RetrogeneDB ID: retro_chof_1615

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_34081:930..1598(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BYSL
• Ensembl ID: ENSCHOG00000011476
• Aliases: None
• Description: bystin-like [Source:HGNC Symbol;Acc:1157]

Sequence

>retro_chof_1615
TGGGAGCAGATCCTTTATGTCACAGAGCCTGAGGCCTCGACTGCAGCTGCCATGTACCAAGCCACCAGGATTTTCACCTC
TAACCTAAAGGAACACATGGCCCAGCGCTTCTACAACTTGTCCTTCTTCCCTGAGTATGAGATGACATAGCTGAATACAA
ATGCCTCAACTTCTACTCTACATGGCTCTCAAGAAGGCCCTCTTCAAGCCTGGAGCCTGGTTCAAAGGGATCCTGATCCC
ACTGTGTGACTCAGGCACCTGTACCCTGAGGAAAGCCATCATTGTGGGTAGCATTGTCACCAAGCGCTCCATCCGTGTGT
TGCACTCCAGTGCAGCCGTGCTGAAAACTGCTGAGATAGAATACAGCAGTGCCAACAGCATCTGCCTCTTACTGCTGCTG
GACAAGAAGTATGCTCTGCCCTACTAGGTGCTGGATGCCCTGGTCTTCCATTTCCTGGGGTTCAGGACAGAGAAGCACAA
ACTCCTCATGCTCTGGCGCCAATGCCTCCTGACCCTGGTCCAGCCTTACAAGGCAGACTGGCCACAGATCAGAAAGAGGC
TCTCCTGGTACTGCTCTGGCTACAGCCCCATCCACAGTCCCCTGAGATCAGGTGTGAGCTTTAGAATGCAGTCCCCGAGA
TGTGGAAGATGTCCCCATCAACATGGAC

Alignment

ORF - retro_chof_1615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.28 %
• Parental protein coverage: 51.72 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  WEQILYITEPEAWTAAAMYQATRIFASNLKERMAQRFYNL-VLLPRVRDDIAEYKRLNFH-LYMALKKAL
          WEQILY.TEPEA.TAAAMYQATRIF.SNLKE.MAQRFYNL.VLLP.V.DDIAEYK.LNF..LYMALKKAL
Retrocopy WEQILYVTEPEASTAAAMYQATRIFTSNLKEHMAQRFYNL<VLLP*V*DDIAEYKCLNFY<LYMALKKAL

Parental  FKPGAWFKGILIPLCESGTCTLREAIIVGSIITKCSIPVLHSSAAMLKIAEMEYSGANSIFLRLLLDKKY
          FKPGAWFKGILIPLC.SGTCTLR.AIIVGSI.TK.SI.VLHSSAA.LK.AE.EYS.ANSI.L.LLLDKKY
Retrocopy FKPGAWFKGILIPLCDSGTCTLRKAIIVGSIVTKRSIRVLHSSAAVLKTAEIEYSSANSICLLLLLDKKY

Parental  ALPYRVLDALVFHFLGFRTEKRKLPVLWHQCLLTLVQRYKAD-LAKDQKEALLELLRLQPHPQLSPEIRR
          ALPY.VLDALVFHFLGFRTEK.KL..LW.QCLLTLVQ.YKAD.LA.DQKEALL.LL.LQPHPQ.SPEIR.
Retrocopy ALPY*VLDALVFHFLGFRTEKHKLLMLWRQCLLTLVQPYKAD<LATDQKEALLVLLWLQPHPQ-SPEIRC

Parental  ELQSAV-PRDVEDVPINMD
          EL..AV.PRDVEDVPINMD
Retrocopy EL*NAV<PRDVEDVPINMD

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_1615 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010101	1 retrocopy	retro_btau_1246,
Choloepus hoffmanni	ENSCHOG00000011476	1 retrocopy	retro_chof_1615 ,
Macropus eugenii	ENSMEUG00000000759	2 retrocopies	retro_meug_1365, retro_meug_608,
Oryctolagus cuniculus	ENSOCUG00000017567	1 retrocopy	retro_ocun_514,