RetrogeneDB ID: retro_chof_1322

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_262365:605..1324(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VTCN1
• Ensembl ID: ENSCHOG00000005097
• Aliases: None
• Description: V-set domain containing T cell activation inhibitor 1 [Source:HGNC Symbol;Acc:28873]

Sequence

>retro_chof_1322
ATCATTAGCATCATAATAATTCTGGCTGGAGCGGCTGCAGTCATCACTGGTTTTGGTATTTCAGGGAGACACTCCATCAC
AGTCACTACTCTCATCTCAGCTGGGAACATTGGAGACAATGGAACACTGAGCTGCACTTTTGAACCTGACATCAAACTTT
CTGATATTGTGATACAGTGGCTGAAGGAAGGTGCTATGGGTTTGGTCCATGAGTCCAAAGAAGGCAAAGATAACCTGTCA
GACCAGGATGAAATGTTCAAGAGCCAGACAGCAGTGTTTACAGATCAAGTGATAGTTGGCAATGCCTCTCTGAGCCTGAA
AAATGTGCAACTCTCAGATGCTGGCACCTACAAATGTTACATCATCACCTCTAAGGGCAAGGGGAATGCTAACCTGGAGT
ATAAAACTGGAGCTTTCAGCATCCCAGAGGCAAGTGTGGACTATAATGCCAGTTCAGAGAGCTTGCCGTGTGAGGCTCCT
CAATGGTTTCCCCCAGCCCACAGTGGTCTGGGCATCCCAAGTTGGCCAGGGAGCCAACTTCTCTGAAGTCTCCAACACAA
GTTTGGAGCTGAACTCTGAGAATGTGACCGAAGGTGGTGTCTGTGCCCTACAGTGTCACAATCAACAACACATACTCCTG
TGTGATTGAGAACGACACTGGCAAAGCCTCAGGGGATATCAAAGTGACAGACTCTGAGATCAAAAGGCGGAGTCACTTA

Alignment

ORF - retro_chof_1322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.66 %
• Parental protein coverage: 88.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IISIIIILAGATALIIGFGISGRHSIAVTTLTSAGNIGEDGILSCTFEPDIKLSDIVIQWLKEGVRGLVH
          IISIIIILAGA.A.I.GFGISGRHSI.VTTL.SAGNIG..G.LSCTFEPDIKLSDIVIQWLKEG..GLVH
Retrocopy IISIIIILAGAAAVITGFGISGRHSITVTTLISAGNIGDNGTLSCTFEPDIKLSDIVIQWLKEGAMGLVH

Parental  EFKEGKDNLSDQDEMFKGRTAVFTDQVIVGNASLRLKNVQLTDAGTYKCYIVTSKGKGNANLEYKTGAFS
          E.KEGKDNLSDQDEMFK..TAVFTDQVIVGNASL.LKNVQL.DAGTYKCYI.TSKGKGNANLEYKTGAFS
Retrocopy ESKEGKDNLSDQDEMFKSQTAVFTDQVIVGNASLSLKNVQLSDAGTYKCYIITSKGKGNANLEYKTGAFS

Parental  IPEVNVDYNASSESLRCEAPRW-FPQPTVVWASQVDQGANFSEVSNTSFELNSENVTMKVVSVLYNVMIN
          IPE..VDYNASSESL.CEAP.W.FPQPTVVWASQV.QGANFSEVSNTS.ELNSENVT...V..L......
Retrocopy IPEASVDYNASSESLPCEAPQW>FPQPTVVWASQVGQGANFSEVSNTSLELNSENVTEGGVCALQCHNQQ

Parental  HTYSCM-IENDIAKATG-DIKVTDSEIKRRSHL
          H...C.......AK..G.DIKVTDSEIKRRSHL
Retrocopy HILLCD<LRTTLAKPQG<DIKVTDSEIKRRSHL

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_1322 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005097	1 retrocopy	retro_chof_1322 ,
Dasypus novemcinctus	ENSDNOG00000013317	1 retrocopy	retro_dnov_1181,
Homo sapiens	ENSG00000134258	1 retrocopy	retro_hsap_2420,
Gorilla gorilla	ENSGGOG00000025814	1 retrocopy	retro_ggor_1505,
Macaca mulatta	ENSMMUG00000016964	1 retrocopy	retro_mmul_611,
Nomascus leucogenys	ENSNLEG00000005256	1 retrocopy	retro_nleu_2811,
Pan troglodytes	ENSPTRG00000001164	1 retrocopy	retro_ptro_1394,