RetrogeneDB ID: retro_chof_2402

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_71887:4872..5102(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VAMP4
• Ensembl ID: ENSCHOG00000000124
• Aliases: None
• Description: vesicle-associated membrane protein 4 [Source:HGNC Symbol;Acc:12645]

Sequence

>retro_chof_2402
ATGCCTCCCAAGTTAAAGCGCCACCTCGATGATGATAATGATGGTGTCACTGGTTCTGTGAAAAGTGAGAGGAGGCATTT
TTGGAAGATGTTTCAGATAAAGAGGAGGACTTTTTTTTTTTTTTAAGGGGACCTTCTGGACCAAGATTTGGACCTAGAAA
TGATAAAATTAAGCATGCTTAGAATCAGGTGGATGAAGTTATTGATGTCATGCAAGAAAATACTACAAAG

Alignment

ORF - retro_chof_2402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.23 %
• Parental protein coverage: 50.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPPKFKRHLNDDD--VSGSVKSERRNL-LED--DSDEEEDFF--GPSGP-FGPRNDKIKHVQNQVDEVID
          MPPK.KRHL.DD...V.GSVKSERR...LED..D..E.......GPSGP.FGPRNDKIKH..NQVDEVID
Retrocopy MPPKLKRHLDDDNDGVTGSVKSERRHF<LEDVSDKEEDXXXXXRGPSGPRFGPRNDKIKHA*NQVDEVID

Parental  VMQENITK
          VMQEN.TK
Retrocopy VMQENTTK

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_2402 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 7 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000124	4 retrocopies	retro_chof_2225, retro_chof_2402 , retro_chof_513, retro_chof_58,
Macropus eugenii	ENSMEUG00000011226	13 retrocopies	retro_meug_1053, retro_meug_115, retro_meug_1257, retro_meug_1406, retro_meug_1489, retro_meug_1587, retro_meug_163, retro_meug_2075, retro_meug_2154, retro_meug_319, retro_meug_386, retro_meug_569, retro_meug_75,
Monodelphis domestica	ENSMODG00000003811	1 retrocopy	retro_mdom_268,
Otolemur garnettii	ENSOGAG00000026745	1 retrocopy	retro_ogar_3369,
Sorex araneus	ENSSARG00000001709	2 retrocopies	retro_sara_234, retro_sara_79,
Sarcophilus harrisii	ENSSHAG00000017179	2 retrocopies	retro_shar_584, retro_shar_747,
Tupaia belangeri	ENSTBEG00000010829	2 retrocopies	retro_tbel_2607, retro_tbel_4488,