RetrogeneDB ID: retro_rnor_838

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 11:77910921..77912199(-)
• Located in intron of: ENSRNOG00000001714

Retrocopy information

• Ensembl ID: ENSRNOG00000001713
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Il13ra1
• Ensembl ID: ENSRNOG00000013170
• Aliases: None
• Description: interleukin-13 receptor subunit alpha-1 precursor [Source:RefSeq peptide;Acc:NP_665732]

Sequence

>retro_rnor_838
ATGGCACGGCCAGCGTGGCTGGGCGAGCTGTTGGTGCTGCTGCTTTTTGCCGCCTCCCTGGACCAAGTTGCCCTGGCCAC
AGAAGTTCAGCCACCTGTAACGAATTTGAGTGTCTCTGTCGAAAATCTCTGCACAATAGTGTGGACATGGAGTCCTCCTG
AGGGAGCCAGTCCAAATTGCAGTCTCAGATATTTTAGTCATTTTGATGACCAACAGGATAAGAAAATTGCTCCTGAAACT
CGTCGTAAAAAGGAATTACCCCTAAATGAGAAAATCTGTCTGCAAGTGGGGTCCCAGTGTAGCACCAATGAAAGTGAGAA
GCCTAGCCCTTTGGTGAAAAAGTGCATCTCACCCCCCGAAGGGGATCCTGAGTCTGCTGTGACCGAACTGCAGTGCATTT
GGCACAACCTGAGCTATATGAAGTGTTCCTGGCTCCCTGGAAAGAATACAAGCCCGGACACCAACTATACTCTTTACTAT
TGGTACAGCAGCCTGGGGAAAAGTCTTCAATGTGAAAACATCCACAGAGAAGGTCAACACATTGGTTGTTCCTTTAAATT
GACTAAAGTGGAATCTAATTATGAACATCATAACATTCAGATAATGGTCAAGGATAATGCTGGGAAAATTAGGCCATCCT
ACAAAATAGTGTCCTTCACTTCCAATGTGAAACCCGGTCCTCCACATATTAAACATCTTTTCCTCAAAAATGGTGCCTTA
TTCGTGCAGTGGAAGAACCCACAGAATTTCAGTAGCAGATGTTTGTCTTATGAAGTAGAAGTCAATAGCACTCAAACTGA
CAGCTATAATTCTAACTCTTTAGAGGTTGAAGAGGACAAATGCCAGAATTCTGAATTTGATAGAAACATGGAGGGTGCAA
GTTGTTTCATATCTCCCGGTGTTCTTGCCAACACTGTCTACACAGTCAGAGTAAGAGTCAAAACAAACAAGTTATGCTTT
GATGACAACGACCTGTGGAGTAATTGGAGCGAAGCGCTGAGTATAGGTAAGGAGCCGAATTCCACCTTCTACACCACCAT
GTTACTCATCATTCCAGTCTTTGTCGCAGTGGTAATCATAATTCTCCTTTTTTACCTGAAAAGGCTTAAGATCATTATAT
TTCCTCCAATTCCTGATCCTGGCAAGATTTTTAAAGAAATGTTTGGAGACCAGAATGATGATACCCTGCACTGGAAAAAG
TATGACATCTATGAGAAACAATCGAAAGAAGAAACCGACTCTGTAGTGCTGATAGAAAACCTGAAGAAAGCGGCTCCA

Alignment

ORF - retro_rnor_838 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARPAWLGELLVLLLFAASLDQVALATEVQPPVTNLSVSVENLCTIVWTWSPPEGASPNCSLRYFSHFDD
          MARPAWLGELLVLLLFAASLDQVALATEVQPPVTNLSVSVENLCTIVWTWSPPEGASPNCSLRYFSHFDD
Retrocopy MARPAWLGELLVLLLFAASLDQVALATEVQPPVTNLSVSVENLCTIVWTWSPPEGASPNCSLRYFSHFDD

Parental  QQDKKIAPETRRKKELPLNEKICLQVGSQCSTNESEKPSPLVKKCISPPEGDPESAVTELQCIWHNLSYM
          QQDKKIAPETRRKKELPLNEKICLQVGSQCSTNESEKPSPLVKKCISPPEGDPESAVTELQCIWHNLSYM
Retrocopy QQDKKIAPETRRKKELPLNEKICLQVGSQCSTNESEKPSPLVKKCISPPEGDPESAVTELQCIWHNLSYM

Parental  KCSWLPGKNTSPDTNYTLYYWYSSLGKSLQCENIHREGQHIGCSFKLTKVESNYEHHNIQIMVKDNAGKI
          KCSWLPGKNTSPDTNYTLYYWYSSLGKSLQCENIHREGQHIGCSFKLTKVESNYEHHNIQIMVKDNAGKI
Retrocopy KCSWLPGKNTSPDTNYTLYYWYSSLGKSLQCENIHREGQHIGCSFKLTKVESNYEHHNIQIMVKDNAGKI

Parental  RPSYKIVSFTSNVKPGPPHIKHLFLKNGALFVQWKNPQNFSSRCLSYEVEVNSTQTDSYNSNSLEVEEDK
          RPSYKIVSFTSNVKPGPPHIKHLFLKNGALFVQWKNPQNFSSRCLSYEVEVNSTQTDSYNSNSLEVEEDK
Retrocopy RPSYKIVSFTSNVKPGPPHIKHLFLKNGALFVQWKNPQNFSSRCLSYEVEVNSTQTDSYNSNSLEVEEDK

Parental  CQNSEFDRNMEGASCFISPGVLANTVYTVRVRVKTNKLCFDDNDLWSNWSEALSIGKEPNSTFYTTMLLI
          CQNSEFDRNMEGASCFISPGVLANTVYTVRVRVKTNKLCFDDNDLWSNWSEALSIGKEPNSTFYTTMLLI
Retrocopy CQNSEFDRNMEGASCFISPGVLANTVYTVRVRVKTNKLCFDDNDLWSNWSEALSIGKEPNSTFYTTMLLI

Parental  IPVFVAVVIIILLFYLKRLKIIIFPPIPDPGKIFKEMFGDQNDDTLHWKKYDIYEKQSKEETDSVVLIEN
          IPVFVAVVIIILLFYLKRLKIIIFPPIPDPGKIFKEMFGDQNDDTLHWKKYDIYEKQSKEETDSVVLIEN
Retrocopy IPVFVAVVIIILLFYLKRLKIIIFPPIPDPGKIFKEMFGDQNDDTLHWKKYDIYEKQSKEETDSVVLIEN

Parental  LKKAAP
          LKKAAP
Retrocopy LKKAAP

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	0.14 RPM	0.50 RPM
SRP017611_kidney	0.07 RPM	4.54 RPM
SRP017611_liver	0.34 RPM	4.50 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_838 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_838 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_838 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011001	1 retrocopy	retro_dnov_1187,
Rattus norvegicus	ENSRNOG00000013170	1 retrocopy	retro_rnor_838 ,