174 , retro_etel_2164, retro_etel_451,
Homo sapiens ENSG000001569762 retrocopies
retro_hsap_593, retro_hsap_878,
Gorilla gorilla ENSGGOG000000058672 retrocopies
retro_ggor_525, retro_ggor_712,
Macropus eugenii ENSMEUG000000117371 retrocopy
retro_meug_237,
Microcebus murinus ENSMICG000000073771 retrocopy
retro_mmur_525,
Macaca mulatta ENSMMUG000000037022 retrocopies
retro_mmul_1055, retro_mmul_2450,
Nomascus leucogenys ENSNLEG000000066331 retrocopy
retro_nleu_2589,
Oryctolagus cuniculus ENSOCUG000000050113 retrocopies
retro_ocun_392, retro_ocun_696, retro_ocun_763,
Otolemur garnettii ENSOGAG000000107292 retrocopies
retro_ogar_2830, retro_ogar_943,
Ochotona princeps ENSOPRG000000041701 retrocopy
retro_opri_498,
Pongo abelii ENSPPYG000000143842 retrocopies
retro_pabe_596, retro_pabe_677,
Pan troglodytes ENSPTRG000000157181 retrocopy
retro_ptro_437,
Rattus norvegicus ENSRNOG000000018152 retrocopies
retro_rnor_1163, retro_rnor_2340,
Ictidomys tridecemlineatus ENSSTOG000000126011 retrocopy
retro_itri_858,
Tupaia belangeri ENSTBEG0000000226811 retrocopies
retro_tbel_114, retro_tbel_1488, retro_tbel_1500, retro_tbel_2048, retro_tbel_2524, retro_tbel_2729, retro_tbel_2733, retro_tbel_3159, retro_tbel_3793, retro_tbel_4599, retro_tbel_841,
Takifugu rubripes ENSTRUG000000056602 retrocopies
retro_trub_14, retro_trub_6,
Tarsius syrichta ENSTSYG000000130503 retrocopies
retro_tsyr_1905, retro_tsyr_903, retro_tsyr_935,


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