RetrogeneDB ID: retro_chof_2502

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_81045:9378..10018(+)
• Located in intron of: None

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_2502
CTGACTCTTCCTGTGTTATTAAAGATGCAATATCCAGAATTCATTACAATATTGAGAAGAAACCATAAAAGCTAACAAAT
TATCCAAGCATATGGCTTTTAGGTTGAATGTCTATAAAAATATGGAAATGCCAAGGTTTGGAAATAATATTTCACAGATA
TATACGATTATCTTCCACCTACAACTTTAGCAGATGGACAGATATTCTGCCTCCCTGGTGGCCTCCATCTATCCATATAT
ACATTGGATCATATAAGAACCCTGGATCATTTACAAGATGCTCCACATGAGGGTACCACTGTATGATTTGTTATGGTCAG
ATCCAGATGATCATGGTGGGTGGTATCTCCACATGGTGCTGGCTACACATCTGGACAAAACATTTCTAAAAATATTTAAC
CATGCCAATGGTCTCACACTGGTTTCTCATGCTCACCAACTTGTAATGGAGGGATACAATAGGTGTCATGATCAGAATGT
GTTTACTACTGTCAGTGCACCCAATTATTGTTATCAATGCGGAAACCAAGCTGTTATCATGGAATTAGATGACACTTTAA
AATATTACTTCCTTCATTATGACCTAGTGCTTCATTGTGGAGAGCCTCATGATACCCAGTGCACTCCAGACTACTTCCTG

Alignment

ORF - retro_chof_2502 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.97 %
• Parental protein coverage: 69.38 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VTLLVALKVRYPERITILRGNHESRQITQVYGFYDECLRKYGNANVWK-YFTDLFDYLPLTALVDGQIFC
          .TL.V.LK..YPE.ITILR.NH.S.QI.Q.YGF..ECL.KYGNA.VWK.YFTD..DYLP.T.L.DGQIFC
Retrocopy LTLPVLLKMQYPEFITILRRNHKS*QIIQAYGF*VECL*KYGNAKVWK*YFTDIYDYLPPTTLADGQIFC

Parental  LHGGLSPSIDTLDHIRALDRLQEVPHEG-PMCDLLWSDPDDRGG-WGISPRGAGYTFGQDISET-FNHAN
          L.GGL..SI.TLDHIR.LD.LQ..PHEG.P..DLLWSDP.D..G.W..SP.GAGYT.GQ.IS...FNHAN
Retrocopy LPGGLHLSIYTLDHIRTLDHLQDAPHEG>PLYDLLWSDP-DDHG<WVVSPHGAGYTSGQNISKN>FNHAN

Parental  GLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYSFLQFDPAPRRGEPHVTR
          GLTLVS.AHQLVMEGYN.CHD.NV.T..SAPNYCY.CGNQA.IMELDDTLKY.FL..D.....GEPH.T.
Retrocopy GLTLVSHAHQLVMEGYNRCHDQNVFTTVSAPNYCYQCGNQAVIMELDDTLKYYFLHYDLVLHCGEPHDTQ

Parental  RTPDYFL
          .TPDYFL
Retrocopy CTPDYFL

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_2502 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,