RetrogeneDB ID: retro_chof_105

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_2030:396..1074(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFATC2IP
• Ensembl ID: ENSCHOG00000011828
• Aliases: None
• Description: nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2 interacting protein [Source:HGNC Symbol;Acc:25906]

Sequence

>retro_chof_105
GTCCAGGACACCTCTCCTCTGCCCTCACCTCCACCTAGGACTAAAAGCAGAAAGCACACGAGGGCCCTCCAGAAGTTAAG
GGAGGTGAGCAGGCGCCTCCACGACCTCCGTTCCTGCCTGAGTCCCCTGCAGCACCAGGGCCAAGACCACTGGAACCAGG
ACGACGAGGTGGTCCTGGTGGAGGGGTCCACTGTCCCAGAGAGCCCCCGACTCTTCCCCCTCAAAATCCGGTGCCGGGCG
GACCTGATCAGATTGCCTGTCGAGATGTCGGAGCCCCTGCAGGGTGTGGTGGACCACCTTGCCGCCCGCCTCGGGGTGTC
CCCAAGTAGGATCCTCTTGCTCTTTGGAGAGGCAGAGCTGTCCTCTACTGCCACCCCCAAGACCCTGAAGCTCGGAGTGG
CTGACATCATCTACTGTGTGGTGCTAGCAAGTTCTCCGGAGGCTACAGAGATGTTCCAGCAGTTCCAGCTCCGGGTGCAG
GGGAAGGAGAAGCACCAGATGCTGGAGGTCTCGCTGGCTCGGGATTCTTCCCTCAAGACCCTCATGTCCCACTACGAGGA
AGCCATGGGACTCTCATGACACAAGCTCTCCTTCTTCTTTGATGGGGCAAAGCTTTCAGGCAAGGAGCTGCCAGCCGATC
TGGGCATGGAATCTGGGGACCTCATTGAGGTCTGGAGC

Alignment

ORF - retro_chof_105 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.02 %
• Parental protein coverage: 68.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VQDTSPLPSPPPRTKSRKHTRALQKLREVSRRLHDLRSCLSPLQHQGQDHWNQDDEVVLVEGSTVPESPR
          VQDTSPLPSPPPRTKSRKHTRALQKLREVSRRLHDLRSCLSPLQHQGQDHWNQDDEVVLVEGSTVPESPR
Retrocopy VQDTSPLPSPPPRTKSRKHTRALQKLREVSRRLHDLRSCLSPLQHQGQDHWNQDDEVVLVEGSTVPESPR

Parental  LFPLKIRCRADLIRLPVEMSEPLQGVVDHLAARLGVSPSRIPLLFGEAELSPTATPKTLILGVADIIDCV
          LFPLKIRCRADLIRLPVEMSEPLQGVVDHLAARLGVSPSRI.LLFGEAELS.TATPKTL.LGVADII.CV
Retrocopy LFPLKIRCRADLIRLPVEMSEPLQGVVDHLAARLGVSPSRILLLFGEAELSSTATPKTLKLGVADIIYCV

Parental  VLASSPEATEMSQQLQLRVQGKEKHQMLEVSLARDSPLKTLMSRYEEAMGLSGHKLSFFFDGAKLSGKEL
          VLASSPEATEM.QQ.QLRVQGKEKHQMLEVSLARDS.LKTLMS.YEEAMGLS.HKLSFFFDGAKLSGKEL
Retrocopy VLASSPEATEMFQQFQLRVQGKEKHQMLEVSLARDSSLKTLMSHYEEAMGLS*HKLSFFFDGAKLSGKEL

Parental  PADLGMESGDLIEVWS
          PADLGMESGDLIEVWS
Retrocopy PADLGMESGDLIEVWS

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_105 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	ENSCHOG00000011828	1 retrocopy	retro_chof_105 ,