RetrogeneDB ID: retro_rnor_2604

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:3537382..3538027(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Snrnp40
• Ensembl ID: ENSRNOG00000012219
• Aliases: Snrnp40, RGD1309198
• Description: U5 small nuclear ribonucleoprotein 40 kDa protein [Source:RefSeq peptide;Acc:NP_001128028]

Sequence

>retro_rnor_2604
AGAGTGAAAAGGCTAAGGGGGCATACTTCCTTTGTGAATTCCTGTTATCCAATTAGGCGGGGCCCCCAACTTGTCTGCAA
GGGCAGTGACGATAGCACCCTAAAGCTTTGAGACATCTGGAAGAAAGCAGCTATCCAGACGTTTTAGAACACATACCAGG
TGTTAGCTGTGACCTTCAATGACACGAGAGATCAGATTATCTCTGTTGGAATAGACAATGATATCAAGGTTTGGGACTTA
CGCCAAAACAAGTTAACCTATACCATAAGAGGCCCTGAAGACTCCGTAGCTCGCTTGAGTTTAAGTTCTGAAGGAATTTG
TCTCTTGTCCAATGCAATGGACAACACAATGTGTGTTTGGGACATCCGGCCATTTGCTCTCAAAGAGAGATGTGTGAAGA
TATTTCAAGGAAATGTTCACAACTTTGAAAAGAACCTCCTGAAGTGATCCTGGTCACCAGATGGAAGCAAGATATCAGCT
GGCTCAGCAGACAGGTTTGTGTATGTGTGGGACACCAGGAGCAGAAGGATTCTGTATAAGTTTCCTGGTCATGCTGGCTT
CATCAGTGAGGTGGCCTTTCATCCCAATGAGCCCATCATCCTCTCAGCATCCAGTGAAAAGAGGCTGTACATGGGCGAGA
CCCAG

Alignment

ORF - retro_rnor_2604 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.58 %
• Parental protein coverage: 60.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVKRLKGHTSFVNSCYPARRGPQLVCTGSDDGTVKLWDIRKKAAIQTFQNTYQVLAVTFNDTSDQIISGG
          RVKRL.GHTSFVNSCYP.RRGPQLVC.GSDD.T.KL.DI.KKAAIQTF.NTYQVLAVTFNDT.DQIIS.G
Retrocopy RVKRLRGHTSFVNSCYPIRRGPQLVCKGSDDSTLKL*DIWKKAAIQTF*NTYQVLAVTFNDTRDQIISVG

Parental  IDNDIKVWDLRQNKLTYTMRGHADSVTGLSLSSEGSYLLSNAMDNTVRVWDVRPFAPKERCVKIFQGNVH
          IDNDIKVWDLRQNKLTYT.RG..DSV..LSLSSEG..LLSNAMDNT..VWD.RPFA.KERCVKIFQGNVH
Retrocopy IDNDIKVWDLRQNKLTYTIRGPEDSVARLSLSSEGICLLSNAMDNTMCVWDIRPFALKERCVKIFQGNVH

Parental  NFEKNLLRCSWSPDGSKIAAGSADRFVYVWDTTSRRILYKLPGHAGSINEVAFHPDEPIILSASSDKRLY
          NFEKNLL..SWSPDGSKI.AGSADRFVYVWDT.SRRILYK.PGHAG.I.EVAFHP.EPIILSASS.KRLY
Retrocopy NFEKNLLK*SWSPDGSKISAGSADRFVYVWDTRSRRILYKFPGHAGFISEVAFHPNEPIILSASSEKRLY

Parental  MGEIQ
          MGE.Q
Retrocopy MGETQ

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	14.38 RPM
SRP017611_kidney	0.00 RPM	10.12 RPM
SRP017611_liver	0.00 RPM	7.93 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2604 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2604 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2604 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000000586	3 retrocopies	retro_mluc_2200, retro_mluc_2609, retro_mluc_318,
Macaca mulatta	ENSMMUG00000019406	1 retrocopy	retro_mmul_1461,
Rattus norvegicus	ENSRNOG00000008212	1 retrocopy	retro_rnor_258,
Rattus norvegicus	ENSRNOG00000012219	1 retrocopy	retro_rnor_2604 ,