RetrogeneDB ID: retro_chof_655

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_131972:3477..4464(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000013258
• Aliases: None
• Description: None

Sequence

>retro_chof_655
CATGTAAAAGAAGGAGTATGGTGTCTCAATTTGATAGCATCTGTGAAGTTCAAAGTGATAAAGCTTCTGTTACTATCACT
AGTTGTTATGATGGAGTCATTAAAAAACTCTATGATAATCTAGAGGAGGTTGCCTGTGTGGGGAAGCCATTAGTAGACAT
AGAAACGGAAGCTTTAAAAGACTCATAGGAAGATGTTGAAACACCTGTCATGTCCCATGGTGAACACACACACCAAGAGA
TAAAGGGCCAAAAAACACTGGCAACTGCAGTTCACCACCTTGCAATGGAAAACAATATTAAGGTGAATGAAGTTGCTGGC
TCAGGAAAAGATGGCAGAATACTTAAGGAAGATATTCTCAACTATTTGGCACAGCAGACAGGAGTTATGTTACTTCCTTC
ACCAAAAGCCGAAATTATGCCACCTCCAGCAACTCCAAAAGACGTGACTATTCCTATACCAATATCAAAACCTCCAGTAT
TCCCAGGGAAAGACAGACTAGAACCCATTAAAGGCTTTCACAAAGCAATGGTCAGGACGGTGACTGTAGCCCTGAAGCAT
CCTCACTTTGGGTATTGTGATGAGGTTGACCTTACTGAACTGGTTAAACTACAGGAAGAATTAAAGGCCGTTGCTTTTGC
TTGTGGAATTAAACTCTCCTTTATGCCCTTCTTTTTAAAGTCTGCTTCTTGGGGTTACTACAGTTCCCCATTCTTAATGC
TTCTGTGGATGAGAACTGCCAGAAGGTAACATATAAGGTGTCTCATAATATCAGGGTAGCAATGGATACTGAGCAAGGGT
TGATTGTTCCTAAGGTAAAAAATGTTCAGATCTGCTCTGTATTTGAGATTGCTAGTGAATTGAACTGTCTCCAGAAATTT
GGGCTCTGCAGGTCAGATTGGAACCACTGATCTTACAGGGGGAACATTTACTCTTTTCCAACATTGGATCAATTGGTGGT
ATCTATGCCAAACCAGTGATATTGCCA

Alignment

ORF - retro_chof_655 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.88 %
• Parental protein coverage: 68.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YVKEG-DTVSQFDSICEVQSDKASVTITSRYDGVIKKLYYNLEEIAYVGKPLVDIETEALKDSEEDVVET
          .VKEG...VSQFDSICEVQSDKASVTITS.YDGVIKKLY.NLEE.A.VGKPLVDIETEALKDS.EDV.ET
Retrocopy HVKEG<SMVSQFDSICEVQSDKASVTITSCYDGVIKKLYDNLEEVACVGKPLVDIETEALKDS*EDV-ET

Parental  PAVSHDEHTHQEIKGQKTLATPAVRRLAMENNIKLSEVVGSGKDGRILKEDILNYLAKQTGAILPPSPKA
          P..SH.EHTHQEIKGQKTLAT.AV..LAMENNIK..EV.GSGKDGRILKEDILNYLA.QTG..L.PSPKA
Retrocopy PVMSHGEHTHQEIKGQKTLAT-AVHHLAMENNIKVNEVAGSGKDGRILKEDILNYLAQQTGVMLLPSPKA

Parental  EIMPPPATPKDRTIPLPVSKPPVFTGKDRTEPIKGFHKAMVKTMTAALKIPHFGYCDEVDLTELVKLREE
          EIMPPPATPKD.TIP.P.SKPPVF.GKDR.EPIKGFHKAMV.T.T.ALK.PHFGYCDEVDLTELVKL.EE
Retrocopy EIMPPPATPKDVTIPIPISKPPVFPGKDRLEPIKGFHKAMVRTVTVALKHPHFGYCDEVDLTELVKLQEE

Parental  LKPIAFSRGIKLSFMPFFLKAAS-LGLLQFPILNASVDENCQNITYKASHNIGVAMDTEQGLIV-NIKNV
          LK..AF..GIKLSFMPFFLK.AS.LGLLQFPILNASVDENCQ..TYK.SHNI.VAMDTEQGLIV...KNV
Retrocopy LKAVAFACGIKLSFMPFFLKSAS<LGLLQFPILNASVDENCQKVTYKVSHNIRVAMDTEQGLIVPKVKNV

Parental  QICSVFEIASELNRLQK-LGSAGQIGTPDLAGGTFTL-SNVGSIGGTYTKPVILP
          QICSVFEIASELN.LQK.LGSAGQIGT.DL.GGTFTL.SN.GSIGG.Y.KPVILP
Retrocopy QICSVFEIASELNCLQK>LGSAGQIGTTDLTGGTFTL>SNIGSIGGIYAKPVILP

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_655 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003998	1 retrocopy	retro_chof_2128,
Choloepus hoffmanni	ENSCHOG00000013258	2 retrocopies	retro_chof_52, retro_chof_655 ,
Microcebus murinus	ENSMICG00000006218	1 retrocopy	retro_mmur_1089,
Oryctolagus cuniculus	ENSOCUG00000014244	1 retrocopy	retro_ocun_952,
Otolemur garnettii	ENSOGAG00000005625	1 retrocopy	retro_ogar_2997,