RetrogeneDB ID: retro_rnor_1455

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 19:40279132..40280108(-)
• 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_1455
ATGGCTGAAGGGGAGCTGAACGTGGACAGTTTCACCACCCACCTGCTGGAGGTACGAGGATATCATCCGGGAAAAATTGT
GCAGATGACTGAAGCAGAAGTCCCAGGACTGTGTATCACGTCTCGTGAAATCTTTCTTAGCCAGCCTATTCTTGGAATTG
GAAGCATCACTGAAGATTTGTGGAGATATTCATGGACAGTATTCAGACTTACTGAGATTATTTGAATATGGAGGTTTTCC
ACCAGAAGCAAACTATCTTTTTGTGGAGATTATATGGACAGAGGAAAGCAGTCTTTGGAAACCATCTGTTTGCCATTGGC
TTACAAAATCAAATACCCGGAGAACTTCTTTCTTCTATGAGGAACCATGAGTGTGCTAGCATCAACGGCATTTATGGATT
CTATGATGAGTGCAAATGAAGATTTAATATTAAATTGTGGAGGACATTCACTATTGTTTTAACTGTCTGCCTATAACTGC
TATTGTTGATGAGAAAATCCTCTGTTGTCGTGGAGGACTGTCACCAGACCCACAGTCTGTGGAACAGATTCGGAGAATTA
TGAGACCCACTGGTGTACCTGATACAGGTTTGCAGTGTGATTTACTGTGCTCCGACCCAGATAAGGATGTACAAGGCTGG
GGAGAAAATGACCGTGGTGTTTCTTTTACTTTTGGAGCTGATGTAGTTAGTAAGTTTCTGAATCGTCATGATTTAGACTT
GATTTGTCGAGCCCATCAGGTGGTAGAAGACGGATAGGAATTTTTTGCTAAAAGACAATTCGTAACTTTATTTTCTGCCC
CAAATTCCTGTGGCGACTTTGACAATGCTGGTGGTATGATGAGTGTGGATGAAACTTTGATGTGTTCATTCCAGATATTG
AAACCATCTGAAAAGAAAGCTAAGTACCAGGATGGTGGGCTGGATTCTGGACGTCCTGTCACTCTACCTCGAACAGCTAA
ACCACCGAAGAAAAGG

Alignment

ORF - retro_rnor_1455 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.01 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MADGELNVDSLITRLLEVRGCRPGKIVQMTEAEVRGLCIKSREI-FLSQPILLELEAPLKICGDIHGQYT
          MA.GELNVDS..T.LLEVRG..PGKIVQMTEAEV.GLCI.SREI.FL.....LELEA.LKICGDIHGQY.
Retrocopy MAEGELNVDSFTTHLLEVRGYHPGKIVQMTEAEVPGLCITSREI>FLAS-LFLELEASLKICGDIHGQYS

Parental  DLLRLFEYGGFPPEANYLFL-GDYVDRGKQSLETICLLLAYKIKYPENFFLLRG-NHECASINRIYGFYD
          DLLRLFEYGGFPPEANYLF..GDY.DRGKQSLETICL.LAYKIKYPENFFLL.G.NHECASIN.IYGFYD
Retrocopy DLLRLFEYGGFPPEANYLFV<GDYMDRGKQSLETICLPLAYKIKYPENFFLL*G<NHECASINGIYGFYD

Parental  ECKRRFNIKLWKTFTD-CFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDTGLLCDLLWS
          ECK.RFNIKLW.TFT..CFNCLPI.AIVDEKI.CC.GGLSPD.QS.EQIRRIMRPT.VPDTGL.CDLL.S
Retrocopy ECK*RFNIKLWRTFTI<CFNCLPITAIVDEKILCCRGGLSPDPQSVEQIRRIMRPTGVPDTGLQCDLLCS

Parental  DPDKDVQGWGENDRGVSFTFGADVVSKFLNRHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFD
          DPDKDVQGWGENDRGVSFTFGADVVSKFLNRHDLDLICRAHQVVEDG.EFFAKRQ.VTLFSAPN.CG.FD
Retrocopy DPDKDVQGWGENDRGVSFTFGADVVSKFLNRHDLDLICRAHQVVEDG*EFFAKRQFVTLFSAPNSCGDFD

Parental  NAGGMMSVDETLMCSFQILKPSEKKAKYQYGGLNSGRPVTPPRTANPPKKR
          NAGGMMSVDETLMCSFQILKPSEKKAKYQ.GGL.SGRPVT.PRTA.PPKKR
Retrocopy NAGGMMSVDETLMCSFQILKPSEKKAKYQDGGLDSGRPVTLPRTAKPPKKR

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	0.79 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_1455 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1455 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1455 has 0 orthologous retrocopies within eutheria group .

---

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,