RetrogeneDB ID: retro_cjac_992

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:82280391..82282299(+)
• Located in intron of: ENSCJAG00000015969

Retrocopy information

• Ensembl ID: ENSCJAG00000022962
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_992
ATGGCGCACTACAACTTCAAGAAAATTACGGTGGTACCGTCCGCCAAGGACTTTATTGACCTGACATTGTCGAAGACTCA
ACGAAAGACTCCAACCGTTATTCATAAACATTACCAAATTCATCACATTAGACATTTTTACATGAGAAAAGTCAAATTTA
CTCAACAGAATTACCACGATAGACTTTCACAAATTCTAACAGATTTTCCTAAGTTGGATGACATTCATCCATTCTACGCA
GACTTGATGAATATTCTGTACGACAAAGATCACTACAAGTTGGCTCTGGGGCAAATAAATATTGCCAAAAATTTAGAGGA
CAATGTTGCTAAAGATTATGTGCGGTTGATGAAGTACGGCGACTCTCTCTACCGCTGCAAGCAGTTGAAGAGTGCGCCCC
TGGGGCGGATGTGCACCGTGATCAAGAGGCAGAAGCAGAGTTTGGAGTATTTGGAGCAAGTGCGTCAGCATTTATCCCGT
TTGCCAACCATTGATCCAAATACCAGGACTCTGCTTTTGTGTGGGTACCCAAATGTAGGCAAGTCCAGCTTCATCAATAA
GGTGACAAGAGCAGATGTGGATGTCCAACCCTATGCGTTCACAACCAAGTCTCTGTTTGTTGGGCACATGGATTATAAGT
ATCTACGTTGGCAGGTTGTAGACACTCCTGGGATACTGGACCACCCTCTGGAGGATAGGAACACCATCGAGATGCAGGCC
ATCACTGCCCTGGCCCACCTCCGTGCTGCGGTCCTGTACGTGATGGATTTGTCTGAGCAGTGTGGGCACCGGCTGAGGGA
GCAGCTAGAACTCTTCCAGAACATCAGACCTCTCTTCATCAACAAGCCTCTTATAGTTGTAGCCAACAAATGTGATGTGA
AGAGAATAGCTGAACTTTCTGAAGATGATCAGAAAATATTTACAAATTTGCAGGCTGAAGGATTCCCTGTAATAGAGACC
AGCACCTTGACTGAGGAAGGTGTTATTAAAGTTAAAACAGAGGCTTGTGATAGGCTTTTGGCTCATCGAGTGGAAACCAA
AATGAAGGGAAATAAAGTGAATGAGGTGCTGAATAGACTACACCTGGCTGTCCCAACCAGGAGGGACGATAAGGAGAGGC
CGCCTTTCATCCCTGAAGGAGTGGTGGCACGCAGGAAGAGAATGGAAATGGAGGAGCCCAAGAAAAAGAGGGAACGAGAT
CTTGAGCTGGAAATGGGAGATGATTATATTTTGGATCTTCAGAAGTACTGGGATTTAATGAATTCATCTGAAAAACATGA
TAAGATACTAGAAATCTGGCAAGGCCATAATATAGCTGATTATATTGATCCAGCCATCATGAAGAAATTGGAAGAATTAG
AAAAAGAAGAAGAGCTGAGAACAGCTGCTGGAGAGTATGACAGTGACTCTGAGAGTGAAGATGAGGAGATGCTGGAGATT
CGACAGCTGGCAAAGCAGATTAGAGAGAAGAAGAAGTTGAAAATTCTGGAGTCCAAAGAAAAGAATACACAGGGACCCAG
GATGCCTCGAACTGTTAAGAAGGTTCAGAGGACAGTTTTGGAGAATGAGATGCGTAGTCTTGGTGTTGACATGGACGATA
AAGACAACGCCCACTACGCAGTCCAGGCAAGAAGATCCCGGAGTGTCACTAGGAAAAGAAAGCGGGAAGACTCTGCTCCC
CGCTCCTCTGTGGCCCGGAGTCGGAGTCGGAGTTGCTCTCGAACTCCACGTGACGTTTCTGGTCTTCGGGATGTCAAGAT
GGTGAAGAAAGCCAAGACTATGATGAAGAATGCTCAGAAGAAGATGAATCGGTTGGGGAAGAAAGGGGAGGCAGATAAAC
ATGTGTTTGATATGAAGCCCAAGCACTTACTCTCTGGAAAGAGGAAAGCTGGCAAAAAGGACAGGAGA

Alignment

ORF - retro_cjac_992 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAHYNFKKITVVPSAKDFIDLTLSKTQRKTPTVIHKHYQIHRIRHFYMRKVKFTQQNYHDRLSQILTDFP
          MAHYNFKKITVVPSAKDFIDLTLSKTQRKTPTVIHKHYQIH.IRHFYMRKVKFTQQNYHDRLSQILTDFP
Retrocopy MAHYNFKKITVVPSAKDFIDLTLSKTQRKTPTVIHKHYQIHHIRHFYMRKVKFTQQNYHDRLSQILTDFP

Parental  KLDDIHPFYADLMNILYDKDHYKLALGQINIAKNLVDNVAKDYVRLMKYGDSLYRCKQLKRAALGRMCTV
          KLDDIHPFYADLMNILYDKDHYKLALGQINIAKNL.DNVAKDYVRLMKYGDSLYRCKQLK.A.LGRMCTV
Retrocopy KLDDIHPFYADLMNILYDKDHYKLALGQINIAKNLEDNVAKDYVRLMKYGDSLYRCKQLKSAPLGRMCTV

Parental  IKRQKQSLEYLEQVRQHLS-VATLIP-ITGLC-FVWVPKCR-KSS-INKVTRADVDVQPYAFTTKSLFVG
          IKRQKQSLEYLEQVRQHLS...T..P.I.GLC.FVWVPKCR.KSS.INKVTRADVDVQPYAFTTKSLFVG
Retrocopy IKRQKQSLEYLEQVRQHLSRLPTIDP>IPGLC>FVWVPKCR>KSSFINKVTRADVDVQPYAFTTKSLFVG

Parental  HMDYKYLRWQVVDTPGILDHPLEDRNTIEMQAITALAHLRAAVLYVMDLSEQCGHGLREQLELFQNIRPL
          HMDYKYLRWQVVDTPGILDHPLEDRNTIEMQAITALAHLRAAVLYVMDLSEQCGH.LREQLELFQNIRPL
Retrocopy HMDYKYLRWQVVDTPGILDHPLEDRNTIEMQAITALAHLRAAVLYVMDLSEQCGHRLREQLELFQNIRPL

Parental  FINKPLIVVANKCDVKRIAELSEDDQKIFTNLQAEGFPVIETSTLTEEGVIKVKTEACNRLLAHRVETKM
          FINKPLIVVANKCDVKRIAELSEDDQKIFTNLQAEGFPVIETSTLTEEGVIKVKTEAC.RLLAHRVETKM
Retrocopy FINKPLIVVANKCDVKRIAELSEDDQKIFTNLQAEGFPVIETSTLTEEGVIKVKTEACDRLLAHRVETKM

Parental  KGNKVNEVLNRLHLAVPTRRDDKERPPFIPEGVVARRKRMEMEEPKKKRERDLELEMGDDYILDLQKYWD
          KGNKVNEVLNRLHLAVPTRRDDKERPPFIPEGVVARRKRMEMEEPKKKRERDLELEMGDDYILDLQKYWD
Retrocopy KGNKVNEVLNRLHLAVPTRRDDKERPPFIPEGVVARRKRMEMEEPKKKRERDLELEMGDDYILDLQKYWD

Parental  LMNSSEKHDKIPEIWEGHNIADYIDPAIMKKLEELEKEEELRTAAGEYDSDSESEDEEMLEIRQLAKQIR
          LMNSSEKHDKI.EIW.GHNIADYIDPAIMKKLEELEKEEELRTAAGEYDSDSESEDEEMLEIRQLAKQIR
Retrocopy LMNSSEKHDKILEIWQGHNIADYIDPAIMKKLEELEKEEELRTAAGEYDSDSESEDEEMLEIRQLAKQIR

Parental  EKKKLKILESKEKNTQGPRMPRTAKKVQRTVLENEMRSLGVDMDDKDNAHYAVQARRSRSVTRKRKREDS
          EKKKLKILESKEKNTQGPRMPRT.KKVQRTVLENEMRSLGVDMDDKDNAHYAVQARRSRSVTRKRKREDS
Retrocopy EKKKLKILESKEKNTQGPRMPRTVKKVQRTVLENEMRSLGVDMDDKDNAHYAVQARRSRSVTRKRKREDS

Parental  APPSSVARSRSRSCSRTPRDVSGLRDVKMVKKAKTMMKNAQKKMNRLGKKGEADRHVFDMKPKHLLSGKR
          AP.SSVARSRSRSCSRTPRDVSGLRDVKMVKKAKTMMKNAQKKMNRLGKKGEAD.HVFDMKPKHLLSGKR
Retrocopy APRSSVARSRSRSCSRTPRDVSGLRDVKMVKKAKTMMKNAQKKMNRLGKKGEADKHVFDMKPKHLLSGKR

Parental  KAGKKDRR
          KAGKKDRR
Retrocopy KAGKKDRR

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	3.17 RPM	14.29 RPM
SRP051959_heart	2.35 RPM	17.47 RPM
SRP051959_kidney	2.33 RPM	21.08 RPM
SRP051959_liver	2.25 RPM	17.48 RPM
SRP051959_lung	2.34 RPM	19.59 RPM
SRP051959_lymph_node	2.12 RPM	25.30 RPM
SRP051959_skeletal_muscle	2.62 RPM	19.06 RPM
SRP051959_spleen	2.82 RPM	20.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_992 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_992 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_992 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,