RetrogeneDB ID: retro_rnor_1961

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:37444660..37446559(+)
• Located in intron of: None

Retrocopy information

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

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_1961
GTGGCACATTACAACTTCAAGAAGATTATGTTGGTGCCATCAGCCAAGGACTTTATTGACCTGGCATTATCCAAGACACA
ACATAAGACTCCAATGGTTATTCATAAACATTATCAAATTCATCGAATTCAACATTTTTATATGAGAAAAGTCAAATTTA
CTCAACAGAATTACCATGACAGACTGTTACAGATTCTGTCTGATTTCCCCAAATTGGATGATAGCCATCCATTTTATGCT
CTCTTGATGAATATTCTCTATTACAAGGATCACTACAAGTTGACTCTAGGTCAAATAAATACTGCCAAAAACTTGGTGGA
AAATGTTACCAAAGATTACATGCGATTTATGAAGTATGGTGATTCTCTTTACCGATGCAAACAGCTGAAACGCAGTGCCC
TGGGACGAATGTGTACAATTATCAAGAGGCAGAGGCAGAGTTTGGAGTACTTGGGACAAGTACGTCAACATTTATCCCTC
TTACCATCCATTGATCCAAATATGAGGAGACTGCTTTTGTGTGGGTATCCGAATGTTGGGAAATCCAGCTTCATCAATAA
GGTGACAAGAGCAGATATGGCTGTTCAGCCCTATGCATTTGCCACCAAGTCTCTGTTTGTCAGGCACATGGATTATAAGT
ATCTGCGCTGGCAGGCTGTAGATACCCCAGGGATTTTGGATCATCCTTTGGAGGATCGGAACACCATTGAAATGCAGGCC
ATCACAGCCCGGGCCCACCTCCGAGCTACAGTTCTGTATGTGATGGATTTGTCTGAGCAGTGTGGACATGGGTTGAAGGA
GCAATTAGAACTCTTCCAGAATATCAGACCTCTGTTTATCAACAAGCCTCTTATTGTTGTAGCAAACAAATGTGATGTGA
AGAGAATAGCTGAACTTTCTGAAGGAGATCAGAAAATATTTCTAGACTTGCAGGCTGAAGGATTTCCTGTCATCGAGACC
AGCACCTTGACTGAGGAAGGTGTCATTCACGTTAAAACAGAGGCTTGTCGTAGGCTTTTGGCTCATCTAGTAGAAAAGAA
AATGAAAGGAAATGAAGTGAATGAGGTTCTGAACAGATTGCACTTAGCTGTGCCCAACAAGAGAGATGAAAAGGAGAGAC
CCCCTTTCATCCCAGAAGGAGTGGTAGCTCGTCAGAAGAGAACGGAGATCTCAGAGCCCAAGAGGAAGAGGGAACAAGAT
CTTGAGCTGGAAATGGGAGATGATTAGATTTTGGATCTTCAGAAATACTGGGACTTAATGAATTTATCTGAGAAGTATGA
TAAGATACCAGAGATTTGGGAAGGCCACAATGTTGCTGATTATATCGAACCTGCTATCATGAAGAATTTAGAAGAGTTGG
AAAAGGAAGAAGAGATCAGAACAGCTGCAGGGGAGTATGACAGTGACTCTGAGAGTGAAGATGAGGAAATGATGGAAATC
CGACAGTTGGCGAAACAAATTAGAGAAAAGAAGATTTTGAAAATTCTACAGTCCAAAGAAAAGAACACACAGGGACCTAG
GATGCCCCGGACTGCTAAGAAGGTTCAATGGGCAGATTTAGAGAATGAGATGCATAGTTTTGGCATGGACATGGATGATA
AAGACAATGCCCACTATGCAGTCCAGGCCAGATCTCGGAGTGTCACCAGGAAAAGAAAATGAGAAGAATCTGCTCCTTCC
TCTTCCATAGCCTGCAGTCCAAGTTGCTCTAAAATGCCACATGATGTTTCTAGTCTTCAGGATGTTAAGACGGTGAAGAA
AGCCAAGACTATGATGAAGAAAATGCAGAAGAAGATGAATTGCTTGGGGAAGAAGGGGGAAGCAGATATACATGTGTTTT
ATATGAAGCCCAAGCACCTACTCTCTGGGAAGAGGAAAGCTGGTAAAAAGGACAGGAGA

Alignment

ORF - retro_rnor_1961 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAHYNFKKITVVPSAKDFIDLTLSKTQRKTPTVIHKHYQIHRIRHFYMRKVKFTQQNYHDRLSQILSDFP
          .AHYNFKKI..VPSAKDFIDL.LSKTQ.KTP.VIHKHYQIHRI.HFYMRKVKFTQQNYHDRL.QILSDFP
Retrocopy VAHYNFKKIMLVPSAKDFIDLALSKTQHKTPMVIHKHYQIHRIQHFYMRKVKFTQQNYHDRLLQILSDFP

Parental  KLDDIHPFYADLMNILYDKDHYKLALGQINIAKNLVDNVAKDYVRLMKYGDSLYRCKQLKRAALGRMCTI
          KLDD.HPFYA.LMNILY.KDHYKL.LGQIN.AKNLV.NV.KDY.R.MKYGDSLYRCKQLKR.ALGRMCTI
Retrocopy KLDDSHPFYALLMNILYYKDHYKLTLGQINTAKNLVENVTKDYMRFMKYGDSLYRCKQLKRSALGRMCTI

Parental  IKRQRQSLEYLEQVRQHLSRLPTIDPNTRTLLLCGYPNVGKSSFINKVTRADVDVQPYAFTTKSLFVGHM
          IKRQRQSLEYL.QVRQHLS.LP.IDPN.R.LLLCGYPNVGKSSFINKVTRAD..VQPYAF.TKSLFV.HM
Retrocopy IKRQRQSLEYLGQVRQHLSLLPSIDPNMRRLLLCGYPNVGKSSFINKVTRADMAVQPYAFATKSLFVRHM

Parental  DYKYLRWQVVDTPGISDHPLEDRNTIEMQAITALAQPRAAVLYVMDLSEQCGHGLKEQLELFQNIRPLFI
          DYKYLRWQ.VDTPGI.DHPLEDRNTIEMQAITA.A..RA.VLYVMDLSEQCGHGLKEQLELFQNIRPLFI
Retrocopy DYKYLRWQAVDTPGILDHPLEDRNTIEMQAITARAHLRATVLYVMDLSEQCGHGLKEQLELFQNIRPLFI

Parental  NKPLIVVANKCDVKRIAELSEEDQKIFLDLQAEGFPVIETSTLTEEGVIQVKTEACDRLLAHRVETKMKG
          NKPLIVVANKCDVKRIAELSE.DQKIFLDLQAEGFPVIETSTLTEEGVI.VKTEAC.RLLAH.VE.KMKG
Retrocopy NKPLIVVANKCDVKRIAELSEGDQKIFLDLQAEGFPVIETSTLTEEGVIHVKTEACRRLLAHLVEKKMKG

Parental  NKVNEVLNRLHLAVPNKRDDKERPPFIPEGVVARRKRMEIAEPKKKRERDLELEMGDDYILDLQKYWDLM
          N.VNEVLNRLHLAVPNKRD.KERPPFIPEGVVAR.KR.EI.EPK.KRE.DLELEMGDD.ILDLQKYWDLM
Retrocopy NEVNEVLNRLHLAVPNKRDEKERPPFIPEGVVARQKRTEISEPKRKREQDLELEMGDD*ILDLQKYWDLM

Parental  NSSEKYDKIPEIWEGHNVADYIDPAIMKKLEELEKEEELRTAAGEYDSESESEDEEMVEIRQLAKQIREK
          N.SEKYDKIPEIWEGHNVADYI.PAIMK.LEELEKEEE.RTAAGEYDS.SESEDEEM.EIRQLAKQIREK
Retrocopy NLSEKYDKIPEIWEGHNVADYIEPAIMKNLEELEKEEEIRTAAGEYDSDSESEDEEMMEIRQLAKQIREK

Parental  KKLKILQSKEKNTQGPRMPRTAKKVQRADLENEMRSLGVDMDDKDNAHYAVQARRSRSVTRKRKREESVP
          K.LKILQSKEKNTQGPRMPRTAKKVQ.ADLENEM.S.G.DMDDKDNAHYAVQA.RSRSVTRKRK.EES.P
Retrocopy KILKILQSKEKNTQGPRMPRTAKKVQWADLENEMHSFGMDMDDKDNAHYAVQA-RSRSVTRKRK*EESAP

Parental  PSSIARSRSRSCSKTPRDVSGLRDVKMVKKAKTMMKKAQKKMNRLGKKGEADRHVFDMKPKHLLSGKRKA
          .SSIA...S.SCSK.P.DVS.L.DVK.VKKAKTMMKK.QKKMN.LGKKGEAD.HVF.MKPKHLLSGKRKA
Retrocopy SSSIA--CSPSCSKMPHDVSSLQDVKTVKKAKTMMKKMQKKMNCLGKKGEADIHVFYMKPKHLLSGKRKA

Parental  GKKDRR
          GKKDRR
Retrocopy GKKDRR

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	9.85 RPM
SRP017611_kidney	0.28 RPM	32.94 RPM
SRP017611_liver	0.07 RPM	5.72 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1961 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1961 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1961 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,