RetrogeneDB ID:

retro_chof_2162

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_54553:941..1353(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MTCH2
Ensembl ID:ENSCHOG00000008473
Aliases:None
Description:mitochondrial carrier 2 [Source:HGNC Symbol;Acc:17587]


Retrocopy-Parental alignment summary:






>retro_chof_2162
CAGCATTACCAGGAATGTGAAAAAGTTGAGGAATTGGGCCTGGGAATGTGCAGAAAGAAGTCTCATCATCCTATGATGGA
GTTATAAAGAAACAACTCTAGAGATGATGGCTTGTTCTGCTGTAATCCTCAGCACAGATCCCTTACACTTGATCATTTTG
AGATCCCTGGTACAATTCATTGGCATAGAATCCAAATACTGTGGACTTTGTGAACCCATAGTAACCATCTGTTGTGAAGA
AGGCATCCCAGGATTTTTTGCAGGTTTTATTCCTCACCTCCTAGGTGACATCATTTTTTTGTGGCTCTGTAACTCACTGG
CCTACCTTGTCAATACCTATGCACTGGACAGTGATGTATCCACCATAAGTTAAATAAAGAGTTCTTCCCACACTGTCACA
GGATTTTTTGCA

ORF - retro_chof_2162 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.14 %
Parental protein coverage: 50.36 %
Number of stop codons detected: 1
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalQHYQECEKVEELG-PGNVQKEVSLSFDRVIK-ETTREMMARSAATLITHPFHVITLRSMVQFIGRESKYC
QHYQECEKVEELG.PGNVQKEVS.S.D.VIK.ETT.EMMA.SA..L.T.P.H.I.LRS.VQFIG.ESKYC
RetrocopyQHYQECEKVEELG<PGNVQKEVSSSYDGVIK<ETTLEMMACSAVILSTDPLHLIILRSLVQFIGIESKYC
ParentalGLCDSIVTIYREEGILGFFAGLIPRLLGDIISLWLCNSLAYLVNTYALDSGVSTMNEMKSYSQVVTGFFA
GLC..IVTI..EEGI.GFFAG.IP.LLGDII.LWLCNSLAYLVNTYALDS.VST....KS.S..VTGFFA
RetrocopyGLCEPIVTICCEEGIPGFFAGFIPHLLGDIIFLWLCNSLAYLVNTYALDSDVSTIS*IKSSSHTVTGFFA

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST - click to see more details

Choloepus hoffmanni was not studied using EST data.

TSS - click to see more details

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab - click to see more details

retro_chof_2162 was not experimentally validated.

Retrocopy orthology:
Choloepus hoffmanni 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 17 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000187421 retrocopy
retro_btau_1321,
Choloepus hoffmanni ENSCHOG00000008473 1 retrocopy
retro_chof_2162 ,
Callithrix jacchus ENSCJAG000000202133 retrocopies
retro_cjac_1551, retro_cjac_2003, retro_cjac_3812,
Dasypus novemcinctus ENSDNOG000000012211 retrocopy
retro_dnov_1867,
Homo sapiens ENSG000001099192 retrocopies
retro_hsap_1041, retro_hsap_1690,
Gorilla gorilla ENSGGOG000000082813 retrocopies
retro_ggor_1267, retro_ggor_3083, retro_ggor_822,
Mustela putorius furoENSMPUG000000038521 retrocopy
retro_mputfur_312,
Mus musculus ENSMUSG000000272821 retrocopy
retro_mmus_2657,
Nomascus leucogenys ENSNLEG000000147042 retrocopies
retro_nleu_1335, retro_nleu_913,
Oryctolagus cuniculus ENSOCUG000000063682 retrocopies
retro_ocun_1197, retro_ocun_983,
Otolemur garnettii ENSOGAG000000116071 retrocopy
retro_ogar_2578,
Pongo abelii ENSPPYG000000032963 retrocopies
retro_pabe_1392, retro_pabe_1894, retro_pabe_872,
Pan troglodytes ENSPTRG000000035732 retrocopies
retro_ptro_1144, retro_ptro_710,
Pteropus vampyrus ENSPVAG000000073481 retrocopy
retro_pvam_954,
Sorex araneus ENSSARG000000013991 retrocopy
retro_sara_705,
Sus scrofa ENSSSCG000000132323 retrocopies
retro_sscr_262, retro_sscr_279, retro_sscr_602,
Tursiops truncatus ENSTTRG000000141692 retrocopies
retro_ttru_1476, retro_ttru_353,


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