RetrogeneDB ID: retro_chof_2679

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_9675:12799..13498(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PNLIP
• Ensembl ID: ENSCHOG00000003948
• Aliases: None
• Description: pancreatic lipase [Source:HGNC Symbol;Acc:9155]

Sequence

>retro_chof_2679
ATGGTGCCCTCTTGGACCACCGGCCTTCTCCTGCTGGCCACCGTCAGAGGGAATGAGATCTGGTATGGACCCCTCGGCTG
CTCTTTTGATGAGAAACCATGGACCCCGATCGTCCAGGAGCTGTTCAAGTTATTTCCCAGCACCCCCAAGGACATCAACA
CCCGCTTTCTTCTGTACACAAATGAAAATGCGGACACCTACCAGCTGGTCACTGCCACTGACCTACCCACCATCGAGGCA
TCAAACTTCCAACGGGACCGCAAGACGCGTTTCATCATCCACGGCTTCACAGACACCGGGGAGGACAGCTGGCTGTCGGG
CATGTGCAAGAAGATGTTTAAAGTGGAGGAGGTGAACTGCATCTGCGTGGACTGGAAAGGTGGGTCCCGGGCGCCGTACC
CCCAAGCCGTCCAGAACATCCAGGTGGTGGGGGCGGAGGTGGCGCTCCTCCTACAGGCGCTCTCGGCGGAGCTGGGCTGC
GCCCTGGAGGACGCGCACCTCATTGGCCACAGCCTGAGTGCGAACGTGGACACGCAAGCTGATCTGTGACTGGTTCCTTG
CGTCCAGACAGTTTTGGGGGGTAGAGGCCAGTTTATGAGATTTCATGGCACATTTTATATATTTAGGTCGTAAATTTCTG
ACTCACAGCTTCTATATCTGATACATTGCCTGACATCGATTGTATTCTTCTCACTAGGG

Alignment

ORF - retro_chof_2679 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.07 %
• Parental protein coverage: 50.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLLIWTLSLLLGA-VTGKEICYSRLGCFSDDSPWAGTVERPLKILPWSPEDINTRFLLYTNENPDNFQEL
          M...WT..LLL.A.V.G.EI.Y..LGC..D..PW...V....K..P..P.DINTRFLLYTNEN.D..Q..
Retrocopy MVPSWTTGLLLLATVRGNEIWYGPLGCSFDEKPWTPIVQELFKLFPSTPKDINTRFLLYTNENADTYQLV

Parental  TA-DQPTIQSSNFKTNRKTRFIIHGFIDKGEESWLSNMCKNFFEVESVNCICVDWKGGSRTGYTQASQNI
          TA.D.PTI..SNF...RKTRFIIHGF.D.GE.SWLS.MCK..F.VE.VNCICVDWKGGSR..Y.QA.QNI
Retrocopy TATDLPTIEASNFQRDRKTRFIIHGFTDTGEDSWLSGMCKKMFKVEEVNCICVDWKGGSRAPYPQAVQNI

Parental  RVVGAEVAYFVEVLQSNFGYSLSDVHIIGHSLGSHAAGEAGRRLNGAVGRITGLDPAEPCFEGTPELVRL
          .VVGAEVA.....L....G..L.D.H.IGHSL.......A...L...V....G.......F.GT....R.
Retrocopy QVVGAEVALLLQALSAELGCALEDAHLIGHSLSANVDTQADL*LVPCVQTVLGGRGQFMRFHGTFYIFRS

Parental  DPSDASFVDVIHTDAAPIIPNLG
          ..SD......IH.........LG
Retrocopy *ISDSQLLYLIHCLTSIVFFSLG

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_2679 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003948	1 retrocopy	retro_chof_2679 ,
Choloepus hoffmanni	ENSCHOG00000006303	1 retrocopy	retro_chof_2680,