RetrogeneDB ID: retro_chof_1417

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_28694:14120..14709(-)
• 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_1417
ATGATGGCACTGGAGGAAACTGTGTGGCTGGAGAGAGATATTTGTAGAGCAATTGTATTGTTAGAAAAACTACAAAGGAG
TGAAGTACCACCACAAAAACTTCAGGCTTTACAAAGGGTCCTTCAAAGTGAGTTGTGCAATGCTGTTAGGGAGGTATATG
AACACATCTATGAAACTGTGGACATCAGTAGCAGTTCTGAAGTGAGAGCTAATGCAACTGCAAAGGCTACAGTCACTGCA
TTTGCTGCCAGTGAAAGGAGATTCTCATCCTTGAGTGGCTGAGCTGCCAAAAACAGAAGATGGCCTTAGAGTCAATATTG
TGGGAGGGAAAAAATGAAACTGTCCAATCTGTGTATCTTGAATAATTCCAGGTGGTATTGCTGATAGACATGGGGGCCTC
AAACGAGGAGACCAACTCCTTTCTGATAATGGAGTTAGAATTGAAGGAGAAAATCATGAGAAAGCTGTAGAGCTACTGAA
AGCAGCTCAAGCAAAGGTTAAATTAGTAGTATGATATACACCCAAAGTCTTAGAAGAAATGGAGTCACAATTTGAAAAAA
TGAGATCAGCAAAACACAGGCAACAAACC

Alignment

ORF - retro_chof_1417 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.84 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAALGEPVRLERDICRAIELLEKLQRSGEVPPQKLQALQRVLQSEFCNAVREVYEHVYETVDISSSPEVR
          M.AL.E.V.LERDICRAI.LLEKLQRS.EVPPQKLQALQRVLQSE.CNAVREVYEH.YETVDISSS.EVR
Retrocopy MMALEETVWLERDICRAIVLLEKLQRS-EVPPQKLQALQRVLQSELCNAVREVYEHIYETVDISSSSEVR

Parental  ANATAKATVAAFAASE-GHSHPRVVELPKTEEGLGFNIMGGKEQNSPIYISRIIPGGIADRHGGLKRGDQ
          ANATAKATV.AFAASE.G.SHP.V.ELPKTE.GL..NI.GGK..N.PI..S.IIPGGIADRHGGLKRGDQ
Retrocopy ANATAKATVTAFAASE>GDSHP*VAELPKTEDGLRVNIVGGKK*NCPICVS*IIPGGIADRHGGLKRGDQ

Parental  LLSVNGVSVEGEHHEKAVELLKAAQGKVKLVVRYTPKVLEEMESRFEKMRSAKRRQQT
          LLS.NGV..EGE.HEKAVELLKAAQ.KVKLVV.YTPKVLEEMES.FEKMRSAK.RQQT
Retrocopy LLSDNGVRIEGENHEKAVELLKAAQAKVKLVV*YTPKVLEEMESQFEKMRSAKHRQQT

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_1417 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,