RetrogeneDB ID: retro_chof_2390

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_7086:156..987(+)
• Located in intron of: None

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_2390
AAAGAAAATGGGGTCCATGAAGAACAAGACCAAGAGCCCCAGGATCTCTCTGCAGATGCCACAGTGGAGCTATCCCTGGA
CAGTGCACAAAATAATCAGAAGATGGTGCCAGCCAAAATGCTCATTCCTCTTCCTTCACAGGAAACCATAAATTCTTCTG
AGTTCCAGCCAAGCTATGAGGAGCTAGCAGAAGAAGAACAGGAGGGCCAATTTGATTTGACAGTTGGTATAATGGATCCT
GGGAAGATAGGAGATGTTATGAATGCCTATGTAGCCTACAAAGTTAAAACACAGACGAGCTTATCAATGTGCAGAAGTAA
ACAGTTTGCAGTGAAAAGATTCAGTGATTATTTGGGTCTTTATGAGAAGCTTTCAGAGAAACACTCTCAGAATGGCGTCA
TTGTCCCTCCTCCACCTGAGAAGAGTCTAATAGGAATGACAAAAGTGAAAGTTGGGAAGGAAGATTCTTCTTCCACAGAA
TTTCTTGAAAAATGGAAGGCTGATCTAGAAAGGTGCCTTCAGAGGATTGTGAATCATCCTACAATGGTACAGGATCCTGA
TGTCAGAGAGTTCTTGGAAAAAGAAGAGCTGCCACATGCCGTGGGAACCCAGACATTGATTGGTGCTGGTCTCCTCAAGA
TGTTCAACAAAGCCACAGAAGCAGTTAGCAAAACGACCATCAAGATGAATGAATCAGACATTTGGTTTGAAGAGAAGCTC
CAGGAGGTAGAGTGTGAGAAGCAGTGCTTACAGAAACTGCATGCTGTTGCAGAAACTCTAATCAACCACAGGAAAGAGCT
AGTGCTTAATACAGCCCAGTTTGCACAGTCT

Alignment

ORF - retro_chof_2390 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.33 %
• Parental protein coverage: 53.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KENGVHEEQDQEPQDLFADATVELSLDSTQNNQKKVPAKMLVSLPSQEATNSSKSQPSYEELEEEEQEDQ
          KENGVHEEQDQEPQDL.ADATVELSLDS.QNNQK.VPAKML..LPSQE..NSS..QPSYEEL.EEEQE.Q
Retrocopy KENGVHEEQDQEPQDLSADATVELSLDSAQNNQKMVPAKMLIPLPSQETINSSEFQPSYEELAEEEQEGQ

Parental  FDLTVGITDPEKIGDGMNAYVAYKVTTQTSLPIFRSKQFAVKRRFSDFLGLYEKLSEKHSQNGFIVPPPP
          FDLTVGI.DP.KIGD.MNAYVAYKV.TQTSL...RSKQFAVKR.FSD.LGLYEKLSEKHSQNG.IVPPPP
Retrocopy FDLTVGIMDPGKIGDVMNAYVAYKVKTQTSLSMCRSKQFAVKR-FSDYLGLYEKLSEKHSQNGVIVPPPP

Parental  EKSLIGMTKVKVGKEDSSSAEFLEKRRAALERYLQRIVNHPTMLQDPDVREFLEKEELPRAVGTQTLSGA
          EKSLIGMTKVKVGKEDSSS.EFLEK..A.LER.LQRIVNHPTM.QDPDVREFLEKEELP.AVGTQTL.GA
Retrocopy EKSLIGMTKVKVGKEDSSSTEFLEKWKADLERCLQRIVNHPTMVQDPDVREFLEKEELPHAVGTQTLIGA

Parental  GLLKMFNKATDAVSKMTIKMNESDIWFEEKLQEVECEEQRLRKLHAVVETLVNHRKELALNTAQFAKS
          GLLKMFNKAT.AVSK.TIKMNESDIWFEEKLQEVECE.Q.L.KLHAV.ETL.NHRKEL.LNTAQFA.S
Retrocopy GLLKMFNKATEAVSKTTIKMNESDIWFEEKLQEVECEKQCLQKLHAVAETLINHRKELVLNTAQFAQS

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_2390 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,