RetrogeneDB ID: retro_chof_2050

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_467221:34..739(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AIMP1
• Ensembl ID: ENSCHOG00000000619
• Aliases: None
• Description: aminoacyl tRNA synthetase complex-interacting multifunctional protein 1 [Source:HGNC Symbol;Acc:10648]

Sequence

>retro_chof_2050
AAACAAATACCATTCTTTTCTGGTACTCCACTACAAGCTAATTCTACTCTTTCTGAAAATGTGATACAGTCTACATCAAT
AACAACTGTATCTTCTGATGCCAACAAACAGATAAATGGAGGTAGAGGAGAAGAAAAGAAGATGAAAGAAAAAATTGAAA
AGAAAGGATAGAAAAAGGAGAAAAAACAGCAGTAATCAATAGCAGGAAGGGCCGATTCTAAGCCAATAGATGTTTCCCTT
CTGGATCTTAGGATTGGTTGTATCATCGCTGCCAGAAAGCACCCTGACGCAGATTCTTTGTATGTAGAAGAAGTAGATGG
GGAGGAAACAGCCCCAAGAACAGTTGTCAGTGGCCTGGTGAATCATGTTCCTCTTGAACAGATGCAAAATTGGATGGTGA
TTTTACTTTGTAACCTCAAACCTGCAAAGATGAGGGGAGTACTATCCCAAGCAATGGTGAGGTGCACAGAGAAAGTCGAA
ATCTTGACTCCTCCAAATGGATCTCTTCCTGGAGACAGAATGACTTTTGATGCTTTTCCTGGAGAGCCTGACAAGGAGCT
AAATCCTAAGAAGAAGATATGGGAGCAGATACAGCCTGATCTTTACACTAATGACGAGTGTGTGGCTACATACAAAGGCA
CTCCCTTTAAGGTGAAAGAGAAGGGAGTGTGCAGGGCTCAAACTATGGCCAACAGTGGAATCAAA

Alignment

ORF - retro_chof_2050 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.93 %
• Parental protein coverage: 71.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KQIPFFSGTALQTNSTLSENLIQSTSITTVSSDANEQINGGRGEEKKIKEKIEKKGEKKEKKQQQSIAES
          KQIPFFSGT.LQ.NSTLSEN.IQSTSITTVSSDAN.QINGGR....................QQ.SIA..
Retrocopy KQIPFFSGTPLQANSTLSENVIQSTSITTVSSDANKQINGGRXXXXXXXXXXXXXXXXXXXXQQ*SIAGR

Parental  ADSKPIDVSRLDLRIGCIITARKHPDADSLYVEEVDVGETAPRTVVSGLVNHVPLEQMQNRMVILLCNLK
          ADSKPIDVS.LDLRIGCII.ARKHPDADSLYVEEVD..ETAPRTVVSGLVNHVPLEQMQN.MVILLCNLK
Retrocopy ADSKPIDVSLLDLRIGCIIAARKHPDADSLYVEEVDGEETAPRTVVSGLVNHVPLEQMQNWMVILLCNLK

Parental  PAKMRGVLSQAMVMCASSPEKVEILTPPNGSLPGDRITFDAFPGEADKELNPKKKIWEQIQPDLYTNDEC
          PAKMRGVLSQAMV.C....EKVEILTPPNGSLPGDR.TFDAFPGE.DKELNPKKKIWEQIQPDLYTNDEC
Retrocopy PAKMRGVLSQAMVRCT---EKVEILTPPNGSLPGDRMTFDAFPGEPDKELNPKKKIWEQIQPDLYTNDEC

Parental  VATYKGAPFEVKGKGVCRAQTMATSGIK
          VATYKG.PF.VK.KGVCRAQTMA.SGIK
Retrocopy VATYKGTPFKVKEKGVCRAQTMANSGIK

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_2050 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000619	2 retrocopies	retro_chof_1176, retro_chof_2050 ,
Callithrix jacchus	ENSCJAG00000015885	1 retrocopy	retro_cjac_2504,
Dipodomys ordii	ENSDORG00000005018	1 retrocopy	retro_dord_540,
Mustela putorius furo	ENSMPUG00000008952	1 retrocopy	retro_mputfur_1606,
Mus musculus	ENSMUSG00000028029	2 retrocopies	retro_mmus_2271, retro_mmus_3334,
Pongo abelii	ENSPPYG00000014981	1 retrocopy	retro_pabe_1780,
Rattus norvegicus	ENSRNOG00000011384	1 retrocopy	retro_rnor_1704,
Ictidomys tridecemlineatus	ENSSTOG00000008178	1 retrocopy	retro_itri_1173,
Tupaia belangeri	ENSTBEG00000004412	1 retrocopy	retro_tbel_4008,