RetrogeneDB ID: retro_rnor_1520

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:114939861..114940656(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tpm2
• Ensembl ID: ENSRNOG00000016731
• Aliases: None
• Description: Tropomyosin beta chain [Source:UniProtKB/Swiss-Prot;Acc:P58775]

Sequence

>retro_rnor_1520
CAGATGCTGAAACTAGACAAGGAGAGTAGCATCAACCACACGGAGCAGGTCGACGCTGACAAGAAGCAAGCTGAAGACTG
AAGCAAGCAGCTGGAGGAAGAGCAGCCGGGCCTCCAGAAGAAGCTGAAGGGGACAGGGGATGAGGTAGAAAAGTACTCCT
GAGTCTGTGACGGATGCCCAGGAGAAACTGGAGCAGGCCAAGAAGAAGGCCACCGACGCTGAAGTAATGTGGCTTCTCTG
AACCGCCGCATTCAGCTCATAGAGGAGGAGTTGAATCGGGCACAGGAGCACCTGACTCTCAGCCTTGCAAAAGCTGGAGG
AGGCTGAGAAAGCCGCTGATGAGAGCAAGAGAGGAATGAAGATCATTGAAAACCGGGCCATGAAGGACGAGGAAAAGATG
AAGCAGCAAGAGATGCGGCTGAAGGAAGCCAAGCACATCACTGAGAACTCAGACGCAAATATGAGGAGGTGGCCAGGAAG
CTGGTGATCCTGGAAGGAGAGCTGGAGCGCTCTGAAGAGAGAGCCGAGGTGGCTGAGAGCAGAACCAGGCAGCTGGAGGA
GGAGCTTCGAACCGTGGACCAATCCCTCAAGTCGCCCATAGTCTCGATAGTCTCGGAGGAGGAGGATTCCACCAAAGAGG
ACAAATTTGAAGAAGAGATCAAACTTCCGGAGGAGAAGCTGAAGGAGGCTGAGACCCGAGCAGAGTTTGCTGAAAGATCT
GTGGCAAAGTTGGAGAAAACCATTGATGACCTGGAAAAGACTTTGGCTAGTGCCAAGGAAGAGAACGTGGAGATT

Alignment

ORF - retro_rnor_1520 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.64 %
• Parental protein coverage: 92.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QMLKLDKENAIDRAEQAEADKKQAEDRCKQLEEEQQALQKKLKGTEDEVEKYS-ESVKDAQEKLEQAEKK
          QMLKLDKE..I...EQ..ADKKQAED..KQLEEEQ..LQKKLKGT.DEVEKYS.ESV.DAQEKLEQA.KK
Retrocopy QMLKLDKESSINHTEQVDADKKQAED*SKQLEEEQPGLQKKLKGTGDEVEKYS>ESVTDAQEKLEQAKKK

Parental  ATDAE-ADVASLNRRIQLVEEELDRAQERLA-TALQKLEEAEKAADESERGMKVIENRAMKDEEKMELQE
          ATDAE...VASLNRRIQL.EEEL.RAQE.L...ALQKLEEAEKAADES.RGMK.IENRAMKDEEKM..QE
Retrocopy ATDAE<SNVASLNRRIQLIEEELNRAQEHLT>SALQKLEEAEKAADESKRGMKIIENRAMKDEEKMKQQE

Parental  MQLKEAKHIAEDSD-RKYEEVARKLVILEGELERSEERAEVAESRARQLEEELRTMDQALKS---LIASE
          M.LKEAKHI.E.SD.RKYEEVARKLVILEGELERSEERAEVAESR.RQLEEELRT.DQ.LKS....I.SE
Retrocopy MRLKEAKHITENSD<RKYEEVARKLVILEGELERSEERAEVAESRTRQLEEELRTVDQSLKSPIVSIVSE

Parental  EEYSTKEDKYEEEIKLLEEKLKEAETRAEFAERSVAKLEKTIDDLEETLASAKEENVEI
          EE.STKEDK.EEEIKL.EEKLKEAETRAEFAERSVAKLEKTIDDLE.TLASAKEENVEI
Retrocopy EEDSTKEDKFEEEIKLPEEKLKEAETRAEFAERSVAKLEKTIDDLEKTLASAKEENVEI

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	10.86 RPM
SRP017611_kidney	0.07 RPM	14.86 RPM
SRP017611_liver	0.00 RPM	3.09 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1520 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1520 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1520 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009627	2 retrocopies	retro_cjac_1839, retro_cjac_1894,
Otolemur garnettii	ENSOGAG00000011793	1 retrocopy	retro_ogar_988,
Rattus norvegicus	ENSRNOG00000016731	1 retrocopy	retro_rnor_1520 ,
Rattus norvegicus	ENSRNOG00000017441	1 retrocopy	retro_rnor_1524,
Rattus norvegicus	ENSRNOG00000018184	1 retrocopy	retro_rnor_734,