RetrogeneDB ID: retro_chof_1203

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_224563:1181..1847(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISOC1
• Ensembl ID: ENSCHOG00000006851
• Aliases: None
• Description: isochorismatase domain containing 1 [Source:HGNC Symbol;Acc:24254]

Sequence

>retro_chof_1203
GCGGAGGAAAGGGGCCAGTACATTGACCTGCCCAAAGGCTTTGCGGTGAATGAGCTCTGCGAAGTGCACTTCTTGCTGCT
GCAGATTCAGCTCACTACTCTGGGAAATCTTACACTTTCAAGCACTGTGTTTTTCTGCTTTAATAAGCTAGAAAGTTTTA
CCAGCCATCAGGTATTCGGGGAATATTATTAGTGTGGGACAAAGATTGTTGCAAGGAGCCTGATTTTAGGAATTCTGGTT
ATTGTAACAGAACAGTACCCTAAAGGTCTTGGAAGCACTGTTCAAGAAATTGGTTCAACCCATGTAAAACTGGTGCTTCC
AAAGACCAAGTTTTCAATGGTATTACCAGAAGTAGAAGCAGCATTAGCAGAGATTCCTGGAGTCAAGAGTGTTGTATTAT
TTGAAGTAGAAACTCATGTGTGCATCCAGCAAACTGCTCTGGAGCTAGTTGGTTGAGGTACTGAGGTTCACGTCATCACT
GATGCCACTGCATCGAGAAGCATGATGAACAGGATGTTTGCTCTTGAGCGTCTTGCTCGAACTGGGATCATAGTTACTAC
AAGTGAGGCTGTTCTGTTACAGCTGGTGGCTGATAAAGACCATCCAACATTCAAGAAGTTCAGAAAAAAGGTAAGTGCTT
CAGAATCAGGTCTGCTTTCCAAAGTA

Alignment

ORF - retro_chof_1203 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AEEWGQYVDLPKGFAVSERCKVRLVPLQIQLTTLGNLTPSSTVFFCCDMQERFRPAIKYFGD-IISVGQR
          AEE.GQY.DLPKGFAV.E.C.V....LQIQLTTLGNLT.SSTVFFC....E.F......FG..IISVGQR
Retrocopy AEERGQYIDLPKGFAVNELCEVHFLLLQIQLTTLGNLTLSSTVFFCFNKLESF-TSHQVFGE>IISVGQR

Parental  LLQGA-RILGIPVIVTEQYPKGLGSTVQEIDLTGVKLVLPKTKFSMVLPEVEAALAEIPGVRSVVLFGVE
          LLQGA..ILGI.VIVTEQYPKGLGSTVQEI..T.VKLVLPKTKFSMVLPEVEAALAEIPGV.SVVLF.VE
Retrocopy LLQGA<LILGILVIVTEQYPKGLGSTVQEIGSTHVKLVLPKTKFSMVLPEVEAALAEIPGVKSVVLFEVE

Parental  THVCIQQTALELVGRGIEVHIVADATSSRSMMDRMFALERLARTGIIVTTSEAVLLQLVADKDHPKFKEV
          THVCIQQTALELVG.G.EVH...DAT.SRSMM.RMFALERLARTGIIVTTSEAVLLQLVADKDHP.FK..
Retrocopy THVCIQQTALELVG*GTEVHVITDATASRSMMNRMFALERLARTGIIVTTSEAVLLQLVADKDHPTFKKF

Parental  QNLIKASAPESGLLSKV
          ....K.SA.ESGLLSKV
Retrocopy RK--KVSASESGLLSKV

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_1203 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006851	1 retrocopy	retro_chof_1203 ,
Oryctolagus cuniculus	ENSOCUG00000017498	1 retrocopy	retro_ocun_449,
Sus scrofa	ENSSSCG00000014258	2 retrocopies	retro_sscr_421, retro_sscr_443,