RetrogeneDB ID: retro_chof_150

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_3427:14517..15600(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CCT6A
• Ensembl ID: ENSCHOG00000000654
• Aliases: None
• Description: chaperonin containing TCP1, subunit 6A (zeta 1) [Source:HGNC Symbol;Acc:1620]

Sequence

>retro_chof_150
ACACTTATGGATGTGGCCAGAACATCTCTGCATACTAAAGTTCATGCAGAACTTGCTGATGTCTTAACAGAGCCTGTAGT
GGACTTCTTTTTGGCCATTAAAAAACAAGATGAGCCTATCGACCTTTTCATGGATGAGATCATGGAGATGAAACATAAAT
CTGAAACAGATACGAACTTAATCAGAAGGCTTGTTTTGGACCATGGGGCATGACATCCTGATATGAAAAAGAGAGTAGAA
GATGCATACATCCTCACATGCAACATGTCATTAGAATATGAAAAAACAGAAGTGAACTCAGGCTTTTTTTTTTTTTTTTT
TTGAGAGTGCAGAAGAGAGAAACTAGCAAAAGCTAAAAGATTCATTGAAGGTAGAGTTTAAAAAAAAAAATAGAACAAAG
GAAAGTCTGCGGGGATTCAGATAAAGGATTTGTTATTAATCAAAAGGGAATTGACCCCTTTTCCTTAGATGTTCTTGCAA
AAGAAGGCATAGTAACTCTGTGCAGAGCTAAAAGGAGACATATGGAGAGGCTGCCTCTTGCTTGTGGTGGGGTAGCTCCA
AATTCTTTGGATGACCTAAATCCTGACTGTTTGGGGCATGCAGGCCTTGTCTATGAGTATACATTGGAAGAAGAGTAGTT
CACCTTTACTGAGAAATTTAACAATCCTCGTTCTGTCACATTATTGGTGAAAGGACCAAATAAGCACACACTCACTCAAA
TCAAAGATGCAATAAGAGATGGCCTGAGGGCTGTCAAAAATGCTCTTGATGATGGCTGTGTGGTTCCAGGTGCCAGTGCC
GGTGCAGTGGAAGTGGCAATGGCAGAAGCTTGGTTAAATATAAGCCCAGTATAAAGGGCAGGGCCCAACTTGAGTCCAAG
CATTTGCAGATGCATTGCTCATTATTCCCAAGGTTCTTGCTCAGAACTCTGGTTTTGACCTTCAGGAAACACTAGTAAAG
GTACAAGCAGAACATTCAGAATCAGGTCAACTTGTAGGTGTAGACTCGAACACAGGTGAGCCAATAGTAGCAGCAGAAGT
AGGCATATGGGATAACTACTGTGTCAAGAAACAGCTTCTGCAC

Alignment

ORF - retro_chof_150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.47 %
• Parental protein coverage: 70.97 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TLTDVARTSLRTKVHAELADVLTEAVVDSILAIRKQDEPIDLFMVEIMEMKHKSETDT-LIRGLVLDHGA
          TL.DVARTSL.TKVHAELADVLTE.VVD..LAI.KQDEPIDLFM.EIMEMKHKSETDT.LIR.LVLDHGA
Retrocopy TLMDVARTSLHTKVHAELADVLTEPVVDFFLAIKKQDEPIDLFMDEIMEMKHKSETDTNLIRRLVLDHGA

Parental  RHPDMKKRVEDAYILTCNVSLEYEKTEVNSGFFYKSAEE--REKLVKAERKFIEDRVTKIIELKKK-VCG
          .HPDMKKRVEDAYILTCN.SLEYEKTEVNSG.......E..REKL.KA.R.FIE.RV......K.K.VCG
Retrocopy *HPDMKKRVEDAYILTCNMSLEYEKTEVNSGXXXXXXXECRREKLAKAKR-FIEGRVXXXX*NKGK<VCG

Parental  DSDKGFVVINQKGIDPFSLDALAKEGIVALRRAKRRNMERLTLACGGVALNSLDDLNPDCLGHAGLVYEY
          DSDKGF.VINQKGIDPFSLD.LAKEGIV.L.RAKRR.MERL.LACGGVA.NSLDDLNPDCLGHAGLVYEY
Retrocopy DSDKGF-VINQKGIDPFSLDVLAKEGIVTLCRAKRRHMERLPLACGGVAPNSLDDLNPDCLGHAGLVYEY

Parental  TLGEEKFTFIEKCNSPRSVTLLVKGPNKHTLTQIKDAIRDGLRAVKNAIDDGCVVPG--AGAVEVAMAEA
          TL.EE.FTF.EK.N.PRSVTLLVKGPNKHTLTQIKDAIRDGLRAVKNA.DDGCVVPG..AGAVEVAMAEA
Retrocopy TLEEE*FTFTEKFNNPRSVTLLVKGPNKHTLTQIKDAIRDGLRAVKNALDDGCVVPGASAGAVEVAMAEA

Parental  -LVKYKPSIKGRAQLG-VQAFADALLIIPKVLAQNSGFDLQETLVKVQAEHSES--QLSVDLNTGEPMVA
          .LVKYKPSIKGRAQL..VQAFADALLIIPKVLAQNSGFDLQETLVKVQAEHSES.....VD.NTGEP.VA
Retrocopy <LVKYKPSIKGRAQLE<VQAFADALLIIPKVLAQNSGFDLQETLVKVQAEHSESGQLVGVDSNTGEPIVA

Parental  AEVGIWDNYCVKKQLLH
          AEVGIWDNYCVKKQLLH
Retrocopy AEVGIWDNYCVKKQLLH

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_150 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016077	1 retrocopy	retro_amel_855,
Canis familiaris	ENSCAFG00000010149	1 retrocopy	retro_cfam_431,
Choloepus hoffmanni	ENSCHOG00000000654	3 retrocopies	retro_chof_1183, retro_chof_1193, retro_chof_150 ,
Callithrix jacchus	ENSCJAG00000021279	2 retrocopies	retro_cjac_1320, retro_cjac_580,
Dipodomys ordii	ENSDORG00000001249	1 retrocopy	retro_dord_617,
Felis catus	ENSFCAG00000027654	2 retrocopies	retro_fcat_1102, retro_fcat_320,
Homo sapiens	ENSG00000146731	2 retrocopies	retro_hsap_2741, retro_hsap_3290,
Gorilla gorilla	ENSGGOG00000011439	1 retrocopy	retro_ggor_133,
Loxodonta africana	ENSLAFG00000012791	1 retrocopy	retro_lafr_808,
Macaca mulatta	ENSMMUG00000015272	1 retrocopy	retro_mmul_2582,
Monodelphis domestica	ENSMODG00000006565	1 retrocopy	retro_mdom_1330,
Nomascus leucogenys	ENSNLEG00000015664	1 retrocopy	retro_nleu_1355,
Oryctolagus cuniculus	ENSOCUG00000017674	1 retrocopy	retro_ocun_468,
Procavia capensis	ENSPCAG00000015532	1 retrocopy	retro_pcap_263,
Pongo abelii	ENSPPYG00000025820	1 retrocopy	retro_pabe_2719,
Pan troglodytes	ENSPTRG00000019206	2 retrocopies	retro_ptro_1854, retro_ptro_2225,
Pteropus vampyrus	ENSPVAG00000001421	1 retrocopy	retro_pvam_663,
Rattus norvegicus	ENSRNOG00000000923	1 retrocopy	retro_rnor_2226,
Tursiops truncatus	ENSTTRG00000015158	1 retrocopy	retro_ttru_1552,