RetrogeneDB ID: retro_rnor_2344

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:27990857..27991839(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ppp1cb
• Ensembl ID: ENSRNOG00000004612
• Aliases: None
• Description: Serine/threonine-protein phosphatase PP1-beta catalytic subunit [Source:UniProtKB/Swiss-Prot;Acc:P62142]

Sequence

>retro_rnor_2344
ATGGTGGACAGGGAGCTGAACATGGACAGCCTCATCACCCGCCTGCTGAAGGTTCGAGGATGTCATCCGGGAAAAATTGT
GCAGATGACTGAAGCAGAAGTCCGAGGGCTGTGTATCAAGTCTCGTGAAGCATTTCTTAGCCAGCCTATTCTTTTGGAAT
TGGAAGCACCACTGAAGATTTGTGGAGATATTCATGGACAGTATACAGACTTACTGAGATTATTTGAATATGGAGGTTTT
CCACCAGAAGCCAACTATCTTTTCGTAGGAGATTATGTGGACAGAGGAAAGTTGTCTTTGGAAACCATCTGTTTGCTATT
GGCTTACAAAATCAAACACCCGGAGAATTTCTTTCTTCTACAAGGAAACCAAGACTGTGCTAGCATCAACTGTATTTATG
GATTCTATGATGAGTGCAAACGAAGATTTAATATTAAATTGTGGAAGACATTCCCTGATTATTTTAACTATATGCCTATA
GCTGCTATTGTTGATGAGGGAATCTTCTGTTGTCATGAAGGACTGTCACCAGACCTACAGTCTATGGAACAGATTCAGAG
AATTATGAGACCCACTGATGTACCTGATACAGGTTTGCTTTGGAATTTACTATGGTCCGACCCGGATAAGGATGTACAAG
GCTGGAGAGAAAATGATCATGGTCTTTCTTTTACTTTTGAAGCTGATGTAGTCAGTAAATTTCTGAATTGTCATGATTTT
AGACTTGATTTGTTGAGCCCATCAGGTGGTAGAAGACGGATAGGAATTTTTTGCTAAACGACAATTAGTAACTTTATTTT
CTGCTCCAAATTACTGTAGCGAATTTAACAATGCTGGTGGTATGATGAGTGTGGATAAAACTTTGATGTGTTCATTCCAG
ATATTGAAACCATCTGAAAAGAAAGCTAAGTACCAGTATGTTGGGCTGAATTCTGGATGTCCTGTCACTCTGCCTCGAAA
AGCTAATCCACTGAAGAAAAGG

Alignment

ORF - retro_rnor_2344 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.41 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADGELNVDSLITRLLEVRGCRPGKIVQMTEAEVRGLCIKSREIFLSQPILLELEAPLKICGDIHGQYTD
          M.D.ELN.DSLITRLL.VRGC.PGKIVQMTEAEVRGLCIKSRE.FLSQPILLELEAPLKICGDIHGQYTD
Retrocopy MVDRELNMDSLITRLLKVRGCHPGKIVQMTEAEVRGLCIKSREAFLSQPILLELEAPLKICGDIHGQYTD

Parental  LLRLFEYGGFPPEANYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECK
          LLRLFEYGGFPPEANYLF.GDYVDRGK.SLETICLLLAYKIK.PENFFLL.GN..CASIN.IYGFYDECK
Retrocopy LLRLFEYGGFPPEANYLFVGDYVDRGKLSLETICLLLAYKIKHPENFFLLQGNQDCASINCIYGFYDECK

Parental  RRFNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDTGLLCDLLWSDPDK
          RRFNIKLWKTF.D.FN..PIAAIVDE.IFCCH.GLSPDLQSMEQI.RIMRPTDVPDTGLL..LLWSDPDK
Retrocopy RRFNIKLWKTFPDYFNYMPIAAIVDEGIFCCHEGLSPDLQSMEQIQRIMRPTDVPDTGLLWNLLWSDPDK

Parental  DVQGWGENDRGVSFTFGADVVSKFLNRHD-LDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAG
          DVQGW.END.G.SFTF.ADVVSKFLN.HD.LDLIC.AHQVVEDG.EFFAKRQLVTLFSAPNYC.EF.NAG
Retrocopy DVQGWRENDHGLSFTFEADVVSKFLNCHD>LDLIC*AHQVVEDG*EFFAKRQLVTLFSAPNYCSEFNNAG

Parental  GMMSVDETLMCSFQILKPSEKKAKYQYGGLNSGRPVTPPRTANPPKKR
          GMMSVD.TLMCSFQILKPSEKKAKYQY.GLNSG.PVT.PR.ANP.KKR
Retrocopy GMMSVDKTLMCSFQILKPSEKKAKYQYVGLNSGCPVTLPRKANPLKKR

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	262.35 RPM
SRP017611_kidney	0.00 RPM	212.56 RPM
SRP017611_liver	0.00 RPM	85.26 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2344 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2344 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2344 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000859	5 retrocopies	retro_chof_2023, retro_chof_2063, retro_chof_2076, retro_chof_2154, retro_chof_539,
Echinops telfairi	ENSETEG00000015038	2 retrocopies	retro_etel_1223, retro_etel_1364,
Rattus norvegicus	ENSRNOG00000004612	2 retrocopies	retro_rnor_1455, retro_rnor_2344 ,
Ictidomys tridecemlineatus	ENSSTOG00000029081	2 retrocopies	retro_itri_1200, retro_itri_1618,