RetrogeneDB ID: retro_chof_656

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_13220:19675..20257(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STOML3
• Ensembl ID: ENSCHOG00000012681
• Aliases: None
• Description: stomatin (EPB72)-like 3 [Source:HGNC Symbol;Acc:19420]

Sequence

>retro_chof_656
CTTGGACCTTGTGGATGGATTTTGGTGGCTGTCTCATTTTTATTCACAGTTATAACTTTCCCCTTATCGATATGGATGTG
CATAAAGATCATAAAAGAATATGAAAGAGCCATCATCTTTAGACTGGGTCGTATTTTACAAGGAGGAGCCAAAGGACCTG
GTTTGTTTTTTATTCTGCCCTGCACTGACAACTTCATCAAAGTGGACATGAGAACTATTTCATTTGACATTCCTCCACAG
GAGACCCTCACCAAGGATTCAGTGACAATTAGTGTGGATGGTGTAGTCTATTATCGTGTGCAGAATGCAACCCTGGCTGT
GGCAAATATCACCAATGCTGACTCAGCAACTCGTCTTTTGGCTCAGACTACTCTGAGGAATGTTCTGGGCACCAAGAACC
TTTCGCAGATCCTCTCTGACAGAGAAGAAATTGCATACAACATGCAGTGTACTCTGGATGATGCTACTGATGACTGGGGA
ATAAAGGTGGAGCGTGTGGAAATTAAGGACGTGAAACTACCTGTACAGCTCCAGAGAGCTATGGCTGCAGAAGCAGAAGC
ATCCCGGGAGGCCCGAGCTAAG

Alignment

ORF - retro_chof_656 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.56 %
• Parental protein coverage: 97.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGVCAWLLVFLSFLLMIITFPISIWMCLKIIKEYERAVVFRLGRIQADKAKGPGLILVLPCVDVFVKVDL
          LG.C.W.LV..SFL...ITFP.SIWMC.KIIKEYERA..FRLGRI....AKGPGL...LPC.D.F.KVD.
Retrocopy LGPCGWILVAVSFLFTVITFPLSIWMCIKIIKEYERAIIFRLGRILQGGAKGPGLFFILPCTDNFIKVDM

Parental  RTITCNIPPQEILTRDSVTTKVDGVVYYRIYSAVSAVANVNDVHQATFLLAQTTLRNVLGTQTLSQILAG
          RTI...IPPQE.LT.DSVT..VDGVVYYR...A..AVAN......AT.LLAQTTLRNVLGT..LSQIL..
Retrocopy RTISFDIPPQETLTKDSVTISVDGVVYYRVQNATLAVANITNADSATRLLAQTTLRNVLGTKNLSQILSD

Parental  REEIAHSIQTMLEDVTEMWGIHVARVEIKDVSIPVQLQRSMAAEAEATREARAK
          REEIA...Q..L.D.T..WGI.V.RVEIKDV..PVQLQR.MAAEAEA.REARAK
Retrocopy REEIAYNMQCTLDDATDDWGIKVERVEIKDVKLPVQLQRAMAAEAEASREARAK

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_656 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012681	1 retrocopy	retro_chof_656 ,