RetrogeneDB ID: retro_chof_1240

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_234805:1496..2173(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_chof_1240
TCTGCCCCCTCAGGACCACTCTGAAGCAGCAGTGGAATAGGAGGAGGAGCTCTGTATCACAAGGAAGTGATCATTATAGA
GGCCCACCACGAAGGGAATGCCTCCTCTTTCATAGAGATGTTTATTTGTCCCCAAGAGATGAAGGATATTCTACTTACAA
TAGCTATTCAAGCAGAGATTACCCAAATTCTTGGGCTACAAGGATTATGTACCACCACCAAGAGATTATGCATACCATGA
TCATGGTCATTCCAGGTCATGCGATGACTATCCATCAAGAGGCTTTAGTGATAGAGATTGCTATGGTCATGATCGAGACT
ATTAGATCATCTGAGTGGAGGGCCCTACAGAGATTCATAAGATAGTTATGGCAACTCAAGTAGTGCTCAACCTACACGAG
GGCCCCTGCCATCTTAAGATAGAAGCGGTCACTATGATGATTACAGCCACTCACCTGATGGATATGGTGGAAGTTGAGAC
AGTTACTCAAGTGCCAGAGTGCTCTCCACTCAAGTGGTCATGATTTTGTTGGCAGACAAGGAAGAGGGCTTCCCTCTTCT
ATGGAAAGAGGGTACCCTCCTCCACATGATTCCTACAATAGTTCAAGCTGCAGAGCACCGAGAGGTGGTGGTGGTGGAGG
AAGCCAATCTGATAAAGGGGAAGGCAGATGCAGATAC

Alignment

ORF - retro_chof_1240 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.86 %
• Parental protein coverage: 80.21 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SAPSGPVRSNSGMGG-RAPVSRGRDSYGGPPRREPLPSRRDVYLSPRDDGYSTKDSYSSRDYPSSRDTR-
          SAPSGP..S.SG.GG.R..VS.G.D.Y.GPPRRE.L...RDVYLSPRD.GYST..SYSSRDYP.S..TR.
Retrocopy SAPSGPL*SSSGIGG<RSSVSQGSDHYRGPPRRECLLFHRDVYLSPRDEGYSTYNSYSSRDYPNSWATR<

Parental  DYAPPPRDYTYRDYGHSSSRDDYPSRGYSDRDGYGRDRDY-SDHPSGGSYRDSYESYGNSRSAPPTRGPP
          DY.PPPRDY.Y.D.GHS.S.DDYPSRG.SDRD.YG.DRDY..DH.SGG.YRDS..SYGNS.SA.PTRGP.
Retrocopy DYVPPPRDYAYHDHGHSRSCDDYPSRGFSDRDCYGHDRDY<LDHLSGGPYRDS*DSYGNSSSAQPTRGPL

Parental  PSYGGSSRYDDYSSSRDGYGGSRDSYSSSR-SDLYSSGRDRVGRQERGLPPSMERGYPPPRDSYSSSSRG
          PS...S..YDDYS.S.DGYGGS.DSYSS.R.S.L.SSG.D.VGRQ.RGLP.SMERGYPPP.DSY.SSS..
Retrocopy PS*DRSGHYDDYSHSPDGYGGS*DSYSSAR<SALHSSGHDFVGRQGRGLPSSMERGYPPPHDSYNSSSCR

Parental  APRGGGRGGSRSDRGGGRSRY
          APRGGG.GGS.SD.G.GR.RY
Retrocopy APRGGGGGGSQSDKGEGRCRY

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_1240 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,