RetrogeneDB ID: retro_chof_1500

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_309575:850..1289(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000006159
• Aliases: None
• Description: None

Sequence

>retro_chof_1500
CTCATTTTGCTGTGTGGCTGGATTTTCTTACTGCTTGCCCTTTTTACTTTAATCATTTCTGTGACTACCTCATGGCTCAA
CTCATTTAAATCTTTTTAGTTTATCTGAAAGAATAAGAAGAGAAGAATGAGAAAAGGCAAAAACTTGTGCAAAACAAATA
GCAAGAGACAGAGTGAAAAGGCCAGCAGATTACGTAGAGGAGGTTTTAAACCCTCACCAGGAAATGAAATTGAAAAAACT
GGAAGAGTGCTTTTATCAAATGTCGGGTGAAAACTGGAAGTTAAGCAATGGTCACAAACTTGGGGGTAATGAAGAGGTGT
TACTTGAAAATGCCAGTCAAACATCCTCTGAGACTTCAAACAGAGAAGCTGGAAGGAGCAGAACTTGCCTGAGCCTGAAA
CCAAATTTTCAATGACCTCCTGACCAGCCCACAAAGAAG

Alignment

ORF - retro_chof_1500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.66 %
• Parental protein coverage: 54.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LVLLCGRIFLLLALLTLIISVTTSWLNSFKS-SQVYLKEEEEEKNGKRQKLVLNRQQETQ-SEKASRYIE
          L.LLCG.IFLLLAL.TLIISVTTSWLNSFKS...VYLK.E.EEKN.KRQKLV.N..QET........Y.E
Retrocopy LILLCGWIFLLLALFTLIISVTTSWLNSFKS<FLVYLK-E*EEKNEKRQKLVQNK*QETE<VKRPADYVE

Parental  KVLKPHQEMKLKKLEERFYQMSGETWKLSNGHKLGGDEGLVLENASQT-SETSNREAARRR-NLPEPVTK
          .VL.PHQEMKLKKLEE.FYQMSGE.WKLSNGHKLGG.E...LENASQT.SETSNREA.R.R.NLPEP.TK
Retrocopy EVLNPHQEMKLKKLEECFYQMSGENWKLSNGHKLGGNEEVLLENASQTSSETSNREAGRSR<NLPEPETK

Parental  LSR-PPDQPTKK
          .S..PPDQPTKK
Retrocopy FSM>PPDQPTKK

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_1500 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 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001600	2 retrocopies	retro_amel_1272, retro_amel_1326,
Choloepus hoffmanni	ENSCHOG00000006159	4 retrocopies	retro_chof_1161, retro_chof_1175, retro_chof_1383, retro_chof_1500 ,
Myotis lucifugus	ENSMLUG00000016846	1 retrocopy	retro_mluc_606,