RetrogeneDB ID: retro_fcat_1086

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:50059116..50059933(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CA
• Ensembl ID: ENSFCAG00000029685
• Aliases: None
• Description: protein phosphatase 2, catalytic subunit, alpha isozyme [Source:HGNC Symbol;Acc:9299]

Sequence

>retro_fcat_1086
AAAGAGCTGCATGTGTGTAAACAGCTTAACAGAACCAAGTACAGATGCTGTGCAAAAAGGCTAAGGAAATTTTAACAAAA
GAATAAAATGTGCAAGAGGTTTGTTGTTCTGTTACCGTGTCGGAGATGTGCATGGTCAATTTCTTAAGCTTACTGAACTC
TTCAGAACTGGTGGAAAATCACCAGGTACAAACTGTCTGTTCATGGGCGACTGTGTAGACAGAGGCTATTATTCAGTGGA
GACTGTGACTCTCCTTGTGGCCTTAAAGGCGTATTACTCAGAACACATTACAATATTGAGAGGAAACCACGAAAGCTGCG
AAATTACCCAAGTATATGGCTTTTATAACGAATGTCTGTGAAAGTATAGAAATGCCGATGTTTGGAAATATGTTACAGAT
CTATCTGATTATCTTCTACTTACAACTTTAGTAGATGGACAGATATTCTGCCTCCACAGTGGCCTCTCTCCATCCCTAGA
TGTGCTGGATCATATAAGAGACTTGGATCCTTTACAGGAAGTTCCACATGAGGGCCCAATGTGTGATGTGTAGTGGTTAG
ATCCAGATGATTGTGGTGGGTGGGGTATTTCACCATGTGGTGCTGGCTGCGCATGTGGATAAGACTTTTCTGAAACATTT
AACCATGGGAATGGCCTCACACTGGCTTCTCGAGCTCACCAGCTTGTAATGGAGGGATACAATTGGTGTCATGATTAGAA
TGTGGTTACCATTTTTAGTGCTCCCAGTTACTGTTATCGTTGTGGGAACCAGGCTGCTCTCATGGAATTAGATGACACTT
TAAAATACTCCTTCCTT

Alignment

ORF - retro_fcat_1086 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.27 %
• Parental protein coverage: 88.35 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EQLNECKQLS-ESQVKSLCEKAKEILTKESNVQEVRCPVTVC-GDVHGQFHDLMELFRIGGKSPDTNYLF
          ..L..CKQL....QV..LC.KAKEILTKE.NVQEV.C.VTV..GDVHGQF..L.ELFR.GGKSP.TN.LF
Retrocopy KELHVCKQLN<QNQVQMLCKKAKEILTKE*NVQEVCCSVTVS<GDVHGQFLKLTELFRTGGKSPGTNCLF

Parental  MGDYVDRGYYSVETVTLLVALKVRYRERITILRGNHESRQITQVYGFYDECLRKYGNANVWKYFTDLFDY
          MGD.VDRGYYSVETVTLLVALK..Y.E.ITILRGNHES..ITQVYGFY.ECL.KY.NA.VWKY.TDL.DY
Retrocopy MGDCVDRGYYSVETVTLLVALKAYYSEHITILRGNHESCEITQVYGFYNECL*KYRNADVWKYVTDLSDY

Parental  LPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYTFGQ
          L.LT.LVDGQIFCLH.GLSPS.D.LDHIR.LD.LQEVPHEGPMCD..W.DPDD.GGWGISP.GAG...G.
Retrocopy LLLTTLVDGQIFCLHSGLSPSLDVLDHIRDLDPLQEVPHEGPMCDV*WLDPDDCGGWGISPCGAGCACG*

Parental  DISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYSFL
          D.SETFNH.NGLTL.SRAHQLVMEGYNWCHD.NVVTIFSAP.YCYRCGNQAA.MELDDTLKYSFL
Retrocopy DFSETFNHGNGLTLASRAHQLVMEGYNWCHD*NVVTIFSAPSYCYRCGNQAALMELDDTLKYSFL

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	206.36 RPM
SRP017611_kidney	0.00 RPM	112.75 RPM
SRP017611_liver	0.00 RPM	64.60 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1086 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1086 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002653	1 retrocopy	retro_acar_69,
Bos taurus	ENSBTAG00000000469	1 retrocopy	retro_btau_1754,
Dasypus novemcinctus	ENSDNOG00000013011	4 retrocopies	retro_dnov_1025, retro_dnov_1844, retro_dnov_2100, retro_dnov_2122,
Echinops telfairi	ENSETEG00000007561	2 retrocopies	retro_etel_1233, retro_etel_659,
Felis catus	ENSFCAG00000014171	1 retrocopy	retro_fcat_1043,
Felis catus	ENSFCAG00000025139	1 retrocopy	retro_fcat_1884,
Felis catus	ENSFCAG00000029685	1 retrocopy	retro_fcat_1086 ,
Mustela putorius furo	ENSMPUG00000010169	1 retrocopy	retro_mputfur_633,
Sorex araneus	ENSSARG00000005447	3 retrocopies	retro_sara_296, retro_sara_385, retro_sara_715,
Sarcophilus harrisii	ENSSHAG00000016632	3 retrocopies	retro_shar_313, retro_shar_428, retro_shar_471,
Tursiops truncatus	ENSTTRG00000016859	1 retrocopy	retro_ttru_1584,