RetrogeneDB ID:

retro_etel_1968

Retrocopy
location
Organism:Lesser hedgehog tenrec (Echinops telfairi)
Coordinates:scaffold_320316:50347..51227(-)
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:ENSETEG00000008329
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_etel_1968
GTCCCTGTTGCCATGTTCCGGGACCTGTTCCTCAGGGACCCTAACAAGCTGGTGTTCTGTGAAGTCTTTAAGGACAACCG
AAAGCCTGCAGAGACCAACTTAAGGCACACCTGTAAATGGATTATGGACATGGTGACCAGCCAACACCCCTGGTTTGGAA
TGGAGCAGGAGTACACCCTCATGGGGACAGATGGGCACCCCTTTGGTTGGCCTTCCAATGGCTTTCCTGGACCCCAAGGT
CCGGATTATTGCAGTGTGGGGGCAGACAAAGCCTATGGCAGGGACATTGTGGAGGCTCTCTACGGGGCCCGCTTGTAAGC
TGGCATCAGGATTGGCGGGACGAATGCCGAGGTCATGCCTGCCCAGTGGGAGTTCCAGATAGGACCCTGTGAAGGAATCG
ACATGGGGGGTCATCTCTGGGTGGCCCGCTTCATCCTGCACCGTGTGTGTGAAGACTTTGGAGTGATAGCAACCTTTGAT
CCTAAGCCCATCCTGGGAACTGGAATGGTGCAGGCTGTCATACCAACTTCAGCACCAAGGCCATGCGGGAAGAGAATGGT
CTGAAGTACATTGAGGAGTCCATCGAGAGGCTAAGCAAGCGGCACCAATACCCCATCCGGGCCTACGACCCCAAAGGGGG
CCTGGACAATGCCGGACACCTCACTGAATTCCACGAAACCTCCAACATCAACGACTTTTCCGCCAGCGTGGCCAACCGAG
GTGCCAGCATCCGCATTCCTCGGATCACCGGCCAGGAGAAGAGGGCTACTTTGAAGACCACCGCCCCTCCGCCAACTGTG
ACCCCTTCACAGTGACCGAAGCCCTCTTCTGCACGTATTTTCTCAACGAGACCGGCGAGGAGCCCTTCCAGTATAAAAAC

ORF - retro_etel_1968 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.86 %
Parental protein coverage: 78.82 %
Number of stop codons detected: 1
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalIPVAMFRDPFRRDPNKLVFCEVFKYNRKPAETNLRHTCKRIMDMVTSQHPWFGMEQEYTLMGTDGHPFGW
.PVAMFRD.F.RDPNKLVFCEVFK.NRKPAETNLRHTCK.IMDMVTSQHPWFGMEQEYTLMGTDGHPFGW
RetrocopyVPVAMFRDLFLRDPNKLVFCEVFKDNRKPAETNLRHTCKWIMDMVTSQHPWFGMEQEYTLMGTDGHPFGW
ParentalPSNGFPGPQGPYYCGVGADKAYGRDIVEAHYRACLYAGIKIGGTNAEVMPAQWEFQIGPCEGIDMGDHLW
PSNGFPGPQGP.YC.VGADKAYGRDIVEA.Y.A.L.AGI.IGGTNAEVMPAQWEFQIGPCEGIDMG.HLW
RetrocopyPSNGFPGPQGPDYCSVGADKAYGRDIVEALYGARL*AGIRIGGTNAEVMPAQWEFQIGPCEGIDMGGHLW
ParentalVARFILHRVCEDLGVIATFDPKPI-PGNENGAGCHTNFSTKAMREENGLKYIEESIERLSKRHQYHIRAY
VARFILHRVCED.GVIATFDPKPI.PGN.NGAGCHTNFSTKAMREENGLKYIEESIERLSKRHQY.IRAY
RetrocopyVARFILHRVCEDFGVIATFDPKPI<PGNWNGAGCHTNFSTKAMREENGLKYIEESIERLSKRHQYPIRAY
ParentalDPKGGLDNARRLTGFHETSNINDFSAGVANRGASIRIPRMTGQEKK-GYFEDRRPSANCDPFAVTEALIR
DPKGGLDNA..LT.FHETSNINDFSA.VANRGASIRIPR.TGQEK..GYFED.RPSANCDPF.VTEAL..
RetrocopyDPKGGLDNAGHLTEFHETSNINDFSASVANRGASIRIPRITGQEKR<GYFEDHRPSANCDPFTVTEALFC
ParentalTCLLNETGEEPFQYKN
T..LNETGEEPFQYKN
RetrocopyTYFLNETGEEPFQYKN

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_1968 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 24 parental genes, and 57 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000136314 retrocopies
retro_btau_1050, retro_btau_1474, retro_btau_336, retro_btau_824,
Canis familiaris ENSCAFG000000131022 retrocopies
retro_cfam_1691, retro_cfam_2143,
Callithrix jacchus ENSCJAG000000046541 retrocopy
retro_cjac_2837,
Dasypus novemcinctus ENSDNOG000000139484 retrocopies
retro_dnov_1386, retro_dnov_1870, retro_dnov_2393, retro_dnov_842,
Equus caballus ENSECAG000000158651 retrocopy
retro_ecab_979,
Echinops telfairi ENSETEG00000008329 3 retrocopies
retro_etel_143, retro_etel_189, retro_etel_1968 ,
Felis catus ENSFCAG000000105511 retrocopy
retro_fcat_1811,
Homo sapiens ENSG000001358214 retrocopies
retro_hsap_2364, retro_hsap_3255, retro_hsap_848, retro_hsap_935,
Gorilla gorilla ENSGGOG000000247123 retrocopies
retro_ggor_1794, retro_ggor_2216, retro_ggor_754,
Loxodonta africana ENSLAFG000000007001 retrocopy
retro_lafr_196,
Macropus eugenii ENSMEUG000000017746 retrocopies
retro_meug_1013, retro_meug_1394, retro_meug_1561, retro_meug_409, retro_meug_433, retro_meug_746,
Macaca mulatta ENSMMUG000000228842 retrocopies
retro_mmul_2047, retro_mmul_954,
Monodelphis domestica ENSMODG000000067874 retrocopies
retro_mdom_1268, retro_mdom_488, retro_mdom_823, retro_mdom_892,
Mus musculus ENSMUSG000000264733 retrocopies
retro_mmus_1730, retro_mmus_1767, retro_mmus_696,
Nomascus leucogenys ENSNLEG000000180073 retrocopies
retro_nleu_1388, retro_nleu_293, retro_nleu_416,
Pongo abelii ENSPPYG000000004401 retrocopy
retro_pabe_2698,
Pan troglodytes ENSPTRG000000017514 retrocopies
retro_ptro_2201, retro_ptro_2823, retro_ptro_589, retro_ptro_647,
Sarcophilus harrisii ENSSHAG000000001161 retrocopy
retro_shar_553,
Sus scrofa ENSSSCG000000155451 retrocopy
retro_sscr_726,
Ictidomys tridecemlineatus ENSSTOG000000145292 retrocopies
retro_itri_1083, retro_itri_743,
Tupaia belangeri ENSTBEG000000035223 retrocopies
retro_tbel_2230, retro_tbel_3079, retro_tbel_3992,
Tarsius syrichta ENSTSYG000000020661 retrocopy
retro_tsyr_385,
Tursiops truncatus ENSTTRG000000107811 retrocopy
retro_ttru_543,
Drosophila melanogaster FBgn00011451 retrocopy
retro_dmel_44,


Copyright © RetrogeneDB 2014-2017