RetrogeneDB ID: retro_chof_1983

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_44289:4854..5451(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000000618
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNX10
• Ensembl ID: ENSCHOG00000000291
• Aliases: None
• Description: sorting nexin 10 [Source:HGNC Symbol;Acc:14974]

Sequence

>retro_chof_1983
ATGTTTCCAGAACAACAGAAAGAGGAATTTTTAAAGGTTTGGATTCTAGATCCTGGGATTCAGAAGGAGGATTTGGGGCC
TTCTTATATTGACTATGAGCCATGCCTTCACACCAATAGCATGTGTTTTAAAATGAAAATATCCTGTGTGAAAAGAAGAT
ATAGACAATTTGTGTGGCTGAGGCAGAGACTCCAAAATAATGCATTGCTGGTACAACTGCCAGAATGTCCATCTAAAAAC
CTATTTTTCAACATGAACAATTGCCAGCACATAGATCAAAATCATCAAAGTTTGGAAGATTTCCTCAGAAAGGTCCTACA
GAATACACTTTTGCTTTCAGGTCGCAGCCTTCACCTGTTTTTGCAGAGCCATCTGAATTCAGAAGACACCAGGGTGTACG
TTTCTAGGCAATCCAAGCCTTGGTGGAAGAAGCAATTCCACCATCTTGCCTCGATGGACAACTGTTTCCCTGAAGAAGAT
GAAGAAAGAAAAAAAGAAAATGATATAGATTATGATTCAGGAAGTTCATCCTCCGGGCTTGGACACAGATGTGATGATAG
CAGCTCATATGGATGTAAAACAAGCATGACTCTGCAG

Alignment

ORF - retro_chof_1983 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.35 %
• Parental protein coverage: 99.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFPEQQKEEFVSVWVRDPRIQKEDFWHSYIDYEICIHTNSMCFTMKTSCVRRRYREFVWLRQRLQNNALL
          MFPEQQKEEF..VW..DP.IQKED...SYIDYE.C.HTNSMCF.MK.SCV.RRYR.FVWLRQRLQNNALL
Retrocopy MFPEQQKEEFLKVWILDPGIQKEDLGPSYIDYEPCLHTNSMCFKMKISCVKRRYRQFVWLRQRLQNNALL

Parental  VQLPELPSKNLFFNMNNRQHVDQRRQGLEDFLRKVLQNALLLSDSSLHLFLQSHLNSEDIEACVSGQTKY
          VQLPE.PSKNLFFNMNN.QH.DQ..Q.LEDFLRKVLQN.LLLS..SLHLFLQSHLNSED....VS.Q.K.
Retrocopy VQLPECPSKNLFFNMNNCQHIDQNHQSLEDFLRKVLQNTLLLSGRSLHLFLQSHLNSEDTRVYVSRQSKP

Parental  SVEEAIHKFALMNRRFPEEDEERKKENDIDYDSESSSSGLGHSSDDSSSHGCKISTAPQ
          ......H..A.M...F...........DIDYDS.SSSSGLGH..DDSSS.GCK.S...Q
Retrocopy WWKKQFHHLASMDNCFXXXXXXXXXXXDIDYDSGSSSSGLGHRCDDSSSYGCKTSMTLQ

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_1983 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000291	2 retrocopies	retro_chof_1983 , retro_chof_445,
Myotis lucifugus	ENSMLUG00000000285	1 retrocopy	retro_mluc_488,
Mus musculus	ENSMUSG00000038301	1 retrocopy	retro_mmus_2736,
Oryctolagus cuniculus	ENSOCUG00000004744	1 retrocopy	retro_ocun_918,