RetrogeneDB ID: retro_rnor_1263

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:41575943..41576408(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ppp2ca
• Ensembl ID: ENSRNOG00000005389
• Aliases: Ppp2ca, Pp2a1
• Description: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform [Source:UniProtKB/Swiss-Prot;Acc:P63331]

Sequence

>retro_rnor_1263
GTTTATTGGCAATTTCATGACCTCATGGAACTCTTTAGAATGGTGGTAAACCACCAGATACAACTCACTTGCTTATGGGT
GATTATGTGGACAGAGGATATTACTCAGTTGAAACAGTTACACTGCTTGTAACTCTTAAGGTTCCTTACCAAGAAAGTAT
CCCCATACTCCGAGGCAATTGTGAGAACAGACAGATCACACAAGTTTATGATTTCTACGATGAGTGTTTAAGGAAATACA
GGAATGCAAATGTTTGGAAATACTTCACAGACCTTTTTTGACTATCTTCCTCTCACTGCCTTGGAGGATGGACAGATCTT
CTGTCTACGTGGTGGTCTCCCACCATCCATAGACACACTGGATCACATCCAAGTACTTGAACACCTACACGAAGTTTCTC
ATGAGGGTCCAATGTGTAACTTGCTGTGGTCAGATTCAGATGACCATGATGTCTGGGGGATATCT

Alignment

ORF - retro_rnor_1263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.62 %
• Parental protein coverage: 50.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VHGQFHDLMELFRI-GGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNHESRQITQV
          V..QFHDLMELFR..GGK.PDT..L.MGDYVDRGYYSVETVTLLV.LKV.Y.E.I.ILRGN.E.RQITQV
Retrocopy VYWQFHDLMELFRM<GGKPPDTTHLLMGDYVDRGYYSVETVTLLVTLKVPYQESIPILRGNCENRQITQV

Parental  YGFYDECLRKYGNANVWKYFTDL-FDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPM
          Y.FYDECLRKY.NANVWKYFTDL.FDYLPLTAL.DGQIFCL.GGL.PSIDTLDHI..L..L.EV.HEGPM
Retrocopy YDFYDECLRKYRNANVWKYFTDL>FDYLPLTALEDGQIFCLRGGLPPSIDTLDHIQVLEHLHEVSHEGPM

Parental  CDLLWSDPDDRGGWGIS
          C.LLWSD.DD...WGIS
Retrocopy CNLLWSDSDDHDVWGIS

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	64.06 RPM
SRP017611_kidney	0.00 RPM	45.29 RPM
SRP017611_liver	0.00 RPM	21.38 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1263 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1263 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1263 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002653	1 retrocopy	retro_acar_69,
Callithrix jacchus	ENSCJAG00000013634	2 retrocopies	retro_cjac_1346, retro_cjac_4113,
Homo sapiens	ENSG00000113575	1 retrocopy	retro_hsap_369,
Nomascus leucogenys	ENSNLEG00000026729	1 retrocopy	retro_nleu_2441,
Otolemur garnettii	ENSOGAG00000009695	2 retrocopies	retro_ogar_3414, retro_ogar_921,
Rattus norvegicus	ENSRNOG00000005389	5 retrocopies	retro_rnor_1263 , retro_rnor_1264, retro_rnor_1265, retro_rnor_1266, retro_rnor_817,
Sarcophilus harrisii	ENSSHAG00000016632	3 retrocopies	retro_shar_313, retro_shar_428, retro_shar_471,
Ictidomys tridecemlineatus	ENSSTOG00000010560	1 retrocopy	retro_itri_258,