RetrogeneDB ID: retro_rnor_2882

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:2409628..2411526(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000009609
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Gtpbp4
• Ensembl ID: ENSRNOG00000016217
• Aliases: None
• Description: nucleolar GTP-binding protein 1 [Source:RefSeq peptide;Acc:NP_446141]

Sequence

>retro_rnor_2882
ATGGCGCATTACAACTTCAAGAAGATTACGGTGGTGCCGTCAGCCAAGGACTTTATTGACCTGACATTATCCAAGACACA
ACGAAAGACTCCAACGGTTATTCATAAACATTATCGAATTCGACATTTTTATATGAGAAAAGTCAAATTTACTCAACAGA
ATTATCATGACAGACTGTCACAGATTCTGTCCGATTTCCCCAAATTGGATGATATCCATCCATTTTATGCTGACTTGATG
AATATTCTCTATGACAAGGATCACTACAAGTTGGCTCTAGGACAAATAAATATTGCCAAAAACTTGGTGGACAATGTTGC
TAAAGATTACGTGCGACTTATGAAGTATGGTGATTCTCTCTACCGATGCAAGCAGCTGAAGTGCGCTGCCCTGGGGCGAA
TGTGTACGATTATCAAGAGCAGAGGCAGAGTTTGGAGTACTTGGAACAAGTACGTCAACATCTATCCCGCTTGCCAACCA
TTGATCCAAATACAAGGACTCTACTTTTGTGTGGGTATCCAAATGTTGGGAAATCCAGCTTCATCAATAAGGTGACAAGA
GCAGATGTGGATGTTCAGCCCTATGCATTTACCACCAAGTCTCTGTTTGTCGGGCACATGGATTATAAGTATCTGCGCTG
GCAGGTTGTAGATACCCCAGGGATTTTGGATCATCCTTTGGAAGATCGGAACACCATTGAGATGCAGGCCATCACAGCCC
TGGCCCACCTCCGAGCTGCAGTTCTGTATGTGATGGATTTGTCTGAGCAGTGTGGACATGGGTTGAAGGAGCAATTAGAA
CTCTTCCAGAATATCAGACCCCTGTTTATCAACAAGCCTCTTATTGTTGTAGCAAACAAATGTGATGTGAAGAGAATAGC
TGAACTTTCTGAAGAAGATCAGAAAATATTTCTAGACTTGCAGGCTGAAGGATTTCCTGTCATCGAGACCAGCACCCTGA
CTGAGGAAGGTGTCATTCAAGTTAAAACGGAGGCTTGTGATAGGCTTTTGGCTCACCGAGTAGAAACGAAAATGAAAGGA
AATAAAGTGAATGAGGTTCTGAACAGATTGCACTTAGCTGTGCCCAACAAGAGAGATGACAAGGAGAGACCCCCTTTCAT
CCCAGAAGGAGTGGTAGCTCGTCGGAAGAGAATGGAGATCGCAGAACCCAAGAAGAAGAGGGAACGAGATCTTGAGCTGG
AAATGGGAGATGATTATATTTTGGATCTTCAGAAATACTGGGACTTAATGAATTCATCTGAGAAGTATGATAAGATACCA
GAGATTTGGGAAGGCCACAATGTTGCTGATTATATCGATCCTGCTATCATGAAGAAATTAGAAGAGTTGGAAAAGGAAGA
AGAGCTCAGAACAGCTGCTGGGGAGTATGACAGTGAGTCTGAGAGTGAAGACGAGGAAATGGTGGAAATCCGACAGCTGG
CAAAACAAATTAGAGAGAAGAAGAAGTTGAAAATTCTACAGTCCAAAGAAAAGAACACACAGGGACCCCGGATGCCCCGG
ACTGCTAAGAAGGTTCAACGGGCAGATTTAGAGAATGAGATGCGTAGTCTTGGCGTGGACATGGATGATAAAGACAATGC
CCACTATGCAGTCCAGGCCAGAAGATCTCGGAGTGTCACCAGGAAAAGAAAACGAGAAGAGTCTGTTCCTCCCTCTTCCA
TAGCCCGCAGTCGCAGTCGGAGTTGCTCTAAAACGCCACGTGATGTTTCTGGTCTTCGGGATGTCAAGATGGTGAAGAAA
GCCAAGACCATGATGAAGAAAGCCCAGAAGAAGATGAATCGCTTGGGGAAGAAGGGGGAAGCAGATAGGCATGTGTTTGA
TATGAAGCCCAAGCACCTACTCTCTGGGAAGAGGAAAGCTGGTAAAAAGGACAGGAGA

Alignment

ORF - retro_rnor_2882 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAHYNFKKITVVPSAKDFIDLTLSKTQRKTPTVIHKHYQIHRIRHFYMRKVKFTQQNYHDRLSQILSDFP
          MAHYNFKKITVVPSAKDFIDLTLSKTQRKTPTVIHKHY...RIRHFYMRKVKFTQQNYHDRLSQILSDFP
Retrocopy MAHYNFKKITVVPSAKDFIDLTLSKTQRKTPTVIHKHY---RIRHFYMRKVKFTQQNYHDRLSQILSDFP

Parental  KLDDIHPFYADLMNILYDKDHYKLALGQINIAKNLVDNVAKDYVRLMKYGDSLYRCKQLKRAALGRMCTI
          KLDDIHPFYADLMNILYDKDHYKLALGQINIAKNLVDNVAKDYVRLMKYGDSLYRCKQLK.AALGRMCTI
Retrocopy KLDDIHPFYADLMNILYDKDHYKLALGQINIAKNLVDNVAKDYVRLMKYGDSLYRCKQLKCAALGRMCTI

Parental  IK-RQRQSLEYLEQVRQHLSRLPTIDPNTRTLLLCGYPNVGKSSFINKVTRADVDVQPYAFTTKSLFVGH
          IK..QRQSLEYLEQVRQHLSRLPTIDPNTRTLLLCGYPNVGKSSFINKVTRADVDVQPYAFTTKSLFVGH
Retrocopy IK<EQRQSLEYLEQVRQHLSRLPTIDPNTRTLLLCGYPNVGKSSFINKVTRADVDVQPYAFTTKSLFVGH

Parental  MDYKYLRWQVVDTPGISDHPLEDRNTIEMQAITALAQPRAAVLYVMDLSEQCGHGLKEQLELFQNIRPLF
          MDYKYLRWQVVDTPGI.DHPLEDRNTIEMQAITALA..RAAVLYVMDLSEQCGHGLKEQLELFQNIRPLF
Retrocopy MDYKYLRWQVVDTPGILDHPLEDRNTIEMQAITALAHLRAAVLYVMDLSEQCGHGLKEQLELFQNIRPLF

Parental  INKPLIVVANKCDVKRIAELSEEDQKIFLDLQAEGFPVIETSTLTEEGVIQVKTEACDRLLAHRVETKMK
          INKPLIVVANKCDVKRIAELSEEDQKIFLDLQAEGFPVIETSTLTEEGVIQVKTEACDRLLAHRVETKMK
Retrocopy INKPLIVVANKCDVKRIAELSEEDQKIFLDLQAEGFPVIETSTLTEEGVIQVKTEACDRLLAHRVETKMK

Parental  GNKVNEVLNRLHLAVPNKRDDKERPPFIPEGVVARRKRMEIAEPKKKRERDLELEMGDDYILDLQKYWDL
          GNKVNEVLNRLHLAVPNKRDDKERPPFIPEGVVARRKRMEIAEPKKKRERDLELEMGDDYILDLQKYWDL
Retrocopy GNKVNEVLNRLHLAVPNKRDDKERPPFIPEGVVARRKRMEIAEPKKKRERDLELEMGDDYILDLQKYWDL

Parental  MNSSEKYDKIPEIWEGHNVADYIDPAIMKKLEELEKEEELRTAAGEYDSESESEDEEMVEIRQLAKQIRE
          MNSSEKYDKIPEIWEGHNVADYIDPAIMKKLEELEKEEELRTAAGEYDSESESEDEEMVEIRQLAKQIRE
Retrocopy MNSSEKYDKIPEIWEGHNVADYIDPAIMKKLEELEKEEELRTAAGEYDSESESEDEEMVEIRQLAKQIRE

Parental  KKKLKILQSKEKNTQGPRMPRTAKKVQRADLENEMRSLGVDMDDKDNAHYAVQARRSRSVTRKRKREESV
          KKKLKILQSKEKNTQGPRMPRTAKKVQRADLENEMRSLGVDMDDKDNAHYAVQARRSRSVTRKRKREESV
Retrocopy KKKLKILQSKEKNTQGPRMPRTAKKVQRADLENEMRSLGVDMDDKDNAHYAVQARRSRSVTRKRKREESV

Parental  PPSSIARSRSRSCSKTPRDVSGLRDVKMVKKAKTMMKKAQKKMNRLGKKGEADRHVFDMKPKHLLSGKRK
          PPSSIARSRSRSCSKTPRDVSGLRDV..................RLGKKGEADRHVFDMKPKHLLSGKRK
Retrocopy PPSSIARSRSRSCSKTPRDVSGLRDVXXXXXXXXXXXXXXXXXXRLGKKGEADRHVFDMKPKHLLSGKRK

Parental  AGKKDRR
          AGKKDRR
Retrocopy AGKKDRR

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	2.88 RPM	9.85 RPM
SRP017611_kidney	5.58 RPM	32.94 RPM
SRP017611_liver	2.89 RPM	5.72 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2882 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2882 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2882 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008494	2 retrocopies	retro_cjac_2592, retro_cjac_992,
Cavia porcellus	ENSCPOG00000013736	1 retrocopy	retro_cpor_996,
Rattus norvegicus	ENSRNOG00000016217	2 retrocopies	retro_rnor_1961, retro_rnor_2882 ,
Sarcophilus harrisii	ENSSHAG00000014713	1 retrocopy	retro_shar_654,
Ictidomys tridecemlineatus	ENSSTOG00000010042	1 retrocopy	retro_itri_1466,