RetrogeneDB ID: retro_rnor_512

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:192143318..192144620(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000020477
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Trnt1
• Ensembl ID: ENSRNOG00000006432
• Aliases: None
• Description: tRNA-nucleotidyltransferase 1, mitochondrial [Source:RefSeq peptide;Acc:NP_001019432]

Sequence

>retro_rnor_512
ATGCAGAGCCTCTTGTACCCTTGGCACAGGCAGGTCCTGAGCTGTAGTTGGAGTAGATTGTGCCTTCTAAAGCGATACCT
ATTTACAATGAAGTTGCAGTCTCCAGAATTCCAGTCACTTTTCACAGAAGGATTGAAGAGCCTGACAGAATTATTTGCCA
AAGAGAATCATGAATTAAGAATAGCAGGAGGGGCGGTGAGAGATTTACTAAATGGGGTGAAGCCTCAGGATGTGGATTTC
GCCACCACTGCCACCCCTACTGAGATGAAGGAGATGTTCCAGGCGGCTGGCATTCGCATGATAAACAACAAAGGCGAGAA
GCATGGGACCATCATTGCCAGGCTTCATGAAGAAAATTTTGAGGTTACTACACTCCGGATTGATGTTAGCACTGACGGAA
GACATGCGGAGGTAGAGTTCACAACTGACTGGCAGAAGGATGCCGAACGAAGAGACCTCACTATAAACTCCATGTTTCTA
GGTTTTGATGGTACACTGTTTGATTACTTTAATGGTTATGCAGATTTAAAGAATAAAAAGGTTCGATTTGTTGGACATGC
TAAGCAGAGAATTCAGGAAGATTATCTTCGAATTTTAAGGTATTTCAGATTTTATGGCAGAATTGTCGACAAACCTGGTG
ACCATGACCGTGAGACTCTAGAAGCAATTGCAGAAAATGCCAAAGGCTTGGCTGGAATATCAGGAGAGAGGATTTGGGTA
GAACTGAAGAAAATTCTTACTGGTGACCATGTAAACCATTTGATCCACCTGATCTATGATCTTGATGTGGCTTCTCACAT
AGGTTTACCTGCTAATGCAAATTTAGAAGAATTTAACAAAGTCAGTAAAAATGTTGAAGGCTTTTCACCGAAACCAATGA
CTGTTTTGGCCTCTTTATTCAAAGTACAAGATGATGTCACAAAACTGGATTTGAGATTGAAAATTTCAAAAGAGGAGAAA
AACCTGGGTTTATTTATAGTTAAAAACAGGAAAGATTTGATTAAAGCAACAGATAGTTCAGAACCATTGAAACCATATCA
AGACTTTGTTATAGATTCTAGGGAACCGGATGCAACTGCCCGTGTTTGTGAGCTGCTGAAGTACCAAGGAGAGCATGCTC
TTCTCAAGGAGATGCAGCAGTGGTCTGTGCCGCCATTCCCTGTGAGTGGACACGACATCAGGAAAGTGGGCATTTCTTCA
GGGAAGGAAATTGGGGCCCTGTTACAGCAGTTGCGTGAACAGTGGAAGAAAAGTGGTTACCAAATGGAAAAAGATGAACT
ACTAAATTACATAAAGAAGACA

Alignment

ORF - retro_rnor_512 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQSLLYPWHRQVLSCSWSRLCLLKRYLFTMKLQSPEFQSLFTEGLKSLTELFAKENHELRIAGGAVRDLL
          MQSLLYPWHRQVLSCSWSRLCLLKRYLFTMKLQSPEFQSLFTEGLKSLTELFAKENHELRIAGGAVRDLL
Retrocopy MQSLLYPWHRQVLSCSWSRLCLLKRYLFTMKLQSPEFQSLFTEGLKSLTELFAKENHELRIAGGAVRDLL

Parental  NGVKPQDVDFATTATPTEMKEMFQAAGIRMINNKGEKHGTITARLHEENFEVTTLRIDVSTDGRHAEVEF
          NGVKPQDVDFATTATPTEMKEMFQAAGIRMINNKGEKHGTI.ARLHEENFEVTTLRIDVSTDGRHAEVEF
Retrocopy NGVKPQDVDFATTATPTEMKEMFQAAGIRMINNKGEKHGTIIARLHEENFEVTTLRIDVSTDGRHAEVEF

Parental  -TDWQKDAERRDLTINSMFLGFDGTLFDYFNGYADLKNKKVRFVGHAKQRIQEDYLRILRYFRFYGRIVD
          .TDWQKDAERRDLTINSMFLGFDGTLFDYFNGYADLKNKKVRFVGHAKQRIQEDYLRILRYFRFYGRIVD
Retrocopy TTDWQKDAERRDLTINSMFLGFDGTLFDYFNGYADLKNKKVRFVGHAKQRIQEDYLRILRYFRFYGRIVD

Parental  KPGDHDRETLEAIAENAKGLAGISGERIWVELKKILTGDHVNHLIHLIYDLDVASHIGLPANANLEEFNK
          KPGDHDRETLEAIAENAKGLAGISGERIWVELKKILTGDHVNHLIHLIYDLDVASHIGLPANANLEEFNK
Retrocopy KPGDHDRETLEAIAENAKGLAGISGERIWVELKKILTGDHVNHLIHLIYDLDVASHIGLPANANLEEFNK

Parental  VSKNVEGFSPKPMTVLASLFKVQDDVTKLDLRLKISKEEKNLGLFIVKNRKDLIKATDSSEPLKPYQDFV
          VSKNVEGFSPKPMTVLASLFKVQDDVTKLDLRLKISKEEKNLGLFIVKNRKDLIKATDSSEPLKPYQDFV
Retrocopy VSKNVEGFSPKPMTVLASLFKVQDDVTKLDLRLKISKEEKNLGLFIVKNRKDLIKATDSSEPLKPYQDFV

Parental  IDSREPDATARVCELLKYQGEHALLKEMQQWSVPPFPVSGHDIRKVGISSGKEIGALLQQLREQWKKSGY
          IDSREPDATARVCELLKYQGEHALLKEMQQWSVPPFPVSGHDIRKVGISSGKEIGALLQQLREQWKKSGY
Retrocopy IDSREPDATARVCELLKYQGEHALLKEMQQWSVPPFPVSGHDIRKVGISSGKEIGALLQQLREQWKKSGY

Parental  QMEKDELLSYIKKT
          QMEKDELL.YIKKT
Retrocopy QMEKDELLNYIKKT

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	0.72 RPM	19.48 RPM
SRP017611_kidney	1.95 RPM	19.05 RPM
SRP017611_liver	0.87 RPM	10.22 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_512 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_512 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_512 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
Dipodomys ordii	ENSDORG00000014035	1 retrocopy	retro_dord_414,
Echinops telfairi	ENSETEG00000018177	2 retrocopies	retro_etel_1871, retro_etel_905,
Gorilla gorilla	ENSGGOG00000015286	1 retrocopy	retro_ggor_300,
Petromyzon marinus	ENSPMAG00000002236	1 retrocopy	retro_pmar_17,
Rattus norvegicus	ENSRNOG00000006432	1 retrocopy	retro_rnor_512 ,