RetrogeneDB ID: retro_cjac_3926

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286269.1:42537..43467(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GRK6
• Ensembl ID: ENSCJAG00000006775
• Aliases: None
• Description: None

Sequence

>retro_cjac_3926
ATGGAGCTCGAGAACATCGTAACAAACACGGTGCTACTCAAGGCCCAGGAAGGTGGTGGTGGGAATCGCAAAGGCAAAAG
CAAGAAACGGCGGCAGATGCTGCAGTTCCCCCAAATCAGCCAGTGTGAAGAGCTGCGGCTCAGCCTCAAGCGTGACTACC
ACAGCCTGTGCGAGCAGCAGCCCATCGGGCACCTGCTGTTTCGACAGCTCTGTGCCACGAGGCCGGAGCTGAGCCACTGT
ATCACCTTCCTGGATGAGGTGGCCGAGTATGAAGTGACCACGGATGAGAAGCGGAAGGCATGTGGGCGGCGGCTAATGCA
GAATTTTCTGAGCTACATGGGTCCTGACCTCATCCTGGAGGTCCCCCAGCAACTGGTGATGAACTGCGCCCAGCGACTGG
AGCAGGGGCCCTGCAAAGACCTCTTCCAGGAACTCACCCGGCTGACCCACGAGTACATGGCCCCATGTGCCGACTACCTC
GACAGCATCTACTTCAACCGTTTCCTGCACTGGAAGCGGCTAGAAAGGCAGCCAGTGACCAAAAACACCTTCAGGCAGTA
CCGAGTCCTGGGCAAAGGTGGCTTTGGGGAGGTGGGCGCCTGCCAGGTGCGGGCCACAGGCAAGATGTAAGCCTGCAAGA
AGCTAGAGAAAAAGCGGATCAAGAAGCGGAAAGGGGAGGCCATGGCGCTGAAGGAGAAGCAGATCCTGGAGAAAGTGAAC
AGCAGGTTTGTAGTGAGCTTGGCCTATGCCTGAGACCAAGGACCGCTGTGCCTGGTGCTGACGCTGATGAACGGAGGTGA
CCTCAAGTTCCACATCTACCACATGGGCCATGCTGGCTTCTCTGAAGCATGGGCTGTCTTCTACACCTCCGAGATCTGCT
GCGGCCTGGAGGACCTGCACCCGCAGCGCATCGTGTACAGGGACGCCAGA

Alignment

ORF - retro_cjac_3926 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.14 %
• Parental protein coverage: 53.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MELENIVANTVLLKAREGGGGNRKGKSKKWRQMLQFPHISQCEELRLSLERDYHSLCERQPIGRLLFREF
          MELENIV.NTVLLKA.EGGGGNRKGKSKK.RQMLQFP.ISQCEELRLSL.RDYHSLCE.QPIG.LLFR..
Retrocopy MELENIVTNTVLLKAQEGGGGNRKGKSKKRRQMLQFPQISQCEELRLSLKRDYHSLCEQQPIGHLLFRQL

Parental  CATRPELSHCITFLDGVAEYEVTPDEKRKACGRRLMQNFLSHMGPDLIPEVPQQLVMNCAQRLEQGPCKD
          CATRPELSHCITFLD.VAEYEVT.DEKRKACGRRLMQNFLS.MGPDLI.EVPQQLVMNCAQRLEQGPCKD
Retrocopy CATRPELSHCITFLDEVAEYEVTTDEKRKACGRRLMQNFLSYMGPDLILEVPQQLVMNCAQRLEQGPCKD

Parental  LFQELTRLTHEYLSVAPFADYLDSIYFNRFLQWKWLERQPVTKNTFRQYRVLGKGGFGEVCACQVRATGK
          LFQELTRLTHEY...AP.ADYLDSIYFNRFL.WK.LERQPVTKNTFRQYRVLGKGGFGEV.ACQVRATGK
Retrocopy LFQELTRLTHEYM--APCADYLDSIYFNRFLHWKRLERQPVTKNTFRQYRVLGKGGFGEVGACQVRATGK

Parental  MYACKKLEKKRIKKRKGEAMALNEKQILEKVNSRFVVSLAYAYETKDALCLVLTLMNGGDLKFHIYHMGH
          M.ACKKLEKKRIKKRKGEAMAL.EKQILEKVNSRFVVSLAYA......LCLVLTLMNGGDLKFHIYHMGH
Retrocopy M*ACKKLEKKRIKKRKGEAMALKEKQILEKVNSRFVVSLAYA*D-QGPLCLVLTLMNGGDLKFHIYHMGH

Parental  AGFSEARAVFYTAEICCGLEDLHRERIVYRDLK
          AGFSEA.AVFYT.EICCGLEDLH..RIVYRD..
Retrocopy AGFSEAWAVFYTSEICCGLEDLHPQRIVYRDAR

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	0.02 RPM	9.78 RPM
SRP051959_heart	0.18 RPM	6.88 RPM
SRP051959_kidney	0.04 RPM	6.92 RPM
SRP051959_liver	0.00 RPM	6.56 RPM
SRP051959_lung	0.05 RPM	24.04 RPM
SRP051959_lymph_node	0.02 RPM	61.37 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.70 RPM
SRP051959_spleen	0.00 RPM	20.71 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3926 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3926 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3926 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006775	1 retrocopy	retro_cjac_3926 ,
Homo sapiens	ENSG00000198055	1 retrocopy	retro_hsap_1172,
Gorilla gorilla	ENSGGOG00000009669	1 retrocopy	retro_ggor_912,