RetrogeneDB ID: retro_chof_2223

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_59521:6776..8091(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IFNAR1
• Ensembl ID: ENSCHOG00000001895
• Aliases: None
• Description: interferon (alpha, beta and omega) receptor 1 [Source:HGNC Symbol;Acc:5432]

Sequence

>retro_chof_2223
TTGTCATTTCAAAAAGCTCAGACTGGTCCTCCAGAAGTACATTTAGAAGCTGAAGGTAAGGCAATAATCATCAACATCTC
CCCTCCTGGAACAAGATAGTGTCATGTGGGCCATGGATAGTTCCAGCTTTATATATAGTTTAGTTATCTGGAAAAATTCT
TCAAGTGTAGAAAAAAGGACTGCAACTGTTTATTCTGGAGATAAGATTTATAAACTCTCACCAGAGACTACTTCTTGTTT
AAAAGTTAAAGCAAGACTACGTTTGCAGAGAAAAGTTGGTTTCTATAGTCCAGTGTCTTGTATAAATACCACGGTGGAAA
ATAAACTGCCTCCACCTGAAAATACAGAAATTGGTGCTAAAAATCAGAGCTATATTCTTAAATGGGATTACTCACATGAA
AACGTGACCTTTCAAGTCCAGTGGCTTCATGGTCTTTTTAAAAAGACTCTTGGGAACCATTCAGACAAATGGAAACAAAT
ACCTCAGTGTAAAAACTTCAAAACTACCCAGTGTGTCTTTCCTTGGAAAGCTTTCCAAAAAGGGCTTTACTTCCTCCGTG
TACAAGCACCTAATGGAAATAACACCTCTCTCTGATCTGAAGAGAAACAATTTGTTACTGAAATACAAACTGTCACGTTT
CCATAGTCAGCAACACGGAATCTGGGAACAGTTCCTTGCGCATCTATCTCAGTGCCCCAGAAGAGTCAGAAAACAAGTCT
GTAACCACTGCTACCCAATACTTTATGAAATTGTTTTTTGGGAAAACACATCAACTTCCGAGAACAAAATGCTAGAGAAT
AAAACTGATTTTACTCTTTCTAATTTACAACCGCTGACTGTGTATTGTGTCAAAGTGAGAGCACTTGTTGAAGATGAAAA
ATGGAATAAAAGCAGTGTTTTCAGTGATATGGTGTGCGAGAAAACACAACCAGGAAAGACCTCCATATCCTGGATTATAA
CTGGAATTTGTGATGCATTATTTTCCTTCCCACTTGTCATTTATGCTGTGAAAGCCTTCTTGAAATGTATCAATTATGTG
TTCTTTCCATCACATAATGCTCCTTCCAGGATAGATGAGTATTTCTCGGAAAAGCCACTAAAGAATCTACTCCTTTCCAC
TTCTGAGGAACAAACTGAAAGATGTTTCATGATTGAAATACAAGCCCTATTGCTACCTTTGAAGATACTTATCAAATTGA
CAAAAATCACATAAAATACAATTCCCAGACTAATCAAGACTTAAGAAACGATTCTAATGAAGATGAAAATAGCGAAGATA
AAGCAAGTGAAGAATTTTTACAGCAGGAGACCATG

Alignment

ORF - retro_chof_2223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.63 %
• Parental protein coverage: 78.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IPFQKAQIGPPEVHLEAEDKAIII-NISPPGTEDSVMWAMDSFSFTYSLVIWKNSSSVEKRIATVYSGDK
          ..FQKAQ.GPPEVHLEAE.KA.II...SP....DSVMWAMDS.SF.YSLVIWKNSSSVEKR.ATVYSGDK
Retrocopy LSFQKAQTGPPEVHLEAEGKA-II>STSPLLEQDSVMWAMDSSSFIYSLVIWKNSSSVEKRTATVYSGDK

Parental  IYKLSPETTYCLKVKARLRLQRKVGFYSPVYCINTTVENELPPPENIEIDAKNQNYVLKWDYSYENVTFQ
          IYKLSPETT.CLKVKARLRLQRKVGFYSPV.CINTTVEN.LPPPEN.EI.AKNQ.Y.LKWDYS.ENVTFQ
Retrocopy IYKLSPETTSCLKVKARLRLQRKVGFYSPVSCINTTVENKLPPPENTEIGAKNQSYILKWDYSHENVTFQ

Parental  VQWLHAFFKKTLGNHSDKWKQIPECKNVKTTQCVFPRRVFQKGIYFLRVKASNGINTSLWSEEKKFVPEI
          VQWLH..FKKTLGNHSDKWKQIP.CKN.KTTQCVFP...FQKG.YFLRV.A.NG.NTSL.SEEK.FV.EI
Retrocopy VQWLHGLFKKTLGNHSDKWKQIPQCKNFKTTQCVFPWKAFQKGLYFLRVQAPNGNNTSL*SEEKQFVTEI

Parental  QTAVFP-PVISLKPINNSLRIYLGAPKESENKSV-NQYYPIIYEIVFWENTSTAESKMLENKTDFTLHNL
          QT..FP..V......N.SLRIYL.AP.ESENKSV.N..YPI.YEIVFWENTST.E.KMLENKTDFTL.NL
Retrocopy QTVTFP<IVSNTESGNSSLRIYLSAPEESENKSV<NHCYPILYEIVFWENTSTSENKMLENKTDFTLSNL

Parental  QPLTVYCVKARALVEDEKWNKSSVFSDIVCEKTQPGKTSKTWIIIGICIALFSFPLVIYAVKGLLKCIKY
          QPLTVYCVK.RALVEDEKWNKSSVFSD.VCEKTQPGKTS..WII.GIC.ALFSFPLVIYAVK..LKCI.Y
Retrocopy QPLTVYCVKVRALVEDEKWNKSSVFSDMVCEKTQPGKTSISWIITGICDALFSFPLVIYAVKAFLKCINY

Parental  VFFPSHKPPSSIDEYFSEKPLKNLLLSTSEEQTERCFIIE-NTSTITTFEETHEIDENHKQYNSQTSRDS
          VFFPSH..PS.IDEYFSEKPLKNLLLSTSEEQTERCF.IE.NTS.I.TFE.T..ID.NH..YNSQT..D.
Retrocopy VFFPSHNAPSRIDEYFSEKPLKNLLLSTSEEQTERCFMIE<NTSPIATFEDTYQIDKNHIKYNSQTNQDL

Parental  GNYSNEDENSEDKASEELLQQKTM
          .N.SNEDENSEDKASEE.LQQ.TM
Retrocopy RNDSNEDENSEDKASEEFLQQETM

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_2223 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	ENSCHOG00000001895	1 retrocopy	retro_chof_2223 ,