RetrogeneDB ID: retro_chof_1226

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_23125:9152..9593(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFAP2C
• Ensembl ID: ENSCHOG00000011025
• Aliases: None
• Description: transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma) [Source:HGNC Symbol;Acc:11744]

Sequence

>retro_chof_1226
TCCCTTCTCAGCTCCACATCTAAATATACAGTGGCAGTTGCTGAAGTATGGAAGCAACTGTCACCACCTGAATGCTTAAA
TGACTCATTACTGGGAGTTTCTCAGAAGAGCCAAATCTAAAAATTGAGGCAGGTCCTTGCGGGAGAAGTTGGATTAGATT
GAGTTGAATCTTCCTGCCAGGAGATGGAAAGCTGCACACGTTACGCTCCTGACATCCTTAGTGGAAGGTGAAGCTGTTCA
TTTGGCTCACGACTCTGCATATGTCTGTGAAGAACAATTTGCTAGTAAATCAGTGGCCAACTATTTAACCAAACCACATG
TAGGAAAATGGAATGAGATGGGAACTCGGAAGAACATGCTAGGGCTGCACAGTAACTGTGTAAAGAATTCTCAGACCTTC
TCAATCAAGTCCAAACACCCATTGGGAACAACAGGCCCACC

Alignment

ORF - retro_chof_1226 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78. %
• Parental protein coverage: 58.04 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLLSSTSKYKVTVAEVQRRLSPPECLNASLLGGV-LRRAKSKNGGRSLREKLDKIGLNLPAGRRKAAHVT
          SLLSSTSKY.V.VAEV...LSPPECLN.SLL.GV.LRRAKSKN.GRSLREKLD.I.LNLPA.R.KAAHVT
Retrocopy SLLSSTSKYTVAVAEVWKQLSPPECLNDSLL-GV>LRRAKSKN*GRSLREKLD*IELNLPARRWKAAHVT

Parental  LLTSLVEGEAVHLARDFAYVCEAEFPSKPVAEYLTRPHLGGRNEMATRKNML-LAAQQVCKEFTDLLNQD
          LLTSLVEGEAVHLA.D.AYVCE..F.SK.VA.YLT.PH.G..NEM.TRKNML..AAQ..CKEF.DLLNQ.
Retrocopy LLTSLVEGEAVHLAHDSAYVCEEQFASKSVANYLTKPHVGKWNEMGTRKNML<RAAQ*LCKEFSDLLNQV

Parental  RTPNGNNRPT
          .TP.GNNRPT
Retrocopy QTPIGNNRPT

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_1226 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011025	1 retrocopy	retro_chof_1226 ,
Macropus eugenii	ENSMEUG00000007703	1 retrocopy	retro_meug_166,
Myotis lucifugus	ENSMLUG00000010003	2 retrocopies	retro_mluc_284, retro_mluc_5,
Monodelphis domestica	ENSMODG00000016445	1 retrocopy	retro_mdom_728,
Otolemur garnettii	ENSOGAG00000033901	1 retrocopy	retro_ogar_1767,
Pan troglodytes	ENSPTRG00000013654	1 retrocopy	retro_ptro_1933,
Ictidomys tridecemlineatus	ENSSTOG00000014299	3 retrocopies	retro_itri_1741, retro_itri_1801, retro_itri_1813,
Tursiops truncatus	ENSTTRG00000005983	1 retrocopy	retro_ttru_535,