RetrogeneDB ID: retro_fcat_1884

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: JH408876.1:30494..31041(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CB
• Ensembl ID: ENSFCAG00000025139
• Aliases: None
• Description: protein phosphatase 2, catalytic subunit, beta isozyme [Source:HGNC Symbol;Acc:9300]

Sequence

>retro_fcat_1884
CAGATGCATTACCCAGAACACATTATAATATTGCAAGGAAAACAAGAAAGCTGACAAATTACCCAATTATAAGGCTTTTA
TGACGAATGTCTACGAAAGTATGCAAATACCAATGTTTGGACATATTTTACAGATCTAGTTGATTACCTTCCACTTAAAG
CTTTAGTAGATGGACAGATATTTTGCCTCTACAGCATGGCATCTCTCCACCCATAGATAACACTGGATCATATAAGAGCC
TAGGATCGTTTACAAGAAGTTCCACGTGAGGACCCAAAGTGTGATCTGTTTTGGCCAGATTCAGATGATCCTAGTGGGTG
GGGCATTTCATCACGGGGTACTAGCTACACATTTGGACATTCTGAAACATGTAATCATGCCAGTGGTCTTACCCTGGTTT
CTCCAGCTCACCAACTTATAATGGGAGGATACAATTGGTGTCATGATCAAAATGTGCTTACCATTTTCAGTGCACCCAAC
TACTGTAAGACTTGTGGGAACGAGGCCGCTTTTCATGGGATTAGATGACACTTCAAAATGTTCCTTC

Alignment

ORF - retro_fcat_1884 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.97 %
• Parental protein coverage: 75. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KVRYPERITILRGNHESRQITQVYGFYDECLRKYGNANVWKYFTDLFDYLPLTALVDGQIFCLH--GGLS
          ...YPE.I.IL.G..ES.QITQ..GFYDECLRKY.N.NVW.YFTDL.DYLPL.ALVDGQIFCL.....L.
Retrocopy QMHYPEHIIILQGKQES*QITQL*GFYDECLRKYANTNVWTYFTDLVDYLPLKALVDGQIFCLYSMASLH

Parental  PSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYTFGQDISETFNHANGLTLVSRAH
          P.I.TLDHIRA.DRLQEVP.E.P.CDL.W.D.DD..GWGIS.RG..YTFG...SET.NHA.GLTLVS.AH
Retrocopy P*I-TLDHIRA*DRLQEVPREDPKCDLFWPDSDDPSGWGISSRGTSYTFGH--SETCNHASGLTLVSPAH

Parental  QLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAA-IMELDDTLKYSF
          QL.M.GYNWCHD.NV.TIFSAPNYC..CGN.AA..M.LDDT.K.SF
Retrocopy QLIMGGYNWCHDQNVLTIFSAPNYCKTCGNEAA>FMGLDDTSKCSF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	151.73 RPM
SRP017611_kidney	0.31 RPM	88.63 RPM
SRP017611_liver	0.10 RPM	27.80 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1884 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1884 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001615	1 retrocopy	retro_amel_663,
Bos taurus	ENSBTAG00000009245	3 retrocopies	retro_btau_1199, retro_btau_1750, retro_btau_704,
Dasypus novemcinctus	ENSDNOG00000010906	1 retrocopy	retro_dnov_2211,
Echinops telfairi	ENSETEG00000018123	4 retrocopies	retro_etel_1607, retro_etel_1923, retro_etel_680, retro_etel_702,
Felis catus	ENSFCAG00000014171	1 retrocopy	retro_fcat_1043,
Felis catus	ENSFCAG00000025139	1 retrocopy	retro_fcat_1884 ,
Felis catus	ENSFCAG00000029685	1 retrocopy	retro_fcat_1086,
Monodelphis domestica	ENSMODG00000019001	2 retrocopies	retro_mdom_192, retro_mdom_632,
Otolemur garnettii	ENSOGAG00000002488	1 retrocopy	retro_ogar_3188,
Tursiops truncatus	ENSTTRG00000000102	1 retrocopy	retro_ttru_1576,