RetrogeneDB ID: retro_cjac_2592

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:11146679..11148578(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTPBP4
• Ensembl ID: ENSCJAG00000008494
• Aliases: None
• Description: nucleolar GTP-binding protein 1 [Source:RefSeq peptide;Acc:NP_001240708]

Sequence

>retro_cjac_2592
ATGGCACACTACAACTTCAAGAAAATTACGGTGGTGCCGTCTGCCAAGGACTTTATTGACTTGAAGTTGTCAAAGACTCA
ACAGAAGACTCCAGCTGTTACTCATAAACATTGCCAAATTCATCGCATTGGACATTTTTACATGAGAAAAGTCAAATTTG
CTCAACAGAATTACCATGATAGACTTTCGCAAATTCTAACAGATTTCCCTAAGTTGGATGACATTCATCTGTTCTATGCT
GATTTGATGAATATTCTCTACAACAAGATCACTACAATTTGGCTCTGGGGCAAATAAATGTTGCCAAAAATTTAGTGGAC
AATGTTGCTAAAGATGACTTTGGCTGATGAAGTACAGCGACCCCCGACTCCCTCTACGCAAGCAGCTGAAGTGTGCAGCC
CCAGGGCGGATGTGCACCATGATCAAGAGGCAGAAGCAGAGTTTGGAGTATTTGGAGCAAGTGCATCAGCATTTATCCCC
TTTGCCACAACCATTGATCCAAATACCAGGACTCTGCTTTTGGGTGGGTATCCAAATGTTGGGAAGTCCAGCTTCATCAA
TAAGGTGACAAGAGCAGATGTGGATGTCTGACCCTCTGCGTTCATAATCAAGTCTCTGTTTGTTGGGCACATGGATTCTA
ACTGTCTACACTGGCAGACTGTAGATGCTCCTGGGATCCTGGACCATCCTCTGGAGGACAGGAACACCATTGCGATGCAG
ATCACTGCCCTTGCCCATCTCCGTGCTGCAGTCCCGTACGTGATGGATTTGTCTGAGCAGTGTAGGCACGGGCTGAGGGA
GCAGCTAGAACTCTTCCAGAACATCAGACCTCTCCTCATCAACAAGACTCTTATAGTTGTAGCCAACAAGTGTGATGTGA
AAAGAATAGCCAAACTTTCTGAAGACGATCAGAAAATATTTACAGATTTGCAGGCTGAAGGATTCCCTGTAATAAAGACC
AGAATCCTGACTGAGGAAGGTGTTATTAAAGTTAAAACAAAGGCTTGCGATAGACTTTTGGCTCATCGAGTGGAAACCAA
AATGAAGGGAAATAAAGTGAATGAAGCGCTGAATAGACTGCACCTGGCTGTCCCAACCAGGAGGAACGATAAGCAGAGGC
CCCCTTTGATCCCCGAAGGAGTGGTGGCACGCAGAAAGAGGATGGAAATGGAGGAGCCCAAGAAGAAGAGGAAATGAGAT
CTTGAGCTGGAAATTGGAGGTGATTAAATTTTGGGTCTTCAGAAGTACTGGGATTTAATGAATTCGTCTGAAAAACATGA
TAAGATACCAGAAATCTGGGAAGGCCATAATATAGCTGATTATATTGATCCAGCCATCATGAAGAAATGGGAAGAATTAG
AAAAAGGAGAAGGACTGAGAACAGCTGCCAGAGAGTATGACAGTGACTCAGAGTGAAGATGAGGAGATGCTGGAAATCTG
ACAGCAGGCAAAGCAGATTAGAGAGAAAAAGAAGTTGAAAATTCTGGAGTCCAAAGAAAAGAATACACAGGGACCCAGGA
TGCCTCGAACTGCTAAGAAGCTTCAGAGAACAGTTTTGGAGAATGAGTCACGTAGTCTTGGTGTTGACATTGACAATAAA
GACAACGCCCACTACGCAGTCCAGGCAAGACGATCCCGGAGCGTCACTAGGAAAAGAAAGGGGAAGACTCTGCTCCCGCC
TCCTCTGTGGCCCAGAGTTGGAGTTGCCCTCGAACTCCAAGTGAGGTTTCTGGTCTTTGGGATGTCAAGATGGTGGAGAA
AGCCAAGACTATGATGAAGAATGCTCAGAAGAAGATGAATCGATTAGGGAAGAAAGGGGAGGCGGATGGACATGTGTTTG
ATATGAAGCCCAAGCACTTACTCTCCAGAGAGAGGAAAGCTGGCAGAAAGGACAGGAGA

Alignment

ORF - retro_cjac_2592 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MAHYNFKKITVVPSAKDFIDLTLSKTQRKTPTVIHKHYQIHRIRHFYMRKVKFTQQNYHDRLSQILTDFP
          MAHYNFKKITVVPSAKDFIDL.LSKTQ.KTP.V.HKH.QIHRI.HFYMRKVKF.QQNYHDRLSQILTDFP
Retrocopy MAHYNFKKITVVPSAKDFIDLKLSKTQQKTPAVTHKHCQIHRIGHFYMRKVKFAQQNYHDRLSQILTDFP

Parental  KLDDIHPFYADLMNILYDK-DHYKLALGQINIAKNLVDNVAKDY-VRLMKYGDS-LYRCKQLKRAALGRM
          KLDDIH.FYADLMNILY.K.DHY.LALGQIN.AKNLVDNVAKD....LMKY.D..L...KQLK.AA.GRM
Retrocopy KLDDIHLFYADLMNILYNK<DHYNLALGQINVAKNLVDNVAKDD<LWLMKYSDPRLPLRKQLKCAAPGRM

Parental  CTVIKRQKQSLEYLEQVRQHLSVAT--LIPITGLCFV-WV-PKCRKSS-INKVTRADVDVQPYAFTTKSL
          CT.IKRQKQSLEYLEQV.QHLS.....LI.I.GLCF..WV.P...KSS.INKVTRADVDV.P.AF..KSL
Retrocopy CTMIKRQKQSLEYLEQVHQHLSPLPQPLIQIPGLCFW>WV>PNVGKSSFINKVTRADVDV*PSAFIIKSL

Parental  FVGHMDYKYLRWQVVDTPGILDHPLEDRNTIEMQAITALAHLRAAVLYVMDLSEQCGHGLREQLELFQNI
          FVGHMD...L.WQ.VD.PGILDHPLEDRNTI.MQ.ITALAHLRAAV.YVMDLSEQC.HGLREQLELFQNI
Retrocopy FVGHMDSNCLHWQTVDAPGILDHPLEDRNTIAMQ-ITALAHLRAAVPYVMDLSEQCRHGLREQLELFQNI

Parental  RPLFINKPLIVVANKCDVKRIAELSEDDQKIFTNLQAEGFPVIETSTLTEEGVIKVKTEACNRLLAHRVE
          RPL.INK.LIVVANKCDVKRIA.LSEDDQKIFT.LQAEGFPVI.T..LTEEGVIKVKT.AC.RLLAHRVE
Retrocopy RPLLINKTLIVVANKCDVKRIAKLSEDDQKIFTDLQAEGFPVIKTRILTEEGVIKVKTKACDRLLAHRVE

Parental  TKMKGNKVNEVLNRLHLAVPTRRDDKERPPFIPEGVVARRKRMEMEEPKKKRERDLELEMGDDYILDLQK
          TKMKGNKVNE.LNRLHLAVPTRR.DK.RPP.IPEGVVARRKRMEMEEPKKKR..DLELE.G.D.IL.LQK
Retrocopy TKMKGNKVNEALNRLHLAVPTRRNDKQRPPLIPEGVVARRKRMEMEEPKKKRK*DLELEIGGD*ILGLQK

Parental  YWDLMNSSEKHDKIPEIWEGHNIADYIDPAIMKKLEELEKEEELRTAAGEYDSDSE-SEDEEMLEIRQLA
          YWDLMNSSEKHDKIPEIWEGHNIADYIDPAIMKK.EELEK.E.LRTAA.EYDSDSE....E.MLEI.Q.A
Retrocopy YWDLMNSSEKHDKIPEIWEGHNIADYIDPAIMKKWEELEKGEGLRTAAREYDSDSE>EDEE-MLEI*QQA

Parental  KQIREKKKLKILESKEKNTQGPRMPRTAKKVQRTVLENEMRSLGVDMDDKDNAHYAVQARRSRSVTRKR-
          KQIREKKKLKILESKEKNTQGPRMPRTAKK.QRTVLENE.RSLGVD.D.KDNAHYAVQARRSRSVTRKR.
Retrocopy KQIREKKKLKILESKEKNTQGPRMPRTAKKLQRTVLENESRSLGVDIDNKDNAHYAVQARRSRSVTRKR<

Parental  KREDSAPPSSVARSRSRSCSRTPRDVSGLRDVKMVKKAKTMMKNAQKKMNRLGKKGEADRHVFDMKPKHL
          K.EDSAP.SSVA...S.SC.RTP..VSGL.DVKMV.KAKTMMKNAQKKMNRLGKKGEAD.HVFDMKPKHL
Retrocopy KGEDSAPASSVA--QSWSCPRTPSEVSGLWDVKMVEKAKTMMKNAQKKMNRLGKKGEADGHVFDMKPKHL

Parental  LSGKRKAGKKDRR
          LS..RKAG.KDRR
Retrocopy LSRERKAGRKDRR

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
SRP051959_colon	0.27 RPM	14.29 RPM
SRP051959_heart	0.00 RPM	17.47 RPM
SRP051959_kidney	0.00 RPM	21.08 RPM
SRP051959_liver	0.00 RPM	17.48 RPM
SRP051959_lung	0.00 RPM	19.59 RPM
SRP051959_lymph_node	0.00 RPM	25.30 RPM
SRP051959_skeletal_muscle	0.04 RPM	19.06 RPM
SRP051959_spleen	0.00 RPM	20.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2592 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2592 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2592 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,