RetrogeneDB ID: retro_chof_2352

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_67580:3269..3743(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS26A
• Ensembl ID: ENSCHOG00000007324
• Aliases: None
• Description: vacuolar protein sorting 26 homolog A (S. pombe) [Source:HGNC Symbol;Acc:12711]

Sequence

>retro_chof_2352
GGCACTGAAGATTGTCTACACACAGAATTTGAATACAATGAATCAAAGTATCATTTAAAGGATGTGACTGTTGGAAAAAT
TTACTTCTTATTAGTAAGAATAAAAATGCAACACATGGAGTTATAACAGATCAAAAAAGAGACCACAGGAATTGGACCCA
GTACCACAAAAGAAACAGAAACAATTGCCAAATGGGAAGTAATGGAGGGGGCACAAGTAAAAGGCGAATCAATCCAATAA
GACTATTTGTAGCGAGGTATGCCCCAACCCCAACAAGGAGAGATGTGAACAAAAACTTTCAGTAAGGTGCTTTTTGAATC
TAGTCCTTGCTGTTGAGGAAGACAGAAGGTACTTCAAGCAGCAGGAGATCATTTGTGGCAGAAAAGCACCTGAAAAACTG
AGGATACCGAGACAAACTTTCACCAGTGAACTGAATCTCTGGAATCACAGGCATCTGCTGAACAGCCTGAAATG

Alignment

ORF - retro_chof_2352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.01 %
• Parental protein coverage: 55.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GIQDCLHIQFEYNKSKYHLKDVIVGKIYFLLVRIKIQHMELQLIKKEITGIGPSTTTETETIAKYEIMDG
          G..DCLH..FEYN.SKYHLKDV.VGKIYFLLVRIK.QHMEL..IKKE.TGIGPSTT.ETETIAK.E.M.G
Retrocopy GTEDCLHTEFEYNESKYHLKDVTVGKIYFLLVRIKMQHMEL*QIKKETTGIGPSTTKETETIAKWEVMEG

Parental  APVKGESI-PIRLFLAGYDPTPTMRDVNKKF-SVRYFLNLVLVDEEDRRYFKQQEIILWRKAPEKLRKQR
          A.VKGESI.PIRLF.A.Y.PTPT.RDVNK.F.SVR.FLNLVL..EEDRRYFKQQEII..RKAPEKLR..R
Retrocopy AQVKGESI<PIRLFVARYAPTPTRRDVNKNF<SVRCFLNLVLAVEEDRRYFKQQEIICGRKAPEKLRIPR

Parental  -INFHQRFESPESQASAEQPEM
          ..NFHQ..ES.ESQASAEQPEM
Retrocopy <TNFHQ*TESLESQASAEQPEM

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_2352 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013827	1 retrocopy	retro_cfam_1133,
Choloepus hoffmanni	ENSCHOG00000007324	5 retrocopies	retro_chof_1303, retro_chof_1663, retro_chof_1796, retro_chof_2352 , retro_chof_242,
Callithrix jacchus	ENSCJAG00000012907	1 retrocopy	retro_cjac_1420,
Equus caballus	ENSECAG00000009507	1 retrocopy	retro_ecab_17,
Homo sapiens	ENSG00000122958	1 retrocopy	retro_hsap_2688,
Gorilla gorilla	ENSGGOG00000010433	1 retrocopy	retro_ggor_1875,
Microcebus murinus	ENSMICG00000014940	1 retrocopy	retro_mmur_1070,
Mustela putorius furo	ENSMPUG00000004519	1 retrocopy	retro_mputfur_146,
Nomascus leucogenys	ENSNLEG00000011548	1 retrocopy	retro_nleu_1187,
Pongo abelii	ENSPPYG00000002386	1 retrocopy	retro_pabe_2293,
Pan troglodytes	ENSPTRG00000002567	3 retrocopies	retro_ptro_1815, retro_ptro_2245, retro_ptro_4,
Tupaia belangeri	ENSTBEG00000015348	1 retrocopy	retro_tbel_1425,
Vicugna pacos	ENSVPAG00000000630	1 retrocopy	retro_vpac_385,