RetrogeneDB ID: retro_chof_2063

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_47116:8049..8938(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1CB
• Ensembl ID: ENSCHOG00000000859
• Aliases: None
• Description: protein phosphatase 1, catalytic subunit, beta isozyme [Source:HGNC Symbol;Acc:9282]

Sequence

>retro_chof_2063
AAACTCAACATCGACAGCATCATCCAACGGCTGCTGGAAGTGAGAGGGTCAAGCCTGGTAAGAATGTCCAGCTACAGGAG
AATGAAATCAGAGGATTGTGCTTAAAGTCTCGTGAGATCTTCTCAGTCAGCCTATCCTACTAGAACTTGAAGCACCACTC
AAAATATGTGGTGATATCCATGGGCAATACTATGATTTGCTTCGACTTTTTGAGTACGGTGGTTTCCCACCAGAAAGCAA
CTACCTGTTTCTTGGGGACTATGTTGACAGAGGGAAGCAGTCATTGGAGACTATATGCCTCTTACTGGCCTACAAAATCA
AATATCCCGAGAATTTTTTTCTTCTCCGAGGAAACCACGAATGTGCCAGCATCAATAGAATTTATGGATTTTATGATGAA
TGTAAAAGAAGATACAACATTAAACTATGGAAAACTTTCACAGACTGCTTTAACTGTTTACCGATAGCAGCCATCGTTGA
TGAGAAAATATTCTGCTGTCATGGAGGTTTATCACCAGATCTTCAATCTATGGAGCAGATACGGCGAATTATGCGACCAA
CTGATGTACCAGATCAAGGTCTTCTTTGTGATCTTTTGTGGTCTGACCCCGATAAAGATGTCTTAGGCTGGGGTGAAAAT
GACAGAGGAGTGTCCTTCACATTTGGTGCAGAAGTGGTTGCAAAATTTCTCCATAAGCATGATTTGGATCTTATATGTAG
AGCCCATCAGGTGGTTGAAGATGGATATGAATTTTTTGCCAAGAGGCAGTTGGTCACTCTGTTTTCCGCACCCAATTATT
GTGGAGAGTTTGACAATGCAGGTGCCATGATGAGTGTGGATGAAACGCTAATGTGTTCTTTTCAGATTTTAAAGCCTGCA
GAGAAAAAG

Alignment

ORF - retro_chof_2063 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.3 %
• Parental protein coverage: 81.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELNVDSLITRLLEVRGC-RPGKIVQMTEAEVRGLCIKSREIF-LSQPILLELEAPLKICGDIHGQYTDLL
          .LN.DS.I.RLLEVRG...PGK.VQ..E.E.RGLC.KSREIF.LSQPILLELEAPLKICGDIHGQY.DLL
Retrocopy KLNIDSIIQRLLEVRGS<KPGKNVQLQENEIRGLCLKSREIF<LSQPILLELEAPLKICGDIHGQYYDLL

Parental  RLFEYGGFPPEANYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRR
          RLFEYGGFPPE.NYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRR
Retrocopy RLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRR

Parental  FNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDTGLLCDLLWSDPDKDV
          .NIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPD.GLLCDLLWSDPDKDV
Retrocopy YNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDV

Parental  QGWGENDRGVSFTFGADVVSKFLNRHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGGMM
          .GWGENDRGVSFTFGA.VV.KFL..HDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAG.MM
Retrocopy LGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMM

Parental  SVDETLMCSFHILKPSEKK
          SVDETLMCSF.ILKP.EKK
Retrocopy SVDETLMCSFQILKPAEKK

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_2063 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 4 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000859	5 retrocopies	retro_chof_2023, retro_chof_2063 , retro_chof_2076, retro_chof_2154, retro_chof_539,
Echinops telfairi	ENSETEG00000015038	2 retrocopies	retro_etel_1223, retro_etel_1364,
Myotis lucifugus	ENSMLUG00000003785	1 retrocopy	retro_mluc_1907,
Rattus norvegicus	ENSRNOG00000004612	2 retrocopies	retro_rnor_1455, retro_rnor_2344,