RetrogeneDB ID: retro_chof_2475

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_78588:10604..11109(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BNIP3L
• Ensembl ID: ENSCHOG00000007732
• Aliases: None
• Description: BCL2/adenovirus E1B 19kDa interacting protein 3-like [Source:HGNC Symbol;Acc:1085]

Sequence

>retro_chof_2475
AGCTTCAATGGTAATGATAATGGCAACAGGAAAAATGGGGGGCTTGCACATGTACCCCCCTTCATCCTCCATGCACAACA
GAGACACAGAGAAGATTCCTTAGGCTGTACAGCATGAATCAGGAAGGGGCGGTTCTCATTATTGACGGCCCTTCCCCACA
GGAAGAGGGACAGATGATGTTTGATGTGGAGATGCACACCAGCAGGAATCACAGCACTCAGTCAGAAGAAGTTGGAGGAG
AGAAAAAAGTTGAGGCTTTGAAGAAAAGTGTAGACTGCGTATCTGACTGGTCCAGGAGATCTGAAATCATTTCACCTATA
GAGTTCCACTTCAGGTGCCCTAAATATTATGCTTCCTTAAGCCCGAGAAAAAGTGGAGCCATGAAGAAAGGGGGTATTTT
CTTTGCAGAATTTCTTAAGGTGTTCATCTATCCCTCCTCATTTCTCACATTTTGGCTTTGGGGCTCTCCCCAAAACAACT
GAGCACAACTTCTGCCAGCACCTAC

Alignment

ORF - retro_chof_2475 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.11 %
• Parental protein coverage: 80.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SSNGNDNGNGKNGGLEHVPS-SSSIHNGDMEKILLDAQHESGQSSSRGSSH-CDSPSPQEDGQIMFDVEM
          S.NGNDNGN.KNGGL.HVP..SSS.HN.D.EKI....QHESG....RG.SH..D.PSPQE.GQ.MFDVEM
Retrocopy SFNGNDNGNRKNGGLAHVPP>SSSMHNRDTEKIP*AVQHESG----RGGSH>IDGPSPQEEGQMMFDVEM

Parental  HTSRDHSSQSEEEVGEGEKEAEGMKKSVDWVSDWSSRPENIPPKEFHFRHPKRSASLSMRKSGAMKKGGI
          HTSR.HS.QSEE.VG.GEK..E..KKSVD.VSDWS.R.E.I.P.EFHFR.PK..ASLS.RKSGAMKKGGI
Retrocopy HTSRNHSTQSEE-VG-GEKKVEALKKSVDCVSDWSRRSEIISPIEFHFRCPKYYASLSPRKSGAMKKGGI

Parental  FSAEFLKVFI-PSLFISHVLALGLGIYIGKRLSTSSASTY
          F.AEFLKVFI..SL.ISH.LALGL.....K.LST.SASTY
Retrocopy FFAEFLKVFI<LSLLISHILALGLS---PKQLSTTSASTY

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_2475 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 22 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021307	4 retrocopies	retro_btau_1148, retro_btau_1170, retro_btau_1790, retro_btau_449,
Choloepus hoffmanni	ENSCHOG00000002150	2 retrocopies	retro_chof_1555, retro_chof_559,
Choloepus hoffmanni	ENSCHOG00000007732	3 retrocopies	retro_chof_2356, retro_chof_2475 , retro_chof_980,
Dasypus novemcinctus	ENSDNOG00000016179	1 retrocopy	retro_dnov_2101,
Dipodomys ordii	ENSDORG00000009336	1 retrocopy	retro_dord_169,
Erinaceus europaeus	ENSEEUG00000006302	1 retrocopy	retro_eeur_269,
Echinops telfairi	ENSETEG00000012037	3 retrocopies	retro_etel_1178, retro_etel_1428, retro_etel_603,
Felis catus	ENSFCAG00000030159	2 retrocopies	retro_fcat_616, retro_fcat_944,
Macropus eugenii	ENSMEUG00000011173	1 retrocopy	retro_meug_962,
Myotis lucifugus	ENSMLUG00000014949	1 retrocopy	retro_mluc_2192,
Mustela putorius furo	ENSMPUG00000000829	1 retrocopy	retro_mputfur_297,
Mus musculus	ENSMUSG00000022051	2 retrocopies	retro_mmus_482, retro_mmus_849,
Oryctolagus cuniculus	ENSOCUG00000010542	1 retrocopy	retro_ocun_1460,
Otolemur garnettii	ENSOGAG00000003163	2 retrocopies	retro_ogar_1039, retro_ogar_2651,
Ochotona princeps	ENSOPRG00000016284	1 retrocopy	retro_opri_1105,
Rattus norvegicus	ENSRNOG00000009820	1 retrocopy	retro_rnor_1183,
Sus scrofa	ENSSSCG00000009658	1 retrocopy	retro_sscr_511,
Ictidomys tridecemlineatus	ENSSTOG00000004029	1 retrocopy	retro_itri_1525,
Tupaia belangeri	ENSTBEG00000006361	2 retrocopies	retro_tbel_3371, retro_tbel_4006,
Tarsius syrichta	ENSTSYG00000011036	4 retrocopies	retro_tsyr_1182, retro_tsyr_1602, retro_tsyr_162, retro_tsyr_1997,
Tursiops truncatus	ENSTTRG00000004862	1 retrocopy	retro_ttru_725,
Vicugna pacos	ENSVPAG00000000509	2 retrocopies	retro_vpac_349, retro_vpac_534,