RetrogeneDB ID:

retro_etel_99

Retrocopy
location
Organism:Lesser hedgehog tenrec (Echinops telfairi)
Coordinates:GeneScaffold_1801:42374..43038(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PSAT1
Ensembl ID:ENSETEG00000004158
Aliases:None
Description:phosphoserine aminotransferase 1 [Source:HGNC Symbol;Acc:19129]


Retrocopy-Parental alignment summary:






>retro_etel_99
CCTGGGACCTCACCCAGATATCTCTTATGTGTTGGGACTGTTCACAGACTGGAGCTTGATTTTTCACCCCGTGCCAGAGG
GGCATCTTAGTTAGCGACATGTCCTCAAACTTCCTATCCAACCCAGTGGACATTGCCAAGTTTGGTGCTTGTTCTTGTTG
GTGCTCAGAATGTTGGCTGTGCTAGGTCAGATGCGGTCGTTCTCAGCAACCTGCTGGGGTAAGCGCTCCTGAAATGCCCT
CTCTCCTGGGCAACAACGCACAAGCTGGAAATAACTTGCACTTTATGCTTCTATGCTACTCATCTCTGTCATGGGCCTAG
GCCTGGAGTGTATTTAAAACCATGGCTGTAAAACAGCTGTGGAAAAGCTTGGCTGCTTCAAGTCCCAAATGATTTTTGAT
ATTGAGAACTCTGAAGGGTTCCGTGTATGTTTAGTGAAACCCTAGAGAAGAAGCAAGGGGAATATGCTGTTCCATATTGG
TAATGCCAAAGGAGATGATCTAGGGGGAAAAAGTTCTCCTAAAGCCCTTGAATTCAACCTGATGTCCTTGAAAGGGCATA
GGCTGGTGGGAGGCAAGTGAGCCTCTTTGGATAGCATGATTACCACTAAAGAAGTTTAAAAGCTGATAGCCTTCAGGAAA
AATAAGGTGGAGATGCATCAGCTA

ORF - retro_etel_99 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 52.81 %
Parental protein coverage: 61.35 %
Number of stop codons detected: 5
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalPEASYVYYCANETVHGVEFDFVPDVKGA-VLVCDMSSNFLSKPVDVSKFG-VIFAGAQKNIGSAGVTVVI
P..S..Y.....TVH..E.DF.P...GA..LV.DMSSNFLS.PVD..KFG.....GAQ.N.G.A....V.
RetrocopyPGTSPRYLLCVGTVHRLELDFSPRARGA<ILVSDMSSNFLSNPVDIAKFG>LVLVGAQ-NVGCARSDAVV
ParentalVREDLLGFALRECP-SVLDYKVQAGNKSLYNTPPCFS-IYVVGLVLEWIKNNGGAAAMEKLGSIKSQMIY
....LLG.AL..CP.S.L....QAGN..L.....C.S.I.V.GL.LE.I.N.G...A.EKLG..KSQMI.
RetrocopyL-SNLLG*ALLKCP<SLLGNNAQAGN-NLHFMLLCYS<ISVMGLGLECI*NHGCKTAVEKLGCFKSQMIF
ParentalEIIDNSQGFYVCPVEPQNRSKMNIPFRIGNAKGDDALEKRFLDKAQEHNMLSLKGHRSVGGIRASLYNAV
.I..NS.GF.VC.V.P..RSK.N..F.IGNAKGDD.L......KA.E.N..SLKGHR.VGG..ASL....
RetrocopyDI-ENSEGFRVCLVKP*RRSKGNMLFHIGNAKGDD-LGGKSSPKALEFNLMSLKGHRLVGGK*ASLDSMI
ParentalTTEDVQKLAAFMTNFLEMHQL
TT..V.KL.AF..N..EMHQL
RetrocopyTTKEV*KLIAFRKNKVEMHQL

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_99 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 28 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000068981 retrocopy
retro_amel_375,
Bos taurus ENSBTAG000000139601 retrocopy
retro_btau_1658,
Canis familiaris ENSCAFG000000015701 retrocopy
retro_cfam_269,
Choloepus hoffmanni ENSCHOG000000038171 retrocopy
retro_chof_2702,
Callithrix jacchus ENSCJAG000000033191 retrocopy
retro_cjac_1203,
Echinops telfairi ENSETEG00000004158 1 retrocopy
retro_etel_99 ,
Homo sapiens ENSG000001350693 retrocopies
retro_hsap_2267, retro_hsap_4054, retro_hsap_412,
Gorilla gorilla ENSGGOG000000154801 retrocopy
retro_ggor_407,
Loxodonta africana ENSLAFG000000179172 retrocopies
retro_lafr_1249, retro_lafr_660,
Macaca mulatta ENSMMUG000000118682 retrocopies
retro_mmul_1029, retro_mmul_2341,
Mustela putorius furoENSMPUG000000125661 retrocopy
retro_mputfur_808,
Nomascus leucogenys ENSNLEG000000029893 retrocopies
retro_nleu_1010, retro_nleu_1288, retro_nleu_2805,
Oryctolagus cuniculus ENSOCUG000000077651 retrocopy
retro_ocun_1092,
Pongo abelii ENSPPYG000000193133 retrocopies
retro_pabe_1950, retro_pabe_308, retro_pabe_3328,
Pan troglodytes ENSPTRG000000210452 retrocopies
retro_ptro_1606, retro_ptro_316,
Rattus norvegicus ENSRNOG000000139711 retrocopy
retro_rnor_1663,
Tupaia belangeri ENSTBEG000000129461 retrocopy
retro_tbel_1577,
Tarsius syrichta ENSTSYG000000000932 retrocopies
retro_tsyr_1073, retro_tsyr_1212,


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