RetrogeneDB ID: retro_cjac_4189

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:73521000..73522542(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPR176
• Ensembl ID: ENSCJAG00000020926
• Aliases: None
• Description: None

Sequence

>retro_cjac_4189
ATGGGACATAACGGGAGCTGGATCTCTCTAAACGCCAGCGAGCCGAGCAAGGCGTCGGGCGTCGAGACTGCAAGCGCAAA
CCGCGGCGCACTCAGGGAGTTCGTCGAGGCGCAGCTGTACCGCCAGTTCACCACCACCTTGCTGGTCGTCATCTTCATAG
GCTCGTTGCTCGGAAACTTCATGGTGTTATGGTTAACTTGCTGCACAACCGTGTTCAAATCTGTCACCAACGGGTTCATT
AAAAACCTGGCCTGCTCGGGATTTGTGCCAGCCTGGACTGTGTGCCCTTTGACATCATCCTCAGCACCAGTCCTCACTGT
TGCTGGTGGATCTACACCATGCTCTTCTGCAAGGTCGTCAAATTTTTTTCACAAAGTATTCTGCTCTGTGACCATCCTCA
GCTTCACTGCTATTGCTTTGGACAGATACTACTCAGTCTTCTATCCGCTGGAGAGGAAAATATCTGATGCCAAGTTCCAT
GAACTGGTGATGTACATCTGGGCCCATGCAGTGGTGGCCAGTGTTCCTGTGTTTGCAGTGACCAATGTGGCCAATATCTA
TGCCACATCCACCTGCACGGAAGTCTGGAGCAACTCCTTGGGCCACCTGGTGTATGTTCTGGTGTAAAACATCACCACAG
TCATTGTGCCTGTGGCGGTGGTGTTCCTCTTCTTGATACTGATCCGAAGGGCCCTGACTGCCAGCCAGAAAAAGAAGGTC
ATTATAGCAGTGCTCTGGACCCCACAGAACACCATCTCCATCCCCTATGCCTCCCAGAGGGAGGCAGAGCTGCACACCAC
TCTGCTCTCCATGGTGATGGTCTTCATCTTGTGTAGCATGCCCTATGCCAGCCTGGTCATCTACCAGACCATGTTCAATG
TCCATGACATTTCCATCTTCTTGCTGCTCACTGCCATTTGGCTGCACAAAGTCTCCCTGCTGGCAAACCCTGTTCTCTTT
CTTACTGTGAACAAATCTTGCCACAAGTGCTTGATAGGGACCCTGGTGCAACTACACCACCAGTACAGTCGCCATAATGT
GATCAGTACCGGGAGCATCCTGGCTGAGGCTAGCCCGGAACCCAGCATACATTGGGGCAGCCAGCTCCTGGAGATCTTCC
ACATTGGGCAGCAACATATCTTTAAGCCCACAGAGGATAAGGAAGAGAGTGAGGCCAAGTACATTGGCTCAGCTGACTTC
CAGGCCAAGGAGATATTTAGCATCTGCCTGGAGGGAGAGCAGGGGCCACAGTTTGCACCCTCTGCCCCACCCCTGGGCAC
AGTGGACTCTGTATCCCAGGTAGCACCAGCAGCTCCTGTGGAATCTGAAACATTCTCTGATACGTATTGCCTGCAGTTTG
GCTTTGGGCCTTTTGAGTTGCCTCCTCTGTGGCTCTCAGAAACCTGAAACAGAAGAAGCGGCTGCTTCCCCCCTTTGGTA
ACACCCCAGAAGAGCTGATCCAGACAAGATTCCCAAGGTAGGCAGGGTGGAGTGGAAGATGAGTAGAAAGAATAAAGTGA
GCATTTTCCAAAGGTGGATTCC

Alignment

ORF - retro_cjac_4189 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MGHNGSWISQNASEPRNASGAETAGVNRSALGEFGEAQLYRQFTTTVQVVIFIGSLLGNFMVLWSTCRTT
          MGHNGSWIS.NASEP..ASG.ETA..NR.AL.EF.EAQLYRQFTTT..VVIFIGSLLGNFMVLW.TC.TT
Retrocopy MGHNGSWISLNASEPSKASGVETASANRGALREFVEAQLYRQFTTTLLVVIFIGSLLGNFMVLWLTCCTT

Parental  VFKSVTNRFIKNLACS-GICASLVCVPFDIALSTSPHCCWWIYSMLFCKVVK-FLHKVFCSVTILSFPAI
          VFKSVTN.FIKNLACS.GICASL.CVPFDI.LSTSPHCCWWIY.MLFCKVVK.F.HKVFCSVTILSF.AI
Retrocopy VFKSVTNGFIKNLACS<GICASLDCVPFDIILSTSPHCCWWIYTMLFCKVVK>FFHKVFCSVTILSFTAI

Parental  ALDRYYSVLYPLERKISDAKSRELVMYIWAHAVVASVPVFAVTNVADIYATSTCTEVWSNSLGHLVYVLV
          ALDRYYSV.YPLERKISDAK..ELVMYIWAHAVVASVPVFAVTNVA.IYATSTCTEVWSNSLGHLVYVLV
Retrocopy ALDRYYSVFYPLERKISDAKFHELVMYIWAHAVVASVPVFAVTNVANIYATSTCTEVWSNSLGHLVYVLV

Parental  YNITTIIVPVVVVFLFLILIRRALSASQKKKVIIAALRTPQNTISIPYASQREAELHATLLSMVMVFILC
          .NITT.IVPV.VVFLFLILIRRAL.ASQKKKVIIA.L.TPQNTISIPYASQREAELH.TLLSMVMVFILC
Retrocopy *NITTVIVPVAVVFLFLILIRRALTASQKKKVIIAVLWTPQNTISIPYASQREAELHTTLLSMVMVFILC

Parental  SVPYATLVIYQTVLNVPDTSVFLLLTAIWLPKVSLLANPVLFLTVNKSVRKCLIGTLVQLHHRYSRRNVV
          S.PYA.LVIYQT..NV.D.S.FLLLTAIWL.KVSLLANPVLFLTVNKS..KCLIGTLVQLHH.YSR.NV.
Retrocopy SMPYASLVIYQTMFNVHDISIFLLLTAIWLHKVSLLANPVLFLTVNKSCHKCLIGTLVQLHHQYSRHNVI

Parental  STGSGLAEASLEPSIRSGSQLLEMFHIGQQQIFKPTEDEEESEAKYIGSADFQAKEIFSTCLEGEQGPQF
          STGS.LAEAS.EPSI..GSQLLE.FHIGQQ.IFKPTED.EESEAKYIGSADFQAKEIFS.CLEGEQGPQF
Retrocopy STGSILAEASPEPSIHWGSQLLEIFHIGQQHIFKPTEDKEESEAKYIGSADFQAKEIFSICLEGEQGPQF

Parental  APSAPPLGTVDSVSQVAPAAPVESETFSDKYSLQFGFGPFELPPQWLSETRN-SKKRLLPPLGNTPEELI
          APSAPPLGTVDSVSQVAPAAPVESETFSD.Y.LQFGFGPFELPP.WLSET.N..KKRLLPP.GNTPEELI
Retrocopy APSAPPLGTVDSVSQVAPAAPVESETFSDTYCLQFGFGPFELPPLWLSET*N<QKKRLLPPFGNTPEELI

Parental  QT-KVPKVGRGERKMSRNNKVSI-FPKVDS
          QT.K.PKVGR.E.KMSR.NKVSI.FPKVDS
Retrocopy QT<KIPKVGRVEWKMSRKNKVSI<FPKVDS

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	0.00 RPM	1.60 RPM
SRP051959_heart	0.00 RPM	2.37 RPM
SRP051959_kidney	0.00 RPM	0.64 RPM
SRP051959_liver	0.00 RPM	0.17 RPM
SRP051959_lung	0.00 RPM	0.26 RPM
SRP051959_lymph_node	0.00 RPM	2.10 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.41 RPM
SRP051959_spleen	0.00 RPM	5.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4189 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4189 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4189 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020926	1 retrocopy	retro_cjac_4189 ,