RetrogeneDB ID: retro_chof_280

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_6127:15343..16201(-)
• Located in intron of: ENSCHOG00000005114

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5C2
• Ensembl ID: ENSCHOG00000004098
• Aliases: None
• Description: 5'-nucleotidase, cytosolic II [Source:HGNC Symbol;Acc:8022]

Sequence

>retro_chof_280
CTCTTGGTCTGTGCACATGGATTTAACTTCATAAGGGGACCAGAAACTAGAGAGCAGTATCCAAATAAATTTATCCAGTG
AGATGACACTGAAAGATTTTACATTCTGAACACACTGTTCAACCTACCAGAGACCTACCTGTTGGCCTGCCTGGTAGATC
TTTTTACTAGTTGTCCTAGGTATACCTGCTGCGAAACAGGATTTAAAGATGGGGACCTCTTCATGTCATACTGGAGTATG
TTCCAGGATGTAAGAGATGCTGTTGACTGAGTTCATTACAAGGGCTCCCTTAAGGAAAAGACAATTGAAAATCTTGAGAA
GTATGTAGTAAAAGATGGAAAACTGCCTTCGCTTCTGAGCCGGATAGAGGAAGTAGGGAAAGTATTTCTTGCCACCAACA
GTGACTATAAATAGACAGATAAAATTATGACTTTCCTGTTTGATTTCCCACATGGCCCCAAGCCTGGGAGCTCCCATCGA
CCATGGCAGTCCTATTTTGACTTGATCCTGGTGGATGCACGGAAACCACTATTTTTTGGAGAAGGCACAGTATTTAGTAT
GGATACTAAAACTGGAAAGCTGAAAATTGGTACCTACACAGGTCCCCTACAGCAAGGCATTGTCTGCTCAGGAGGTTCAT
CTGATACAGTCTGTGATCTGTTGGGAGCCAAGGGCAAGGACATTTTGTATATTGGAGATCACATTTTTGGGGACATTTTA
AAATCAAAACGGCAAGGGTGGTGCACTTTCTTGGTGATCCCTGAACTTGCACAGGAACTGCATGTCTGGACTGACAAGAG
TTCACTTTTTGAGGAGCTTCAGAGCTTGGATATTTTCTTGGCTGAACTCTACAAGCAC

Alignment

ORF - retro_chof_280 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.71 %
• Parental protein coverage: 51.25 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLVCAHGFNFIRGPETREQYPNKFIQRDDTERFYILNTLFNLPETYLLACLVDFFTNCPRYTSCETGFKD
          LLVCAHGFNFIRGPETREQYPNKFIQ.DDTERFYILNTLFNLPETYLLACLVD.FT.CPRYT.CETGFKD
Retrocopy LLVCAHGFNFIRGPETREQYPNKFIQ*DDTERFYILNTLFNLPETYLLACLVDLFTSCPRYTCCETGFKD

Parental  GDLFMSYRSMFQDVRDAVDWVHYKGSLKEKTVENLEKYVVKDGKLPLLLSRMKEVGKVFLATNSDYKYTD
          GDLFMSY.SMFQDVRDAVD.VHYKGSLKEKT.ENLEKYVVKDGKLP.LLSR..EVGKVFLATNSDYK.TD
Retrocopy GDLFMSYWSMFQDVRDAVD*VHYKGSLKEKTIENLEKYVVKDGKLPSLLSRIEEVGKVFLATNSDYK*TD

Parental  KIMTYLFDFPHGPKPGSSHRPWQSYFDLILVDARKPLFFGEGTVLRQVDTKTGKLKIGTYTGPLQYGIVY
          KIMT.LFDFPHGPKPGSSHRPWQSYFDLILVDARKPLFFGEGTV....DTKTGKLKIGTYTGPLQ.GIV.
Retrocopy KIMTFLFDFPHGPKPGSSHRPWQSYFDLILVDARKPLFFGEGTVF-SMDTKTGKLKIGTYTGPLQQGIVC

Parental  SGGSSDTICDLLGAKGKDILYIGDHIFGDILKSKKRQGWRTFLVIPELAQELHVWTDKSSLFEELQSLDI
          SGGSSDT.CDLLGAKGKDILYIGDHIFGDILKS.KRQGW.TFLVIPELAQELHVWTDKSSLFEELQSLDI
Retrocopy SGGSSDTVCDLLGAKGKDILYIGDHIFGDILKS-KRQGWCTFLVIPELAQELHVWTDKSSLFEELQSLDI

Parental  FLAELYKH
          FLAELYKH
Retrocopy FLAELYKH

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_280 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010354	1 retrocopy	retro_cfam_684,
Choloepus hoffmanni	ENSCHOG00000004098	1 retrocopy	retro_chof_280 ,
Microcebus murinus	ENSMICG00000012316	1 retrocopy	retro_mmur_1476,
Rattus norvegicus	ENSRNOG00000020179	1 retrocopy	retro_rnor_430,
Tupaia belangeri	ENSTBEG00000017707	4 retrocopies	retro_tbel_2188, retro_tbel_3201, retro_tbel_3465, retro_tbel_3467,