RetrogeneDB ID: retro_chof_1982

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_44289:1..1084(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IRAK4
• Ensembl ID: ENSCHOG00000005497
• Aliases: None
• Description: interleukin-1 receptor-associated kinase 4 [Source:HGNC Symbol;Acc:17967]

Sequence

>retro_chof_1982
CTTTTGCTACCAGACGCTATTCCCAAAACTGTTAGTACCCTACCTTCAAAGGAAGCTCTAACAGTTCAGCAGAAACCAAT
GCCTCTCTGTGGCAAGGACAGGACATCTGTAGTACCTGTGCAGAATCTTGAACACAGCTGTATGTCACCTGACTCCTCCA
GTCTGGAAAATAAAAGTTTAGAAGTGAGCGATACACGTTTTCACAGCTTCTCATTTTACGAACTGAAGAATGTCACAAAT
AACTTTGACAAACAACCCCTTTCTGCTGGTGGTAATAAAATGGGAGAGGGAGAACTTGGAGTTGTGCATAAAGGCTAAGT
GAACAACAAAACCGTGGCAGTGAAGAAGCTTGCAGCCATGGTTGACATTAATACTGAAGAACTGAAACAACAGTTTGATC
AAGAAATAAAAGTAATGGCAAATTGTCAACATGAAAACTTAGTAGAACTACTTGGTTTTTCTAGTGATGGTGATGACCTC
TGCTTAGTGTATGTTTACATGCCCAATGGATTACTGCTTGACAAACTGTCTTGCTTGGATGGTACTCCACCATTTTCATG
GCACATGCAATGCGAGATTGTTCAGGGTGCAGCTAATGGCATCAGTGTTTTTACATGAAAACTATCATATTCATAGAGAT
ATTAAAAGTGCAAATATCTTACTATAAGAAGCCTTTGTAGCCAAAATATCTGACTTTGGCCTTGCACGGGCTTCTGAGAA
GTTTGCTCAGACAATCATGACTAGCAGAATTGTGGGAACAACAGCTTACATGGCACCTGAAGCTCTATGAGGAGAAATAA
CACCCAAATCTGACATCTACAGTTTTGGTGTGGTTTTACTAGAAATAATAACTGGACTTCCAGCTATGGATGAACACCAT
GAACCTCAGTTATTATTAGATATCAAAGAAGAAATTGAAGATGAAGAAAAGACAATTGAAGATTATATTGATGTGAAGAT
GAATGATGTTGATTCCACTTCAGTTGAAATTATGTACTCTGTTGCTAGTCATGTCTTCATGAAAAGAAAAATAAGAGACC
AGACATTAAGAAGGTTCAACAGCTGCTGCTAGAGATGAGAGTC

Alignment

ORF - retro_chof_1982 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.08 %
• Parental protein coverage: 78.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLLPDAIPKTVNTLPSKEAITVQQKQMPLYGKDRTSVVPLQNLEQNCMSPDSSSLENKNLEVSDTRFHSF
          LLLPDAIPKTV.TLPSKEA.TVQQK.MPL.GKDRTSVVP.QNLE..CMSPDSSSLENK.LEVSDTRFHSF
Retrocopy LLLPDAIPKTVSTLPSKEALTVQQKPMPLCGKDRTSVVPVQNLEHSCMSPDSSSLENKSLEVSDTRFHSF

Parental  SFYELKNVTNNFDERPLSAGGNKMGEGGFGIVYKGYVNNKTVAVKKLAAMVDISTEELKQQFDQEIRVMA
          SFYELKNVTNNFD..PLSAGGNKMGEG..G.V.KG.VNNKTVAVKKLAAMVDI.TEELKQQFDQEI.VMA
Retrocopy SFYELKNVTNNFDKQPLSAGGNKMGEGELGVVHKG*VNNKTVAVKKLAAMVDINTEELKQQFDQEIKVMA

Parental  KCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGIS-FLHENNH
          .CQHENLVELLGFSSDGDDLCLVYVYMPNG.LLD.LSCLDGTPP.SWHM.C.I.QGAANGIS.FLHEN.H
Retrocopy NCQHENLVELLGFSSDGDDLCLVYVYMPNGLLLDKLSCLDGTPPFSWHMQCEIVQGAANGIS>FLHENYH

Parental  IHRDIKSANILLDEAFVAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVL
          IHRDIKSANILL.EAFVAKISDFGLARASEKFAQT.MTSRIVGTTAYMAPEAL.GEITPKSDIYSFGVVL
Retrocopy IHRDIKSANILL*EAFVAKISDFGLARASEKFAQTIMTSRIVGTTAYMAPEAL*GEITPKSDIYSFGVVL

Parental  LEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDVKMNDADSTSVEIMYSVAS-QCLHEKKNKRPD
          LEIITGLPA.DEH.EPQLLLDIKEEIEDEEKTIEDYIDVKMND.DSTSVEIMYSVAS..CLHEKKNKRPD
Retrocopy LEIITGLPAMDEHHEPQLLLDIKEEIEDEEKTIEDYIDVKMNDVDSTSVEIMYSVAS<SCLHEKKNKRPD

Parental  IKKVQQQLLEMTV
          IKKVQQ.LLEM.V
Retrocopy IKKVQQLLLEMRV

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_1982 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005497	1 retrocopy	retro_chof_1982 ,
Monodelphis domestica	ENSMODG00000018536	1 retrocopy	retro_mdom_718,