RetrogeneDB ID: retro_chof_2149

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_5350:5465..6108(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000007723
• Aliases: None
• Description: None

Sequence

>retro_chof_2149
CCCGGGTCAGCCGCAGTCAGCGGCCGCGCAGCCCCAGCCCCGAGCAGCCCCGAGCGCAGGCGGCCCCGGGTGTCGCAGCG
GCCGAGCTGCCTGTGCTTGGATGCCTCCGGGAAGTGGGTGCCGTTCGTTCCTCGCCAGGCCTTAGTGGTCTTCGTGAGGC
ATTTCCTGTGTTTCATCTGCAAGGAATACGTAGAAAATCTGGCCAGAAACCCCAAGAGTTTTTTCATAAGAAGCAGACGT
CACCCTTACAGTAATTGGACAGCCGTCCTACCATCATATTGAGCCTTTCTGCAAATTGACTGGGTATTCTCATGCAATCT
GTGCTGTTCTGAGAGAGAAATTTATAAAAGATTGGGAATAAAAAGAGGTGAAGAAATTGCCTCCTGAGGGCAGAGCCCCC
ATGTAAATTACTTGACAGTCTACTCTCAGGAAGTATTCGGAGCCTGTGGTGGCGGTGACTGGCCCTCTTTTCTTTTCAAG
GGCACCCAGCTCAGAGGAGCGGAACCCTCGTCTTTGATCCAGATAATAACATTCACTTCATATATGGTGATAGGAACAGA
TTGGATCACAAACCCACCAACTACGACCTACAGCTTGTGGAGTGCAGCCTGTGAACTTTACAAGCAGACCTTCAGTTACC
TAT

Alignment

ORF - retro_chof_2149 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.56 %
• Parental protein coverage: 97.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  PVTRQVSGRAAPAPTGSEHGEPLAA-AVAELPVL-DASGKRVPFGALFLERRAVVVFVRHFLCYICKEYV
          P....VSGRAAPAP...E...P....A.AELPVL.DASGK.VP....F..R.A.VVFVRHFLC.ICKEYV
Retrocopy PGSAAVSGRAAPAPSSPERRRPRVS<AAAELPVL>DASGKWVP----FVPRQALVVFVRHFLCFICKEYV

Parental  EDLAKIPKSFLQ-EANVTLIVIGQSSYHHIEPFCKLTGYSHEIYVDPEREIYK-RLGMKRGEEIASSGQS
          E.LA..PKSF...EA.VTL.VIGQ.SYHHIEPFCKLTGYSH.I.........K.RLG.KRGEEIAS.GQS
Retrocopy ENLARNPKSFFI>EADVTLTVIGQPSYHHIEPFCKLTGYSHAICAVLREKFIK<RLGIKRGEEIAS*GQS

Parental  PHVKSNTLSGSIQSLWWAVTG---PLFDFQ-GDPAQQGGTLILGPGNNVHFIHRDRNRLDHKPINSVLQL
          PHV..N.L....Q....A..G...P.F.F..G.PAQ..GTL...P.NN.HFI..DRNRLDHKP.N..LQL
Retrocopy PHV--NYLTVYSQEVFGACGGGDWPSFLFK<GHPAQRSGTLVFDPDNNIHFIYGDRNRLDHKPTNYDLQL

Parental  V-GVQHVNFTSRPSVIH
          V.GVQ.VNFTSRPSV..
Retrocopy V<GVQPVNFTSRPSVTY

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_2149 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 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006422	1 retrocopy	retro_chof_1792,
Choloepus hoffmanni	ENSCHOG00000007723	7 retrocopies	retro_chof_1026, retro_chof_1037, retro_chof_1808, retro_chof_2079, retro_chof_2149 , retro_chof_2642, retro_chof_811,
Callithrix jacchus	ENSCJAG00000005509	1 retrocopy	retro_cjac_4168,
Dasypus novemcinctus	ENSDNOG00000024562	4 retrocopies	retro_dnov_1226, retro_dnov_1419, retro_dnov_1519, retro_dnov_1871,
Homo sapiens	ENSG00000158122	1 retrocopy	retro_hsap_4843,
Macaca mulatta	ENSMMUG00000008295	1 retrocopy	retro_mmul_2586,
Otolemur garnettii	ENSOGAG00000017058	1 retrocopy	retro_ogar_1866,
Procavia capensis	ENSPCAG00000003177	1 retrocopy	retro_pcap_269,
Pongo abelii	ENSPPYG00000019418	1 retrocopy	retro_pabe_3765,
Pan troglodytes	ENSPTRG00000021156	1 retrocopy	retro_ptro_3227,