RetrogeneDB ID: retro_chof_2399

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_71648:6614..7184(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIN7C
• Ensembl ID: ENSCHOG00000000111
• Aliases: None
• Description: lin-7 homolog C (C. elegans) [Source:HGNC Symbol;Acc:17789]

Sequence

>retro_chof_2399
CTGGAGAGAGATATTTGTAGAGCAATTGAATTGTTGGAAAAACTACAAAGGAGTGAAGTACCACCACAAAAACTTCAGGC
TTTACAAAGTGTCCTTCAAAGTGATTGTTAGCATTCCTGCAATGCTGTTAGGGAGGTATGTGAACACATCTATGAAACTG
TGGGCATCAGTAACAGTCCTGAAGTGAGAGCTAATGCAACTGCGAAGGCTACAGTCACTGCATTTGCTGCCAGTGAAGGA
GATTCTCATCCTCGAGTGGTTGAGCTACCAAAAACAGAAGACGGCCTTAGAGTCAATATTATGGGAGGGAAAGAATGAAA
CTCCCCAATCTATGTATCTTGAATAATTCCAAGTGGTATTGCTGATAGACATGGGGGCCTCAAATGAGGAGACCAACTCC
TTTCCATTAATGGAGTTAGTGTTGAAGGAGAACATCATGAGAAATCTGTAGAGCTACTGAAAGCAGCTCAAGGAAAGGTT
AAATTAGTAGTATGATATACACCCAAAGTCTTAGAAGAAATGGAGTCACAATTTGAAAAAATGAGATCAGCAAAATGCAG
GCAACAGACC

Alignment

ORF - retro_chof_2399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.39 %
• Parental protein coverage: 95.43 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LERDICRAIELLEKLQRSGEVPPQKLQALQRVLQSEF---CNAVREVYEHVYETVDISSSPEVRANATAK
          LERDICRAIELLEKLQRS.EVPPQKLQALQ.VLQS.....CNAVREV.EH.YETV.IS.SPEVRANATAK
Retrocopy LERDICRAIELLEKLQRS-EVPPQKLQALQSVLQSDC*HSCNAVREVCEHIYETVGISNSPEVRANATAK

Parental  ATVAAFAASEGHSHPRVVELPKTEEGLGFNIMGGKEQNSPIYISRIIPGGIADRHGGLKRGDQLLSVNGV
          ATV.AFAASEG.SHPRVVELPKTE.GL..NIMGGKE.NSPIY.S.IIP.GIADRHGGLK.GDQLLS.NGV
Retrocopy ATVTAFAASEGDSHPRVVELPKTEDGLRVNIMGGKE*NSPIYVS*IIPSGIADRHGGLK*GDQLLSINGV

Parental  SVEGEHHEKAVELLKAAQGKVKLVVRYTPKVLEEMESRFEKMRSAKRRQQT
          SVEGEHHEK.VELLKAAQGKVKLVV.YTPKVLEEMES.FEKMRSAK.RQQT
Retrocopy SVEGEHHEKSVELLKAAQGKVKLVV*YTPKVLEEMESQFEKMRSAKCRQQT

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_2399 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000111	7 retrocopies	retro_chof_1046, retro_chof_1062, retro_chof_1417, retro_chof_2399 , retro_chof_2401, retro_chof_2515, retro_chof_864,
Microcebus murinus	ENSMICG00000005165	2 retrocopies	retro_mmur_1590, retro_mmur_577,