RetrogeneDB ID: retro_chof_805

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_150598:710..1382(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA7
• Ensembl ID: ENSCHOG00000004243
• Aliases: None
• Description: karyopherin alpha 7 (importin alpha 8) [Source:HGNC Symbol;Acc:21839]

Sequence

>retro_chof_805
TCATCCCTTTACTCCTGCTTGCAGTTTGAGGCAGCCTGGGCTCTGACCAACATTGCTTCAGGGACATTGGAGCAGACCCA
AGCTGTTGTGAAGGGAGGAGCCATCCAACCCTTGGTGGGGCCCCTGTCTTCCCCTGACCTGACTGTGTGTCAACAGGCAG
TGTGGGCTCTGGATAACATAGCAGGTGATGGCCCAGAGTTCAGAAACATCATTATCTCGAGCAACGCCATCCCACATCTG
TTGTCCCTGCTTTTGTCAACCATACCAATCATGTTTCTGCAGAATATCAAGTGGATCTTGTTCAACCTGTGCCAGAACAA
GAACCCATACACTTGCCCCAAAGCAGTGAAGCAAATACTGCCCGTTCTCTCCAACCTCTTGCAGCACTATGACAGTGAGT
TTCTCTCAGACACCTGCTGGGCCCTGTCCTGCCTCACCGATGGCTGCAAGGTGTGCATCGGCCAAGTGGTTGACACGGGG
GTCCTGCCCAGGCTGGTCCACCTTATGAGAAGCTCAGAACTCAGTGTCTTGATCCCTTCTCTCTGCACTGTGGGGAACAT
TGTCTTGGAAGCAGATTACCAGATCCAGGTGGCCACTGATACTGGCTTGCTGAGCATGATGCCCCAGCTCCTAGGTCACC
CCAGTTCTTCCATCCGGAAGGAAGCAGTCTGG

Alignment

ORF - retro_chof_805 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.04 %
• Parental protein coverage: 53.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPLYPCLQFEAAWALTNIASGTSEQTRAVVKGGAIQPLVELLSSPDLTVCEQAVWALGNIAGDGPEFRDI
          S.LY.CLQFEAAWALTNIASGT.EQT.AVVKGGAIQPLV..LSSPDLTVC.QAVWAL.NIAGDGPEFR.I
Retrocopy SSLYSCLQFEAAWALTNIASGTLEQTQAVVKGGAIQPLVGPLSSPDLTVCQQAVWALDNIAGDGPEFRNI

Parental  VISSNAIPHLLSLVSSTIPITFLRNITWTLSNLCRNKNPYPCPKAVKQILPVLFNLLQHYDSEVLSDTCW
          .ISSNAIPHLLSL..STIPI.FL.NI.W.L.NLC.NKNPY.CPKAVKQILPVL.NLLQHYDSE.LSDTCW
Retrocopy IISSNAIPHLLSLLLSTIPIMFLQNIKWILFNLCQNKNPYTCPKAVKQILPVLSNLLQHYDSEFLSDTCW

Parental  ALSYLTDGCNERIGQVVDTEVLPRLVHLMRSSELSVLIPSLRTVGNIVSGTDYQTQVAIDAGLLSVLPQL
          ALS.LTDGC...IGQVVDT.VLPRLVHLMRSSELSVLIPSL.TVGNIV...DYQ.QVA.D.GLLS..PQL
Retrocopy ALSCLTDGCKVCIGQVVDTGVLPRLVHLMRSSELSVLIPSLCTVGNIVLEADYQIQVATDTGLLSMMPQL

Parental  LGHPRSSIQKEAAW
          LGHP.SSI.KEA.W
Retrocopy LGHPSSSIRKEAVW

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_805 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 15 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015125	2 retrocopies	retro_cfam_459, retro_cfam_861,
Choloepus hoffmanni	ENSCHOG00000004243	1 retrocopy	retro_chof_805 ,
Choloepus hoffmanni	ENSCHOG00000008565	2 retrocopies	retro_chof_1082, retro_chof_823,
Callithrix jacchus	ENSCJAG00000015943	1 retrocopy	retro_cjac_2964,
Equus caballus	ENSECAG00000000554	1 retrocopy	retro_ecab_981,
Echinops telfairi	ENSETEG00000000096	1 retrocopy	retro_etel_1548,
Homo sapiens	ENSG00000185467	1 retrocopy	retro_hsap_3337,
Mus musculus	ENSMUSG00000038770	2 retrocopies	retro_mmus_2844, retro_mmus_3301,
Nomascus leucogenys	ENSNLEG00000010827	1 retrocopy	retro_nleu_1680,
Otolemur garnettii	ENSOGAG00000031106	3 retrocopies	retro_ogar_1289, retro_ogar_3237, retro_ogar_353,
Ochotona princeps	ENSOPRG00000015434	2 retrocopies	retro_opri_1101, retro_opri_118,
Pongo abelii	ENSPPYG00000017369	1 retrocopy	retro_pabe_2750,
Pan troglodytes	ENSPTRG00000019446	2 retrocopies	retro_ptro_102, retro_ptro_2142,
Tupaia belangeri	ENSTBEG00000009007	3 retrocopies	retro_tbel_1475, retro_tbel_3862, retro_tbel_3962,
Tursiops truncatus	ENSTTRG00000002998	2 retrocopies	retro_ttru_1426, retro_ttru_430,