RetrogeneDB ID: retro_rnor_1358

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:61304163..61304577(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Txnl4a
• Ensembl ID: ENSRNOG00000017596
• Aliases: None
• Description: thioredoxin-like 4A [Source:MGI Symbol;Acc:MGI:1351613]

Sequence

>retro_rnor_1358
CTTCCACATCTGCATAATGGCTGACAGGTAGACCAGGCCATCCTTTCAGAAGAGGACTGAGTGGTCGTCATTCGCTTCGG
ACATGACTGGGATCACACTTGCTTGAAGATGGATGAGATTCTGTACAGCATCACCGAAAAGGTTAAAAATTTTGCAGTTA
TTTGTCTTGTGGATATTACAGAAGAAGTACCTGACTTCGACAAGATGTACGAGCTCTATGACCCATGCACGGTCATGTTC
TTCTTCAGAAACAAGTGCGTGATGATTGATTTGGGCACTGGTAACAATAACAAGATCAACTGGGCCATGGAAGACAAGCA
TGAAATGGTTGACATCATAGAGACCGTGTACCGTGGCGCCCGCAAAGGCTGAGGCCTGGTGGTGTCGCCCAAGAACTATT
CTACAAAGTACAGA

Alignment

ORF - retro_rnor_1358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.86 %
• Parental protein coverage: 96.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITE-VPDFNKMY
          LPHLHNG.QVDQAILSEED.VVVIRFGHDWD.TC.KMDE.LYSI.EKVKNFAVI.LVDITE.VPDF.KMY
Retrocopy LPHLHNG*QVDQAILSEED*VVVIRFGHDWDHTCLKMDEILYSITEKVKNFAVICLVDITEEVPDFDKMY

Parental  ELYDPCTVMFFFRNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVYRGARKGRGLVVSPKDYSTKYR
          ELYDPCTVMFFFRNK..MIDLGTGNNNKINWAMEDK.EMVDIIETVYRGARKG.GLVVSPK.YSTKYR
Retrocopy ELYDPCTVMFFFRNKCVMIDLGTGNNNKINWAMEDKHEMVDIIETVYRGARKG*GLVVSPKNYSTKYR

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	19.41 RPM
SRP017611_kidney	0.00 RPM	17.31 RPM
SRP017611_liver	0.00 RPM	9.95 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1358 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1358 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1358 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010130	2 retrocopies	retro_cjac_2805, retro_cjac_3659,
Homo sapiens	ENSG00000141759	2 retrocopies	retro_hsap_2185, retro_hsap_4900,
Gorilla gorilla	ENSGGOG00000005285	2 retrocopies	retro_ggor_1731, retro_ggor_3060,
Loxodonta africana	ENSLAFG00000003190	1 retrocopy	retro_lafr_198,
Myotis lucifugus	ENSMLUG00000009188	1 retrocopy	retro_mluc_562,
Macaca mulatta	ENSMMUG00000001613	2 retrocopies	retro_mmul_2636, retro_mmul_913,
Nomascus leucogenys	ENSNLEG00000008378	2 retrocopies	retro_nleu_1268, retro_nleu_314,
Otolemur garnettii	ENSOGAG00000034753	1 retrocopy	retro_ogar_1751,
Pan troglodytes	ENSPTRG00000010136	1 retrocopy	retro_ptro_1663,
Rattus norvegicus	ENSRNOG00000017596	2 retrocopies	retro_rnor_1358 , retro_rnor_2458,
Ictidomys tridecemlineatus	ENSSTOG00000022277	1 retrocopy	retro_itri_1063,
Tarsius syrichta	ENSTSYG00000009428	1 retrocopy	retro_tsyr_240,