RetrogeneDB ID: retro_chof_2120

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_51196:10401..10990(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZC3H15
• Ensembl ID: ENSCHOG00000011958
• Aliases: None
• Description: zinc finger CCCH-type containing 15 [Source:HGNC Symbol;Acc:29528]

Sequence

>retro_chof_2120
GAAGAGAAAGAAGATGAAATTTCATAAGAAGATCTAATTGAAAGAGGGCACTCTGCCCTAGGACCAAATGTTAGCAAAAT
CACTTTAGAATCTTTTCTTGCATGGAAGAAAAGGAAAAGACAAGAAAAGTTTGATCAACTTGAGCAAGATATGGAAAAAA
GGAAAGCAGATATCAAAGCCGGGAAGGCACTAGTGACCGGTGGTCATGAAGTGTTTGAATTCTGTCCTGAACTGGTTGAT
GAGGAAGCAGAAGACACAAGTTACATCTGGAGATCAGCTGGTGTAGAGGTTGATTCTGTGAGTGTGAAGGATTTAGATTT
AAGCCTGTACATCCCAAGAGATGTAGATGAGACAGGTATTACTGTAGCCAGTCTTGAAAGATTCAACCATTATACTTCAG
AAAAAGATGAAAACAAATTAAGTGAAGCTTCTGGCAGTAGGGCTGACAATGGTAGAAGAAGTGATTTGGAAGAGGACAAT
GAAGGAGAGGACAGGAAAATGGAGCCATCGATGCTGTTCCTGTCAATAATTTTGCTGGAGAAGATTGGATGAACTAGAAA
AAGAATTAAACACATTTAATTTAGAAGAA

Alignment

ORF - retro_chof_2120 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 50.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EEKEDEISLEDLIERERSALGPNVTKITLESFLAWKKRKRQEKIDKLEQDMERRKADFKAGKALVISGRE
          EEKEDEIS.EDLIER..SALGPNV.KITLESFLAWKKRKRQEK.D.LEQDME.RKAD.KAGKALV..G.E
Retrocopy EEKEDEIS*EDLIERGHSALGPNVSKITLESFLAWKKRKRQEKFDQLEQDMEKRKADIKAGKALVTGGHE

Parental  VFEFRPELVDDDDEEADDTRYIQGSGGDEVDDSISVNDIDLSLYIPRDVDETGITVASLERFSTYTSEKD
          VFEF.PELVD...EEA.DT.YI..S.G.EV.DS.SV.D.DLSLYIPRDVDETGITVASLERF..YTSEKD
Retrocopy VFEFCPELVD---EEAEDTSYIWRSAGVEV-DSVSVKDLDLSLYIPRDVDETGITVASLERFNHYTSEKD

Parental  ENKLSEASGGMAENGERSDLEEDNEGE-GQENGAVDAVPVDENLFTGED-LDELEEELNTLDLEE
          ENKLSEASG..A.NG.RSDLEEDNEGE.GQENGA.DAVPV..N.F.GED.LDELE.ELNT..LEE
Retrocopy ENKLSEASGSRADNGRRSDLEEDNEGE<GQENGAIDAVPV--NNFAGED<LDELEKELNTFNLEE

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_2120 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 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021762	1 retrocopy	retro_btau_1223,
Choloepus hoffmanni	ENSCHOG00000011958	1 retrocopy	retro_chof_2120 ,
Callithrix jacchus	ENSCJAG00000005931	2 retrocopies	retro_cjac_2883, retro_cjac_3986,
Cavia porcellus	ENSCPOG00000012965	2 retrocopies	retro_cpor_1294, retro_cpor_919,
Dipodomys ordii	ENSDORG00000011664	1 retrocopy	retro_dord_666,
Loxodonta africana	ENSLAFG00000001563	1 retrocopy	retro_lafr_941,
Monodelphis domestica	ENSMODG00000027565	5 retrocopies	retro_mdom_1230, retro_mdom_1321, retro_mdom_1744, retro_mdom_1942, retro_mdom_871,
Oryctolagus cuniculus	ENSOCUG00000011903	1 retrocopy	retro_ocun_886,
Otolemur garnettii	ENSOGAG00000002182	2 retrocopies	retro_ogar_1093, retro_ogar_611,
Ochotona princeps	ENSOPRG00000015790	2 retrocopies	retro_opri_169, retro_opri_609,
Pan troglodytes	ENSPTRG00000012717	1 retrocopy	retro_ptro_348,
Rattus norvegicus	ENSRNOG00000005256	4 retrocopies	retro_rnor_2628, retro_rnor_284, retro_rnor_662, retro_rnor_925,
Sorex araneus	ENSSARG00000012071	1 retrocopy	retro_sara_363,