RetrogeneDB ID: retro_chof_880

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_160515:3290..4057(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000002980
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000012369
• Aliases: None
• Description: None

Sequence

>retro_chof_880
CTTAGCAGTGGAAAAGGAGTAAGTGGAGGAACCAGGGGACCTCCCTCATGTGGAGAGCACGTGGATGATGGTGGCTATTT
CATGAATTTTGACATGCGTTCTTCCAGGGAACCACTTCCAGTAAAAAGAGGACACCACCACAAAGTAGGGGTCCCCCTCC
TAAAAGATCTGCTCCCTCAGGACCAGTTCACAGCAGCAGTGGAATGGGAGGAGAGCTCCTGTATCACGTAGAAGAGATAG
TAATGGAGACCCACCACAAACGGAACCCCTGCCCTCTAGAACTGTTTATTTGTCCCCAAGAGATGATGGATATTCTACTA
AAAATAGCTATTCAAGCAGAGATCACCCAAGTTTTCATGATAAAGTGATTACACACCACCACCAAGAGATTATACTTCCT
GTGATCACAGTCATTCCAGTTCACATGAAGACTACCCATCAAGAGGCTATGGTGATAGAGAGGGCTATGACTGTAATCAA
GACTCTTCAGATCATCTGAGTGGAGGGTCCTACAGAGATTCATGAGAGTTACGGTAACTCACGTAGTGCTCCACCTGCTT
GGGGGAGCCCAGCATCTTATGGTGGAAGCAGTTGCTATGACGACTACAGCAGCTCACGTGACAGATGTGGTGGAAGTTGA
GACAGTTACTCAAGCAGCCAAAGTGATCTCTGCTCCAGTGGTCATGATTAATCGGGTTGGCAGACAAGAAAGAGGGCTCC
CCCCTTTTATGGAAAGGGGGCACCCTCCTCCACGTGATTCCTACAGC

Alignment

ORF - retro_chof_880 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.4 %
• Parental protein coverage: 90.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LRGGRGGSGGTRGPPSRGGHMDDGGYSMNFNMSSSRGPLPVKRG-PPPRSGGPPPKRSAPSGPVRSNSGM
          L..G.G.SGGTRGPPS.G.H.DDGGY.MNF.M.SSR.PLPVKRG..PP.S.GPPPKRSAPSGPV.S.SGM
Retrocopy LSSGKGVSGGTRGPPSCGEHVDDGGYFMNFDMRSSREPLPVKRG<TPPQSRGPPPKRSAPSGPVHSSSGM

Parental  GG-RAPVSRGRDSYGGPPRREPLPSRRDVYLSPRDDGYSTKDSYSSRDYPSSRDT-RDYAPPPRDYTYRD
          GG.RAPVSR.RDS.G.PP..EPLPSR..VYLSPRDDGYSTK.SYSSRD.PS..D...DY.PPPRDYT..D
Retrocopy GG<RAPVSRRRDSNGDPPQTEPLPSRT-VYLSPRDDGYSTKNSYSSRDHPSFHDK<SDYTPPPRDYTSCD

Parental  YGHSSSRDDYPSRGYSDRDGYGRDRDYSDHPSGGSYRDSYESY-GNSRSAPPTRGPPPSYGGSSRYDDYS
          ..HSSS..DYPSRGY.DR.GY....D.SDH.SGGSYRDS.E.........P....P....G.S...D..S
Retrocopy HSHSSSHEDYPSRGYGDREGYDCNQDSSDHLSGGSYRDS*ELR>NSRSAPPAWGSPASYGGSSCYDDYSS

Parental  SSRDGYGGSRDSYSSSRSDLYSSGRDRVGRQER-GLPPSMERG-YPPPRDSYS
          S.RD..GGS.DSYSSS.SDL.SSG.D..G.Q.R...PP....G..PPPRDSYS
Retrocopy S-RDRCGGS*DSYSSSQSDLCSSGHD*SGWQTRKRAPPFYGKG>HPPPRDSYS

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_880 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 21 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013308	1 retrocopy	retro_btau_36,
Canis familiaris	ENSCAFG00000018962	4 retrocopies	retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Choloepus hoffmanni	ENSCHOG00000001130	1 retrocopy	retro_chof_974,
Choloepus hoffmanni	ENSCHOG00000012369	3 retrocopies	retro_chof_1240, retro_chof_2596, retro_chof_880 ,
Cavia porcellus	ENSCPOG00000012164	1 retrocopy	retro_cpor_778,
Dipodomys ordii	ENSDORG00000015481	1 retrocopy	retro_dord_793,
Echinops telfairi	ENSETEG00000013178	1 retrocopy	retro_etel_1952,
Homo sapiens	ENSG00000147274	7 retrocopies	retro_hsap_23, retro_hsap_3074, retro_hsap_3587, retro_hsap_4144, retro_hsap_4846, retro_hsap_800, retro_hsap_91,
Gorilla gorilla	ENSGGOG00000006944	1 retrocopy	retro_ggor_657,
Loxodonta africana	ENSLAFG00000005568	3 retrocopies	retro_lafr_1188, retro_lafr_276, retro_lafr_35,
Myotis lucifugus	ENSMLUG00000013209	5 retrocopies	retro_mluc_1630, retro_mluc_1746, retro_mluc_203, retro_mluc_2180, retro_mluc_80,
Mustela putorius furo	ENSMPUG00000001855	2 retrocopies	retro_mputfur_1539, retro_mputfur_956,
Mus musculus	ENSMUSG00000031134	2 retrocopies	retro_mmus_170, retro_mmus_187,
Oryctolagus cuniculus	ENSOCUG00000007220	1 retrocopy	retro_ocun_3,
Otolemur garnettii	ENSOGAG00000007839	5 retrocopies	retro_ogar_1057, retro_ogar_137, retro_ogar_1586, retro_ogar_2445, retro_ogar_2584,
Ochotona princeps	ENSOPRG00000016593	1 retrocopy	retro_opri_372,
Pongo abelii	ENSPPYG00000020771	3 retrocopies	retro_pabe_2548, retro_pabe_303, retro_pabe_766,
Rattus norvegicus	ENSRNOG00000000866	1 retrocopy	retro_rnor_268,
Sorex araneus	ENSSARG00000000397	1 retrocopy	retro_sara_169,
Tarsius syrichta	ENSTSYG00000009555	1 retrocopy	retro_tsyr_15,
Tursiops truncatus	ENSTTRG00000007322	1 retrocopy	retro_ttru_1450,