RetrogeneDB ID: retro_chof_265

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_584:19301..20391(+)
• Located in intron of: ENSCHOG00000001765

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX1
• Ensembl ID: ENSCHOG00000000707
• Aliases: None
• Description: sorting nexin 1 [Source:HGNC Symbol;Acc:11172]

Sequence

>retro_chof_265
GAAGAAGCAAATGGAGGTATTTTTGATATAGAAATTGGTGTGTCAGATCCAGAGAAAGTTGGTGGTGGCATGAATGCTTA
TGTGGCATATAGGGTAATAACAAAGACTTCCTTTTCCATGTTCAATAAGAGTGAATTTTCTGTTAGAAGAAGATTCAGTG
ACTTTCTTGGCTCGCATGGCAAATTAGCAAGCAAGTATTTACATGTTGGTTATATTGTGCCACCAGCTCCAGAAAAGAGT
ATAGTAAAGCATGACCAAGGTCAAAGTGGGAAAAGAACATTCATAATCCACTAAATCTGTAGAAAAACAGAGAACAGCTC
TTGAAAGATATCTTCAACAAACTGTAAAACATCCAAGTTTACTACAGGATACTGATTTAAGGCAATTTTTGGAGAGTTCT
GAGCTGCCTAGAGCAGTTAATACACAGGCTCTGAGTGGAGAAGGAATATTAAGGATGGTGAACAAGACTGCCGATGCTGT
CAACAAAATGACAGTCAAGATGAACGAATCGGATGCATGGTTTGAAGAAAAGCAGCAGCAATTTGAGAACCTGGATCAGC
AACTTAGGAAACTTCATGCCAGTGTTGAAGCCTTGGTCTTCATAGAAGACCTTTCAGCCAACACAGCTAACTTTACTAAA
AGTGCTGCCATGTTAAGTAATTCTGAGGATCACACTGCTTTATCCAGAGCTTTGTCTCAGCTTGCCAAGGTTGAGGAGAA
GATAGACCAGTTTCATCAAAAACAAGCTTTTGGTGACTTCTATATGTTTTCAGAAGTACTAAGTGACTACAGTCGTCTTA
TTGCTGCAGTGAAAGATGTGTTTGACCATCGAATGAAGTGCTGGCAGAAAAGGGAAGATGCTCAAATTACTTTACTCAAA
AAATGTGAAACTGAGGCAAAAATGATGGTTGCTAACAAACCAGATAAAATACAGCGAGCTAAAAACGAAATAAGATAGTG
AGAGGCTAAAGTGCAACAAGGAAAAGGAAATTTTCAACAGATCTCTAAAATGATTCAAAAAGAAGTTGGAAGATTTGAGG
AAGAATGAGTGAAAGATTTTAAAACTGTTATTATCAAGTACTCAGAATCA

Alignment

ORF - retro_chof_265 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.18 %
• Parental protein coverage: 70.35 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEEQEDQFDLTVGITDPEKIGDGMNAYVAYKVTTQTSLPIFRSKQFAVKRRFSDFLGLYEKLSEKHSQNG
          EE.....FD...G..DPEK.G.GMNAYVAY.V.T.TS...F....F.V.RRFSDFLG...KL..K....G
Retrocopy EEANGGIFDIEIGVSDPEKVGGGMNAYVAYRVITKTSFSMFNKSEFSVRRRFSDFLGSHGKLASKYLHVG

Parental  FIVPPPPEKSLI-GMTKVKVGKEDSSSAEFLEKRRAALERYLQRIVNHPTMLQDPDVREFLEKEELPRAV
          .IVPP.PEKS....MTKVKVGKE.S.S....EK.R.ALERYLQ..V.HP..LQD.D.R.FLE..ELPRAV
Retrocopy YIVPPAPEKSIV>SMTKVKVGKEHS*STKSVEKQRTALERYLQQTVKHPSLLQDTDLRQFLESSELPRAV

Parental  GTQTLSGAGLLKMFNKATDAVSKMTIKMNESDIWFEEKLQEVECEEQRLRKLHAVVETLVNHRKELALNT
          .TQ.LSG.G.L.M.NK..DAV.KMT.KMNESD.WFEEK.Q..E...Q.LRKLHA.VE.LV.....L..NT
Retrocopy NTQALSGEGILRMVNKTADAVNKMTVKMNESDAWFEEKQQQFENLDQQLRKLHASVEALV-FIEDLSANT

Parental  AQFAKSLAMLGSSEDNTALSRALSQLAEVEEKIEQLHQEQANNDFFLLAELLSDYIRLLAIVRAAFDQRM
          A.F.KS.AML..SED.TALSRALSQLA.VEEKI.Q.HQ.QA..DF....E.LSDY.RL.A.V...FD.RM
Retrocopy ANFTKSAAMLSNSEDHTALSRALSQLAKVEEKIDQFHQKQAFGDFYMFSEVLSDYSRLIAAVKDVFDHRM

Parental  KTWQRWQDAQATLQKKREAEARLLWANKPDKLQQAKDEIAEWESRVTYER-DFERISTVVRKEVIRFEKE
          K.WQ...DAQ.TL.KK.E.EA....ANKPDK.Q.AK.EI...E..V......F..IS....KEV.RFE.E
Retrocopy KCWQKREDAQITLLKKCETEAKMMVANKPDKIQRAKNEIR**EAKVQQGKGNFQQISKMIQKEVGRFEEE

Parental  KSKDFKNHVIKYLET
          ..KDFK...IKY.E.
Retrocopy *VKDFKTVIIKYSES

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_265 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000707	2 retrocopies	retro_chof_2390, retro_chof_265 ,
Choloepus hoffmanni	ENSCHOG00000010128	2 retrocopies	retro_chof_1478, retro_chof_2166,
Rattus norvegicus	ENSRNOG00000017029	1 retrocopy	retro_rnor_791,