RetrogeneDB ID:

retro_etel_1406

Retrocopy
location
Organism:Lesser hedgehog tenrec (Echinops telfairi)
Coordinates:scaffold_260469:9073..9957(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP5C1
Ensembl ID:ENSETEG00000010549
Aliases:None
Description:ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1 [Source:HGNC Symbol;Acc:833]


Retrocopy-Parental alignment summary:






>retro_etel_1406
ATGTTCCCTCTGGCGAGCGTTCTTGGGGCCTCAGCCTGGGCTCTGCAGCCGCAATGGACCCAAGTTCGAAATATGGCAAC
TTTGAAAGATATTACCAGGCGACTAAAGTCCATCAAAACCATCCAGAAAATCATCTAGTCTATGAAAATGGTAGCCGCAG
CAAAATATGCCAGAGCTGAGAGGGAGCTGAAACCGGCCCGGGTGTATGGAGTCGGGTCTCTGGCTCTCTATGAAAAAGCT
GATATTAAGGTGCCTGAAGACAAGAACAAACACCTCCTTATTGGTGTCTCCTCCGACCGAGGGCCTTGTGGTGCTATTCA
TTCCTCAGTAGCTAAACGCATGAAAAGGGAGGTGGCCTCACTCACCGCAGCCGGCAAAGAAGTGATGCTTGTTGGAATTG
GTGATAAAATCAGGGGCATACTTTACAGGACTCACTCCGACCAGTTTCTGGTGACATTCAAAGAAGTGGGAAGGAAACCC
TCTACTTTTGGAGATGCGTCTGTTATTGCCCTCGAATTACTAAATTCTGGATATGAGTTTGATGAAGGATTTATCATTTT
TAATCGATTCAGGTTTGTCATCTCCTACAAAACAGACGAGAAGCCCATATTTTCTCTGAATACCATTGCAAGTGCAGAGA
GCATAAGTATCTAGATGAGATTGATGCTGATGCGCTGCAAAATTACCAGGAATACAATCTGGCAAACATCATCTACTACT
TGTTAAAGGAGTCCACCACTAGTGAGCAGAGTGCAAGAATGACAGCTATGGACAACGCTAGCAAGAACGAGTCTGAGATG
ATTGACAAGCTGACTTTGACTTTCAACCGTACCCTCCAAGCTGTCATCACAAAAGAGTTGATTGAAATCATGTCTGGTGC
TGCC

ORF - retro_etel_1406 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.23 %
Parental protein coverage: 99.66 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMFSRASVVGASAWALQPQWTQVRNMATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARVYG
MF..ASV.GASAWALQPQWTQVRNMATLKDITRRLKSIK.IQKI..SMKMVAAAKYARAERELKPARVYG
RetrocopyMFPLASVLGASAWALQPQWTQVRNMATLKDITRRLKSIKTIQKII*SMKMVAAAKYARAERELKPARVYG
ParentalVGSLALYEKADIKVPEDKKKHLLIGVSSDRGLCGAIHSSVAKQIKSEVASLTAAGKEVMLVGIGDKIRGI
VGSLALYEKADIKVPEDK.KHLLIGVSSDRG.CGAIHSSVAK..K.EVASLTAAGKEVMLVGIGDKIRGI
RetrocopyVGSLALYEKADIKVPEDKNKHLLIGVSSDRGPCGAIHSSVAKRMKREVASLTAAGKEVMLVGIGDKIRGI
ParentalLYRTHSDQFLVTFKEVGRKPPTFGDASVIALELLNSGYEFDEGSIIFNRFRSVISYKTDEKPIFSLNTIA
LYRTHSDQFLVTFKEVGRKP.TFGDASVIALELLNSGYEFDEG.IIFNRFR.VISYKTDEKPIFSLNTIA
RetrocopyLYRTHSDQFLVTFKEVGRKPSTFGDASVIALELLNSGYEFDEGFIIFNRFRFVISYKTDEKPIFSLNTIA
ParentalSAESMSI-YDDIDADVLQNYQEYNLANIIYYSLKESTTSEQSARMTAMDNASKNASEMIDKLTLTFNRTR
SAES.SI..D.IDAD.LQNYQEYNLANIIYY.LKESTTSEQSARMTAMDNASKN.SEMIDKLTLTFNRT.
RetrocopySAESISI<LDEIDADALQNYQEYNLANIIYYLLKESTTSEQSARMTAMDNASKNESEMIDKLTLTFNRTL
ParentalQAVITKELIEIISGAA
QAVITKELIEI.SGAA
RetrocopyQAVITKELIEIMSGAA

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_1406 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 43 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000050241 retrocopy
retro_cfam_1781,
Choloepus hoffmanni ENSCHOG000000112293 retrocopies
retro_chof_102, retro_chof_297, retro_chof_673,
Callithrix jacchus ENSCJAG000000206357 retrocopies
retro_cjac_1079, retro_cjac_1293, retro_cjac_1381, retro_cjac_1636, retro_cjac_2506, retro_cjac_4190, retro_cjac_526,
Cavia porcellus ENSCPOG000000105232 retrocopies
retro_cpor_422, retro_cpor_984,
Echinops telfairi ENSETEG00000010549 1 retrocopy
retro_etel_1406 ,
Felis catus ENSFCAG000000001961 retrocopy
retro_fcat_818,
Homo sapiens ENSG000001656291 retrocopy
retro_hsap_1415,
Gorilla gorilla ENSGGOG000000097191 retrocopy
retro_ggor_1094,
Macaca mulatta ENSMMUG000000092071 retrocopy
retro_mmul_2254,
Monodelphis domestica ENSMODG000000167201 retrocopy
retro_mdom_1287,
Mus musculus ENSMUSG000000257814 retrocopies
retro_mmus_1122, retro_mmus_2008, retro_mmus_3451, retro_mmus_3644,
Nomascus leucogenys ENSNLEG000000119171 retrocopy
retro_nleu_1836,
Oryctolagus cuniculus ENSOCUG000000046422 retrocopies
retro_ocun_1171, retro_ocun_363,
Otolemur garnettii ENSOGAG000000152422 retrocopies
retro_ogar_1099, retro_ogar_2738,
Procavia capensis ENSPCAG000000049711 retrocopy
retro_pcap_99,
Pongo abelii ENSPPYG000000020761 retrocopy
retro_pabe_1170,
Pan troglodytes ENSPTRG000000022771 retrocopy
retro_ptro_968,
Pteropus vampyrus ENSPVAG000000065123 retrocopies
retro_pvam_1466, retro_pvam_51, retro_pvam_530,
Ictidomys tridecemlineatus ENSSTOG000000261331 retrocopy
retro_itri_665,
Tupaia belangeri ENSTBEG000000115304 retrocopies
retro_tbel_1763, retro_tbel_2023, retro_tbel_4384, retro_tbel_4406,
Tarsius syrichta ENSTSYG000000030354 retrocopies
retro_tsyr_1268, retro_tsyr_1988, retro_tsyr_465, retro_tsyr_506,


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