RetrogeneDB ID: retro_chof_359

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_951:80281..80804(+)
• Located in intron of: ENSCHOG00000004072

Retrocopy information

• Ensembl ID: ENSCHOG00000004089
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GNAI3
• Ensembl ID: ENSCHOG00000012718
• Aliases: None
• Description: guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 3 [Source:HGNC Symbol;Acc:4387]

Sequence

>retro_chof_359
GAAGTGAGGTTGTTGTTGTTCGTTGCTGGAGATTCTGTTAGATTCACCTTCGTGAACCAGATGAATTCATTCATGAGGAT
GGATATTCAGAGGAAGAACGTGACCAGTATAAAGTGGTTTCTACAGCAATACCATAGAGTCCAGCATTTAATCTTAAGAG
CCATGGGGCGGCTAAAGATTGACTTTGGGGAAGCTTCCGGAGCAGACGATGCCCGGCAATTATTTGTTTTAGCTGGCAGT
GCTGAAGATGGTGTCATTGACTCCAGAACAAGCAGAACGGTTATGGCAAGATGGTGGGGAGCAAGCTTGCTTCAGCAGAT
CCAGGGGATATCAGCTCAATGATGCTGCTTCGTATTACCTAAATGATTTGGATAGAATATCCCAAATCAACTATGTTGCA
ACTCAGCGAGATGTACTACAGGCAAGAGTGAAGACCACAGGCCTTGTGGAAATGCATTTCACTTTCGAAGACCTATACTT
CAAGATGTTTGATGTAGATGGTCAAAGATCAGAACGAGAAAAG

Alignment

ORF - retro_chof_359 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.27 %
• Parental protein coverage: 50.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EVKLLLLGAGESGKSTIVKQM-KIIHEDGYSEEECKQYKVV-VYSNTIQSII-AIIRAMGRLKIDFGEAA
          EV.LLL..AG.S...T.V.QM...IHEDGYSEEE..QYKVV..YSNTI.S.I..I.RAMGRLKIDFGEA.
Retrocopy EVRLLLFVAGDSVRFTFVNQM<EFIHEDGYSEEERDQYKVV<FYSNTIESSI<LILRAMGRLKIDFGEAS

Parental  RADDARQLFVLAGSAEEGV-MTPELAGVIKRLWRDGGVQACFSRSREYQLNDSASYYLNDLDRISQINYI
          .ADDARQLFVLAGSAE.GV..TPE.A....RLW.DGG.QACFSRSR.YQLND.ASYYLNDLDRISQINY.
Retrocopy GADDARQLFVLAGSAEDGV>LTPEQA---ERLWQDGGEQACFSRSRGYQLNDAASYYLNDLDRISQINYV

Parental  PTQQDVLRTRVKTTGIVETHFTFKDLYFKMFDVGGQRSERKK
          .TQ.DVL..RVKTTG.VE.HFTF.DLYFKMFDV.GQRSER.K
Retrocopy ATQRDVLQARVKTTGLVEMHFTFEDLYFKMFDVDGQRSEREK

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_359 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010970	1 retrocopy	retro_acar_40,
Choloepus hoffmanni	ENSCHOG00000003770	4 retrocopies	retro_chof_1344, retro_chof_2083, retro_chof_601, retro_chof_653,
Choloepus hoffmanni	ENSCHOG00000012718	1 retrocopy	retro_chof_359 ,
Ciona intestinalis	ENSCING00000005305	1 retrocopy	retro_cint_14,
Ciona savignyi	ENSCSAVG00000001800	1 retrocopy	retro_csav_19,
Otolemur garnettii	ENSOGAG00000013587	1 retrocopy	retro_ogar_993,
Tupaia belangeri	ENSTBEG00000015771	1 retrocopy	retro_tbel_2449,
Tarsius syrichta	ENSTSYG00000000556	1 retrocopy	retro_tsyr_288,