RetrogeneDB ID: retro_rnor_1524

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:120875212..120875617(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tpm3
• Ensembl ID: ENSRNOG00000017441
• Aliases: Tpm3, TM30nm, Tpm5
• Description: Tropomyosin alpha-3 chain [Source:UniProtKB/Swiss-Prot;Acc:Q63610]

Sequence

>retro_rnor_1524
GGGAGCACCACCATCCAGGAGGTAAAGTGCAAGATCAGGTTCTGCAGCAGCAGACTGAGATGCAGAGGAGAGGGCCGAGA
ACCTCCATCAGGAAGTAGAGGGAGAAAGGAGGGAGAAAGGCAGGCCCAGGAGCAGGTTGAAGCTGAGGTAGGCTCCTTGA
CCTGCAGGATCTAGCTGGTTGAAGAGGAGCTGGACCACACCCAAGAGTCCCTTGCCACTGTTTTACAGAAGCTGGAGGAA
GCAGAAACCTCTGCTGATGAGAGTGAGAGAGGCATGAAGGTGATCAAAAACCGGGTTCTACAAGATGAAGAAAAGATGGA
ACTCTGGGAAATCCAGCTAAAAGAAGCAAAGCACACTGTAGAAGAGGCAGACAGGAAGTAGGAAGAGGTGGCTCATAAGT
TGGTG

Alignment

ORF - retro_rnor_1524 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.94 %
• Parental protein coverage: 53.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GSTTIEAVKRKI-QVLQQQAD-DAEERAERLQREVEGERRAR-EQAEAEV----ASLNRRIQLVEEELDR
          GSTTI..VK.KI.QVLQQQ...DAEERAE.L..EVEGERR....QA...V.....SL..RI.LVEEELD.
Retrocopy GSTTIQEVKCKI<QVLQQQTE<DAEERAENLHQEVEGERREK<RQAQEQVEAEVGSLTCRI*LVEEELDH

Parental  AQERLATALQKLEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLV
          .QE.LAT.LQKLEEAE..ADESERGMKVI.NR.L.DEEKMEL.EIQLKEAKH..EEADRK.EEVA.KLV
Retrocopy TQESLATVLQKLEEAETSADESERGMKVIKNRVLQDEEKMELWEIQLKEAKHTVEEADRK*EEVAHKLV

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	108.28 RPM
SRP017611_kidney	0.00 RPM	113.47 RPM
SRP017611_liver	0.00 RPM	46.73 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1524 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1524 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1524 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009747	9 retrocopies	retro_cjac_1232, retro_cjac_1509, retro_cjac_1580, retro_cjac_1910, retro_cjac_2476, retro_cjac_3121, retro_cjac_527, retro_cjac_785, retro_cjac_798,
Gorilla gorilla	ENSGGOG00000012668	3 retrocopies	retro_ggor_1239, retro_ggor_1817, retro_ggor_2621,
Nomascus leucogenys	ENSNLEG00000010990	8 retrocopies	retro_nleu_1133, retro_nleu_2050, retro_nleu_2119, retro_nleu_2141, retro_nleu_2387, retro_nleu_2523, retro_nleu_921, retro_nleu_922,
Pongo abelii	ENSPPYG00000000787	2 retrocopies	retro_pabe_1230, retro_pabe_3263,
Rattus norvegicus	ENSRNOG00000016731	1 retrocopy	retro_rnor_1520,
Rattus norvegicus	ENSRNOG00000017441	1 retrocopy	retro_rnor_1524 ,
Rattus norvegicus	ENSRNOG00000018184	1 retrocopy	retro_rnor_734,
Sus scrofa	ENSSSCG00000006556	3 retrocopies	retro_sscr_318, retro_sscr_604, retro_sscr_781,
Ictidomys tridecemlineatus	ENSSTOG00000023525	6 retrocopies	retro_itri_1453, retro_itri_1558, retro_itri_1837, retro_itri_231, retro_itri_674, retro_itri_709,