RetrogeneDB ID: retro_chof_1402

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_28311:8437..9176(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAB39L
• Ensembl ID: ENSCHOG00000001915
• Aliases: None
• Description: calcium binding protein 39-like [Source:HGNC Symbol;Acc:20290]

Sequence

>retro_chof_1402
GCTCAAGAACTGTAGACCACTGGGCTCCTGAGAATCCTGGTGGCTGAATTACAATTTGTCGATTTTGAGGGCAAAAAAGA
CATGGCTCAAATTTTCAACAATATTCTCAGAAAACAAATTGGTACAAGAACTCCTACTGTTGAATACAACTGCACACAAC
AGAATATTTTGTTCATGTTATTCAAAGGGTATGAATCTCCAGAAACAGCTCTACATTGTGGAATAATGTTAAGAGAATGC
ATCAGGCATGAACTACTTGCAAAAATCATTTTGTGGTCAGAACACTTTTATGTTTTCTTCAGATATGTCAAAATGTCAAC
ATTTGACATAGCTTCAGATGCATTTGCCAAATTCAAGGATTTACTTACAAGGCATAAATTGCTCAGCAGCAATTTTTGGA
ACAGTGTTAGAAAGATTCTTCAGTGAATATGAGAAGTTACTCCATTCAGAAAATTATGTGACAAAAAGACAGTCACTCAA
GTTTCCCAGTGAACTGTTATTAGATAGACAAAACTTCACAGTTATGACAAAATACATCACTAAATCTGAAAACCTCAAGT
TAATGATGAACCTGCTACAAGACAAAAGCAGTAACATCCAGTTTGAGGCCCTTCATGTTTTTAAGGTATTTGTAGGCAAT
CCTAACAAGACACAGCCTGTCTTAGATACCCTTCTCAAGAACCAGAACAAACTCATACAGTTCCTCAACAAGTTTCAGAA
TGACAAGACCAAGTGTGAG

Alignment

ORF - retro_chof_1402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.27 %
• Parental protein coverage: 76. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AQVLYNTGLLVTLIATLQLIDFKGKKDVTQIFNNILRRQIGTRSPTVEYISAHPHILFMLLQGYEAPQIA
          AQ.L..TGLL..L.A.LQ..DF.GKKD..QIFNNILR.QIGTR.PTVEY......ILFML..GYE.P..A
Retrocopy AQEL*TTGLLRILVAELQFVDFEGKKDMAQIFNNILRKQIGTRTPTVEYNCTQQNILFMLFKGYESPETA

Parental  LRCGIMLRECIRHEPLAKIILFSNQFRDFFKYVELSTFDIASDAFATFKDLLTRHKVLVAD-FLEQ-NYD
          L.CGIMLRECIRHE.LAKIIL.S..F..FF.YV..STFDIASDAFA.FKDLLTRHK.L....FLEQ....
Retrocopy LHCGIMLRECIRHELLAKIILWSEHFYVFFRYVKMSTFDIASDAFAKFKDLLTRHKLLSSN<FLEQ<VLE

Parental  TIFEDYEKLLQSENYVTKRQSLKLLGELILDRHNFAIMTKYISKPENLKLMMNLLRDKSPNIQFEAFHVF
          ..F..YEKLL.SENYVTKRQSLK...EL.LDR.NF..MTKYI.K.ENLKLMMNLL.DKS.NIQFEA.HVF
Retrocopy RFFSEYEKLLHSENYVTKRQSLKFPSELLLDRQNFTVMTKYITKSENLKLMMNLLQDKSSNIQFEALHVF

Parental  KVFVASPHKTPPIVEILLKNQPKLIEFLSTFQKERTDDE
          KVFV..P.KT.P....LLKNQ.KLI.FL..FQ...T..E
Retrocopy KVFVGNPNKTQPVLDTLLKNQNKLIQFLNKFQNDKTKCE

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_1402 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001915	1 retrocopy	retro_chof_1402 ,
Otolemur garnettii	ENSOGAG00000016755	2 retrocopies	retro_ogar_2297, retro_ogar_3157,