RetrogeneDB ID: retro_chof_1162

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_215470:25..690(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTMR10
• Ensembl ID: ENSCHOG00000012336
• Aliases: None
• Description: myotubularin related protein 10 [Source:HGNC Symbol;Acc:25999]

Sequence

>retro_chof_1162
CTGGTGAGACTTGCCCTCATAAAAGATGTATGCAACAGAGAAAAATCAATTGAAGGATCTGTGATGCAATAACTAAAAGT
CACCCACAGAGAAGTGATATTCACAAATTGGCTTTGGATAAGATCTTGCCTATTATCCAAGAAATACAAGTGGCATTTCT
GAAACTGAAGCAAAATGTGCTAATGAGCCTTTTGAAGAAACTAAAGAAAAATGGTTATCTTCATTGGAAAGTACTCAGTG
GTTAGAATATGTAAGGGTATTCCTTAAATGTTCAGTAGAACTTGTATAGATGCTGGAGAGCAAACATCTCTCTCCAATCC
TACAAGAGGAGGAGGGAAGAGATCTGAGTTTTTTCATAGCTTCTCTTACTCAAGTGATGCTGGATCCCTATTTTAGAACA
ATTACTGGATTTCAGAGTCTGATACAGAAGGAGTAGGTCATGGCCAGCTATCTGTTCCTGGACAGGTGCAACCACTTAGA
GATGGGAAAAAGAGTCTCCCTTATTTTTACTATTCTTGGATGCTACTTGGCAACTGTTAAAACAATACCCAGTGGTGTTC
AAGTTCTCTGAAACTTAGCTAGTGGTGCTGTACAATAGTACCCACATCTCACTGTTTGGCAACTTCCTGTTTAACTGTCC
TCACCAGTGGGTGAAGCAAAGAACA

Alignment

ORF - retro_chof_1162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.53 %
• Parental protein coverage: 52.22 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LVRMAFIKDV-LQQRKIDQRICNAITKSHPQRSDVYKSDLDKTLPNIQEIQAAFIKLKQ-LCVNEPFEET
          LVR.A.IKDV..QQRKI..RIC.AITKSHPQRSD..K..LDK.LP.IQEIQ.AF.KLKQ..C.NEPFEET
Retrocopy LVRLALIKDV<MQQRKIN*RICDAITKSHPQRSDIHKLALDKILPIIQEIQVAFLKLKQ<KCANEPFEET

Parental  EEKWLSSLENTRWLEYVRAFLKHSVELVHMLENKHLSVILQEEEGRDLSCFIASLIQVMLDPYFRTITGF
          .EKWLSSLE.T.WLEYVR.FLK.SVELV.MLE.KHLS.ILQEEEGRDLS.FIASL.QVMLDPYFRTITGF
Retrocopy KEKWLSSLESTQWLEYVRVFLKCSVELV*MLESKHLSPILQEEEGRDLSFFIASLTQVMLDPYFRTITGF

Parental  QSLIQKEWVMAGYQFLDRCNHLKRSEKES-PLF-LLFLDATWQLLEQYPAAFEFSEAYLVVLYDSTRISL
          QSLIQKE.VMA.Y.FLDRCNHL......S.P.F.LLFLDATWQLL.QYP..F.FSE..LVVLY.ST.ISL
Retrocopy QSLIQKE*VMASYLFLDRCNHLEMGKRVS<PYF<LLFLDATWQLLKQYPVVFKFSET*LVVLYNSTHISL

Parental  FGTFLFNCPHQRVKQST
          FG.FLFNCPHQ.VKQ.T
Retrocopy FGNFLFNCPHQWVKQRT

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_1162 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	ENSCHOG00000012336	1 retrocopy	retro_chof_1162 ,
Monodelphis domestica	ENSMODG00000011784	2 retrocopies	retro_mdom_1377, retro_mdom_1957,
Ictidomys tridecemlineatus	ENSSTOG00000008851	1 retrocopy	retro_itri_1894,