RetrogeneDB ID: retro_chof_273

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_6027:31250..32177(+)
• Located in intron of: ENSCHOG00000002808

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CB
• Ensembl ID: ENSCHOG00000003467
• Aliases: None
• Description: protein phosphatase 2, catalytic subunit, beta isozyme [Source:HGNC Symbol;Acc:9300]

Sequence

>retro_chof_273
ATGGACGAGAAGGTGTTCACCAAGGAGCTGGACCAGTGGATCGAGCAGCTGCATGAGTGCAAGCAGCTGTCCGAGTCCCA
AGTCAAGAGCCTCTGCGAGAAGGCTAAAGAAATCCTGACAAAAGAATCCAATGTGCAAGAGGTTCGATGTCCAGTCACCG
TCTGTGGAGATGTGCATGGACAATTTCATGATCTCATGGAACTGTTCAGAATTGGTGGCAAATCACCAGATACGAATTAC
TTGTTTATGGGAGATTATGTTGACAGAGGCTATTATTCAGTTGAAACAGTCACACTGCTTGTAGCTCTTAAGGTTCGTTA
CCGTGAACGCATCACTATTCTTCGAGGGAATCATGAAAGCAGACAGATCACACAAGTATATGGTTTCTATGATGAGTGTT
TAAGGAAATATGGAAATGCAAATGTTTGGAAATATTTTACACATCTTTTTGACTATTTTCCTCTCACTGCCTTGGTGGAT
GGGCAGATCTTCTGTCTACATGGTGGCCTCTCACCATCCATAGATAAACTGGATCATATCAGAGCACTCAATCGCCTACA
AGAAGTTCCCCATGAGGGCCCTATGTGTGACTTGCTGTGGTCAGATCCAGATGACCATGGTGGTTGGGGTATATCTCCTC
GAGGAGCAGGTTATACCTTTGGCCAGGATATTTCTGAGACGTTTAATCATGCCAATGGCCTCACATTGGTGTCTAAAGCT
CACTAGCTGGTGATGGAGGGATATAACTGGTGCCATGACCGGAATGTAGTAACAATTTTCAGTGCTCCAAACTATTGTTA
TCGCTGTGGTAACCAAGCTGCAATCATGGAACCTGATGATACTCTAAACTACTCTTTCTTGCAGTTTGACCCAGCACCTC
GCAGAGGCGAGCCACATGTTACTCGTCGTACCCCAGACTACTTCCTG

Alignment

ORF - retro_chof_273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.88 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDYKEFSKELD-WVE-LKECKQFKENQVQTLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFR
          MD.K.F.KELD.W.E.L.ECKQ..E.QV..LCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFR
Retrocopy MDEKVFTKELDQWIEQLHECKQLSESQVKSLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFR

Parental  IGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYPERITILRGNHESRQITQVYGFYDECLRKYGNA
          IGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRY.ERITILRGNHESRQITQVYGFYDECLRKYGNA
Retrocopy IGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNHESRQITQVYGFYDECLRKYGNA

Parental  NVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWG
          NVWKYFT.LFDY.PLTALVDGQIFCLHGGLSPSID.LDHIRAL.RLQEVPHEGPMCDLLWSDPDD.GGWG
Retrocopy NVWKYFTHLFDYFPLTALVDGQIFCLHGGLSPSIDKLDHIRALNRLQEVPHEGPMCDLLWSDPDDHGGWG

Parental  ISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDD
          ISPRGAGYTFGQDISETFNHANGLTLVS.AH.LVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIME.DD
Retrocopy ISPRGAGYTFGQDISETFNHANGLTLVSKAH*LVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMEPDD

Parental  TLKYSFLQFDPAPRRGEPHVTRRTPDYFL
          TL.YSFLQFDPAPRRGEPHVTRRTPDYFL
Retrocopy TLNYSFLQFDPAPRRGEPHVTRRTPDYFL

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_273 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 2 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003467	9 retrocopies	retro_chof_1247, retro_chof_1521, retro_chof_1556, retro_chof_2112, retro_chof_2267, retro_chof_2502, retro_chof_251, retro_chof_273 , retro_chof_446,
Monodelphis domestica	ENSMODG00000019001	2 retrocopies	retro_mdom_192, retro_mdom_632,