RetrogeneDB ID: retro_rnor_817

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 11:89521957..89522884(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000001893
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_817
ATGGACGAGAAGTTGTTCACCAAGGAGCTGGACCAGTGGATCGAGCAGCTGAACGAGTGCAAGCAGCTCTCCGAGTCCCA
GGTCAAGAGCCTCTGCGAGAAGGCTAAAGAAATCCTGACAAAAGAATCTAATGTTCAGGAGGTTCGATGTCCAGTCACTG
TGTGTGGAGATGTGCATGGGCAATTTCATGACCTCATGGAACTCTTTAGAATTGGTGGTAAATCACCAGATACAAATTAC
TTGTTTATGGGAGACTATGTGGACAGAGGATATTACTCAGTTGAAACAGTTACACTGCTTGTAGCTCTTAAGGTTCGTTA
CCGAGAGCGTATCACCATACTCCGAGGGAATCACGAGAGCAGACAGATCACACAAGTTTATGGTTTCTACGATGAGTGTT
TAAGGAAATACGGAAATGCAAATGTTTGGAAATACTTCACAGACCTTTTTGACTACCTTCCTCTCACTGCCTTGGTGGAT
GGGCAGATCTTCTGTCTACATGGTGGTCTTTCACCAACCATAGACACACTGGATCACATCGGAGCACTTGATCGCCTACA
AGAAGTTCCTCATGAGGGTCCAATGTGTGACTTGCTGTGGTCAGATCCAGATGACCGTGGTGGCTGGGGGATATCTCCTC
GGGGAGCTGGTTATACCTTTGGCCAAGATATTTCTGAGACATTTAATCATGCCAATGGCCTCACGTTGGTGTCCAGAGCT
CACCAGCTGGTGATGGAGGGATATAACTGGTGCCATGACCGGAATGTAGTAACAATTTTCAGTGCTCCAAACTATTGCTA
TCGTTGTGGTAACCAAGCTGCAATCATGGAACTTGATGACACTCTTAAGTATTCTTTCTTGCAGTTCGATCCAGCACCTC
GTAGAGGCGAGCCACATGTCACTCGTCGTACCCCAGACTACTTCCTG

Alignment

ORF - retro_rnor_817 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.35 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDEKLFTKELDQWIEQLNECKQLSESQVKSLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFR
          MDEKLFTKELDQWIEQLNECKQLSESQVKSLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFR
Retrocopy MDEKLFTKELDQWIEQLNECKQLSESQVKSLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFR

Parental  IGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNHESRQITQVYGFYDECLRKYGNA
          IGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNHESRQITQVYGFYDECLRKYGNA
Retrocopy IGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNHESRQITQVYGFYDECLRKYGNA

Parental  NVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWG
          NVWKYFTDLFDYLPLTALVDGQIFCLHGGLSP.IDTLDHI.ALDRLQEVPHEGPMCDLLWSDPDDRGGWG
Retrocopy NVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPTIDTLDHIGALDRLQEVPHEGPMCDLLWSDPDDRGGWG

Parental  ISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDD
          ISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDD
Retrocopy ISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDD

Parental  TLKYSFLQFDPAPRRGEPHVTRRTPDYFL
          TLKYSFLQFDPAPRRGEPHVTRRTPDYFL
Retrocopy TLKYSFLQFDPAPRRGEPHVTRRTPDYFL

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	0.65 RPM	64.06 RPM
SRP017611_kidney	0.14 RPM	45.29 RPM
SRP017611_liver	0.07 RPM	21.38 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

5 EST(s) were mapped to retro_rnor_817 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BG016080	89522301	89522430	99.3	128	1	127
BG666516	89521950	89522461	100	510	0	510
CB692026	89522043	89522387	97	321	9	310
CB713956	89522060	89522205	99.4	144	1	143
CB761496	89521967	89522397	100	429	0	428

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_817 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_817 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,