RetrogeneDB ID:

retro_etel_1935

Retrocopy
location
Organism:Lesser hedgehog tenrec (Echinops telfairi)
Coordinates:scaffold_316571:15340..16059(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSETEG00000004648
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_etel_1935
ATGAGTGTGGAGGTAGCTTCTCCCCAAAGCCTTACAGAAGCTTCTGATTCTAGAGACTCTTCACCAACACCTATGATTTT
AGGGCCTGAAGAATATCATACATCCTTGCAAATGTCATCTGCTGAGGCCCCCTACTCAGAGACCGCCGTCTCTCCTCTTT
CTTCTCCGTGGACCTGCTGCTTCAGGAGAGAGCCTGGTTCTTCCACCCGTCCCAAAGTACAGCTGCCCAGTTCAGATGAG
AAATGCCCAGAAGAAGGAGAGTAAGGGCCGGGGCAAGAAAGGGAAGGTCCACACTGTGTTCTCTCAGACCCAGCTGTGCA
TGCTCCAAGACGAATTTCAGAATCAGAAATACCTCAGTCTCCAGCAGATGCAAGAACTTTCCAAAGTCCTGAATCTGAGC
TACAAACACGTTGAGACCTGGCTTCAGCACCAGAGAAGGAAATGTAGGAGGTGCCAGAAAAGCACCAGCCTGTCAAAGAA
CAACCATGGTGCGACTCGGGTCTCTGCACCCACCGATACCTGGACCTCTGTGCTTCCTGCCCCAAGGAGGCCTGCCCTCT
GGAAACTTTCGAATGTGGCGCGATCGGAGCAAGAACAGCCAGACCTGGGACAACCAGAGTTGAAACACTCAGGCTTGGGA
CAACCATACCTGGAACAGGAGCCAGGTGCGAAATAGCCAAGCGTGACGCAAACAAGTCTGGAATAACCAGTCTGGGAAC

ORF - retro_etel_1935 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.97 %
Parental protein coverage: 86.02 %
Number of stop codons detected: 2
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMSVDVASPQNLLEASDSKNSSPVTTSLGTKEDGTSLQMSSAEPPYSETG-SPLPS-SVDLLLQ-KSPDSS
MSV.VASPQ.L.EASDS..SSP....LG..E..TSLQMSSAE.PYSET..SPL.S.SVDLLLQ...P.SS
RetrocopyMSVEVASPQSLTEASDSRDSSPTPMILGPEEYHTSLQMSSAEAPYSETAVSPLSS<SVDLLLQ>REPGSS
ParentalTSP-KVQLPASAETDAARKESKGPGKKQKVRTVFSQTQLCILKDHFQKQKYLSLQQMQELSEVLNLSYKQ
T.P.K...P......A..KESKG.GKK.KV.TVFSQTQLC.L.D.FQ.QKYLSLQQMQELS.VLNLSYK.
RetrocopyTRP>KYSCPVQMR-NAQKKESKGRGKKGKVHTVFSQTQLCMLQDEFQNQKYLSLQQMQELSKVLNLSYKH
ParentalVKTWFQNQRMKCKRWQKTTNWSKNNHAVTQKVSAPTE-YLDVCAS-YHQGCLPSGNLPMWSNQSWNSQAW
V.TW.Q.QR.KC.R.QK.T..SKNNH..T..VSAPT..YLD.CAS...QG.LPSGN..MW...S.NSQ.W
RetrocopyVETWLQHQRRKCRRCQKSTSLSKNNHGAT-RVSAPTD<YLDLCAS<LPQGGLPSGNFRMWRDRSKNSQTW
ParentalNNQSWNSQAWNNQSWN-SQAWNNQTWNSQAWNNPFQN
.NQS.N.QAW.N..WN.SQ..N.Q....Q.WNN...N
RetrocopyDNQS*NTQAWDNHTWNRSQVRNSQA*RKQVWNNQSGN

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_1935 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 23 parental genes, and 67 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000170641 retrocopy
retro_amel_354,
Canis familiaris ENSCAFG000000139141 retrocopy
retro_cfam_724,
Choloepus hoffmanni ENSCHOG000000009724 retrocopies
retro_chof_1267, retro_chof_264, retro_chof_794, retro_chof_987,
Callithrix jacchus ENSCJAG000000189998 retrocopies
retro_cjac_1732, retro_cjac_2234, retro_cjac_2441, retro_cjac_402, retro_cjac_4153, retro_cjac_4177, retro_cjac_880, retro_cjac_989,
Cavia porcellus ENSCPOG000000026211 retrocopy
retro_cpor_1132,
Echinops telfairi ENSETEG00000004648 8 retrocopies
retro_etel_1155, retro_etel_1334, retro_etel_134, retro_etel_1434, retro_etel_1935 , retro_etel_630, retro_etel_818, retro_etel_963,
Felis catus ENSFCAG000000016211 retrocopy
retro_fcat_932,
Homo sapiens ENSG000001117045 retrocopies
retro_hsap_1455, retro_hsap_1549, retro_hsap_3713, retro_hsap_4814, retro_hsap_722,
Gorilla gorilla ENSGGOG000000281964 retrocopies
retro_ggor_1812, retro_ggor_2510, retro_ggor_3000, retro_ggor_608,
Macropus eugenii ENSMEUG000000099492 retrocopies
retro_meug_266, retro_meug_940,
Microcebus murinus ENSMICG000000022281 retrocopy
retro_mmur_575,
Myotis lucifugus ENSMLUG000000293252 retrocopies
retro_mluc_1562, retro_mluc_2054,
Myotis lucifugus ENSMLUG000000305801 retrocopy
retro_mluc_169,
Macaca mulatta ENSMMUG000000321584 retrocopies
retro_mmul_1901, retro_mmul_2466, retro_mmul_964, retro_mmul_979,
Monodelphis domestica ENSMODG000000179792 retrocopies
retro_mdom_1293, retro_mdom_1938,
Mustela putorius furoENSMPUG000000167315 retrocopies
retro_mputfur_1140, retro_mputfur_1553, retro_mputfur_261, retro_mputfur_553, retro_mputfur_691,
Nomascus leucogenys ENSNLEG000000053593 retrocopies
retro_nleu_1086, retro_nleu_2189, retro_nleu_2340,
Oryctolagus cuniculus ENSOCUG000000137831 retrocopy
retro_ocun_971,
Otolemur garnettii ENSOGAG000000263391 retrocopy
retro_ogar_568,
Procavia capensis ENSPCAG000000154602 retrocopies
retro_pcap_143, retro_pcap_429,
Pongo abelii ENSPPYG000000042335 retrocopies
retro_pabe_2157, retro_pabe_3142, retro_pabe_3440, retro_pabe_3742, retro_pabe_623,
Pan troglodytes ENSPTRG000000298074 retrocopies
retro_ptro_1746, retro_ptro_2514, retro_ptro_3203, retro_ptro_990,
Pteropus vampyrus ENSPVAG000000069891 retrocopy
retro_pvam_1251,




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