RetrogeneDB ID: retro_chof_413

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_105558:863..1238(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKIRIN2
• Ensembl ID: ENSCHOG00000012160
• Aliases: None
• Description: akirin 2 [Source:HGNC Symbol;Acc:21407]

Sequence

>retro_chof_413
GAACAAATTCTGCACAACATAAAACAAGAGTATAAATGCATGCAGAAGAGAAGACATTTAGAAACTAGTTTCCAACAGAC
AGATCCAGGTTGTGCCCCTGATGCACAGCCAAATGCATTTCTCCTCCGTGGACCAGCTTTTCTAGGGACTGCATCTGCAA
CATTCTCCCCTTTAAAAAAAGAACAGCCTGTATTCACTCTACAGAAAGTCGGGATGATCTGTGAACATTTGTTGAAAGAA
CATGAAGAGAAAGTTTGAGAAAAGTATGAAGAAATATTGAACACAAAACTTACAGAACAATATGATGCATTTGTGAAGTT
TACGCATGATCAAATAATGTGATGATAAGGAGAACAGCCTACTAGTTGTGTTTCA

Alignment

ORF - retro_chof_413 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.4 %
• Parental protein coverage: 61.58 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EQILYNIKQEYKRMQKRRHLETSFQQTDPCCASDAQPNAFLLSGPASPGTASATSSPLKKEQPLFTLRQV
          EQIL.NIKQEYK.MQKRRHLETSFQQTDP.CA.DAQPNAFLL.GPA..GTASAT.SPLKKEQP.FTL..V
Retrocopy EQILHNIKQEYKCMQKRRHLETSFQQTDPGCAPDAQPNAFLLRGPAFLGTASATFSPLKKEQPVFTLQKV

Parental  GMICDRLLKEREEKVREEYEEILNTKLAEQYDAFVKFTHDQIMRRYGEQPASYVS
          GMIC..LLKE.EEKV.E.YEEILNTKL.EQYDAFVKFTHDQIM...GEQP.S.VS
Retrocopy GMICEHLLKEHEEKV*EKYEEILNTKLTEQYDAFVKFTHDQIM***GEQPTSCVS

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_413 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 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003082	1 retrocopy	retro_cfam_1014,
Choloepus hoffmanni	ENSCHOG00000003010	3 retrocopies	retro_chof_1529, retro_chof_624, retro_chof_672,
Choloepus hoffmanni	ENSCHOG00000012160	1 retrocopy	retro_chof_413 ,
Callithrix jacchus	ENSCJAG00000000769	1 retrocopy	retro_cjac_2231,
Dasypus novemcinctus	ENSDNOG00000000549	1 retrocopy	retro_dnov_1788,
Homo sapiens	ENSG00000135334	1 retrocopy	retro_hsap_2991,
Gorilla gorilla	ENSGGOG00000002448	1 retrocopy	retro_ggor_2071,
Macaca mulatta	ENSMMUG00000002824	1 retrocopy	retro_mmul_1914,
Pongo abelii	ENSPPYG00000016831	1 retrocopy	retro_pabe_2477,
Pan troglodytes	ENSPTRG00000018409	1 retrocopy	retro_ptro_2023,
Rattus norvegicus	ENSRNOG00000008288	1 retrocopy	retro_rnor_1499,
Sorex araneus	ENSSARG00000006084	1 retrocopy	retro_sara_701,
Sarcophilus harrisii	ENSSHAG00000011555	2 retrocopies	retro_shar_363, retro_shar_579,
Sus scrofa	ENSSSCG00000004307	1 retrocopy	retro_sscr_897,