RetrogeneDB ID: retro_chof_1216

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_228196:3056..3845(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000013414
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GORAB
• Ensembl ID: ENSCHOG00000012588
• Aliases: None
• Description: golgin, RAB6-interacting [Source:HGNC Symbol;Acc:25676]

Sequence

>retro_chof_1216
CTGTTTGAACCACAGCAGCGTCTCCCCGTGAAGAAAAGTTGCCAGCAACTTCAGCGAGAAAAAGCTCTTCAAGAGCAAAG
CCAAAAACTTGGACTTCAAGATGGATCAACTTCATTACCTCCAGAGCAGCTACTTTCTACATCAAAACCAAGATTTAATT
CTCAAAAGCCAAATTCTTCTCCACCTACTCCTCCTAGTCTTACAATCATTTCTCCTATTGGTGATAGGAAACAACCGGGT
ATTGAAAGTCAACCAAGCGGACTGGAACTTGAGAATTCCCATGGTGTACAAAACAAAAAAAATTGAGGCTCTTCCTTCAA
AGCCAGATTGCAAATTGGAGAAAAAGAAAATGGAATTGTTAGCAAGAAAAAACTCGTTGGGAAGTCCTCCAACAAGAACA
ACAGCTAATGGAAGAGAAAAATAAACGTAAGAAAGCTCTTTTGGCCAAAGCTATTGCAGAAAGATCTAAAAGAACTCAGG
CAGAGGCCATAAAACTAAAGCAGATCCAGAAGGAGTTACAGACTTTAGATGACATGGTGCCAGCTGACATTGGAATCCTC
AGGAACCGGATTGATCAGGCCAGCCTAGATTATTCATATGCTTGCAAGTGGTTTGACAGGGCTGAAGCAGAGTACATTAC
AGCAAAGCTAGATCTGCAGTGCAAGACTGAGATTAAAGAGCAACTCACTGAACACCTTTGTACAATCATACAACAAAGTG
AGCTCCAGATGCCAAGAGGTTGGAGGATTGATGCAAAAACTGGATGTAGAAGCTGATGAGGAGTCTTTG

Alignment

ORF - retro_chof_1216 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.33 %
• Parental protein coverage: 76.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LFEPQRRLPVKKSRQQLQREKALQEQSQKLGLQDGSTSLPPEQLLTTSKPRFNSQKPNSSPITPPSLLTI
          LFEPQ.RLPVKKS.QQLQREKALQEQSQKLGLQDGSTSLPPEQLL.TSKPRFNSQKPNSSP.TPPSL.TI
Retrocopy LFEPQQRLPVKKSCQQLQREKALQEQSQKLGLQDGSTSLPPEQLLSTSKPRFNSQKPNSSPPTPPSL-TI

Parental  TSPVGDRKELGIESHPSELELENSHDVQNKKI-EALPSKPDCKLE-KKKMEL-QEKTRWEVLQKEQRLME
          .SP.GDRK..GIES.PS.LELENSH.V......EALPSKPDCKLE.K.K....QEKTRWEVLQ.EQ.LME
Retrocopy ISPIGDRKQPGIESQPSGLELENSHGVXXXXX>EALPSKPDCKLE>KRKWNC*QEKTRWEVLQQEQQLME

Parental  EKNKRKKALLAKAIAERSKRTQAETIKLKRIQKELQTLDDMVSADIGILRNRIDQASLDYSYARKRFDRA
          EKNKRKKALLAKAIAERSKRTQAE.IKLK.IQKELQTLDDMV.ADIGILRNRIDQASLDYSYA.K.FDRA
Retrocopy EKNKRKKALLAKAIAERSKRTQAEAIKLKQIQKELQTLDDMVPADIGILRNRIDQASLDYSYACKWFDRA

Parental  EAEYITAKLDLQRKTEIKEQLTEHLCTIIQQNELR-KAKKLEE-LMQQLDVQADEETL
          EAEYITAKLDLQ.KTEIKEQLTEHLCTIIQQ.EL...AK.LE..LMQ.LDV.ADEE.L
Retrocopy EAEYITAKLDLQCKTEIKEQLTEHLCTIIQQSELQ<DAKRLED<LMQKLDVEADEESL

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_1216 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012588	1 retrocopy	retro_chof_1216 ,