RetrogeneDB ID: retro_cjac_845

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:36113585..36115115(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RASGRP2
• Ensembl ID: ENSCJAG00000002861
• Aliases: None
• Description: None

Sequence

>retro_cjac_845
AAAACAAGATACCTGGTCACGTACTGGATCTCTGCCTTCCCACCGGAGTTTGACTTGAACACGGAGCTCACTGAGCAGAT
CAAGGAGCTGAAGGCTCTGCTAGACCAAGCAGGAAACTGGCGGCGCGGCAGCGTCATCGACATAGACAGCGTCCCTACCT
ACAAGTGGAAGAGGCAGGTGACTCAGCGGAACCCTATGGGACAGAAAAAGCGCCAGATGTCCCTGTTGTTCGACCACCTG
GAGCCCCTGGAGCTGGCGGGGCATCTCACCTACTTGGAGTATCACTCCTTCTGCAAGATCCGGTTCCAGGACTATCACAA
TTTTGTGACTCATGGCTACACTGTGGACAACCCCGTCCTGGAGCGGTTCATCTCCCTCTTCAAAAGCATCTCGCAGTGGG
TCATGATCCTCAGCAAACCCACAGCCCCGCAGCGGGGCCTGGTCATCACACACTTTGTCCACGTGGCGGAGAAGCTGCTG
CAGCTGCAGAACTTCAACATACTGATGATAGTGGTCGGGGGCCTGAGCCACAGCTCCATCTCCCGCCTCAAGGAGACCCA
CAGCCACTTTAGCCCTGAGACCATCAAGCTCTGGGATGGTCTCGTGGAACTAGCGACGGCGACAGGCAGCTATGGCAACT
ACCAGCGCCGGCTGGCAGCCTTTGTGGGCTTCCGCTTCCCCATCCTGGGTGTGCACCTCAAGGACCTGGTGGCCCTGCAG
CTGGCATTGCCTGACTGGCTGGACCCAGCCCGGACCCGGCTCCATGAGGGCAAGATGAAGCAGGTCTTCAGCATCCTGGA
GAAGCTGGCCATAGTGACCAGGCTTTGGTCACCAGTACAGGCCAACCGTGATCTGCTCGGCCTGCTCACGGCATCTCTGG
ATCAGTAACAGATGGAGGATGAGCTGCACCAGCTATCCCAGCAGCGGGAGCCGCGCTCCAAGTCCTTGCCAACCAGCCCC
ACGAGCTGTACCCCACCACCCCGGCCCTAGGTGCTGGAGGAGTGGACCTCGGCTGCCAAACCCAAGCTGGATCAGGCCCT
AGTGGTGGAGCACATTGAGAAGATGGTGGAGTCTGTGTTCTGGAACTTTGACGTCGATGGGGATGGCCACATCTCACAGG
AAGAGTTCCAGATCATCCGTGGGAACTTCCCTTACCTCAGCGCCTTTGGGGACCTCGACCAGAACCAGGACTGCTACATC
AGCAGGGAGAAGATGGTCTCCTATTTTCTGCGCTCCAGCTCTGTGCTGGGGGACCGCGTGGGCGTCGTACACAACTTCCA
GGAGAGCAACTCCTTGCGCCCGGTCACCTGCCGCCACTGCAAAGCCCCGATCCTGGGTATCTATAAGCAAGGCCTCAAAT
GCCGAGCCTGTGGTGTGAACTGCCATAAGCAGTGCAAGGATCGCCTGTCAGTGGAGTGTTGGCTCAGGACCCAGAGCGTG
AGCCTGGAGGGGTCTGCACCCTCACCCTTACCCACACACAGCCACCATCATGGCGCCTTCAGCTTCTCCCTTTCCCGCCC
TGCTCGGCGT

Alignment

ORF - retro_cjac_845 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.72 %
• Parental protein coverage: 83.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTCHLVRYWISAFPAEFDLNPELAEQIKELKALLDQEGNRRHSSLIDIDSVPTYKWKRQVTQRNPMGQKK
          KT..LV.YWISAFP.EFDLN.EL.EQIKELKALLDQ.GN.R..S.IDIDSVPTYKWKRQVTQRNPMGQKK
Retrocopy KTRYLVTYWISAFPPEFDLNTELTEQIKELKALLDQAGNWRRGSVIDIDSVPTYKWKRQVTQRNPMGQKK

Parental  RKMSLLFDHLEPLELAEHLTYLEYRSFCKILFQDYHSFVTHGCTVDNPVLERFISLFNSVSQWVQLMILS
          R.MSLLFDHLEPLELA.HLTYLEY.SFCKI.FQDYH.FVTHG.TVDNPVLERFISLF.S.SQWV..MILS
Retrocopy RQMSLLFDHLEPLELAGHLTYLEYHSFCKIRFQDYHNFVTHGYTVDNPVLERFISLFKSISQWV--MILS

Parental  KPTAPQRALVITHFVHVAEKLLQLQNFNTLMAVVGGLSHSSISRLKETHSHVSPETIKLWEGLTELVTAT
          KPTAPQR.LVITHFVHVAEKLLQLQNFN.LM.VVGGLSHSSISRLKETHSH.SPETIKLW.GL.EL.TAT
Retrocopy KPTAPQRGLVITHFVHVAEKLLQLQNFNILMIVVGGLSHSSISRLKETHSHFSPETIKLWDGLVELATAT

Parental  GNYGNYRRRLAACVGFRFPILGVHLKDLVALQLALPDWLDPARTRLNGAKMKQLFSILEELAMVTSLRPP
          G.YGNY.RRLAA.VGFRFPILGVHLKDLVALQLALPDWLDPARTRL...KMKQ.FSILE.LA.VT.L..P
Retrocopy GSYGNYQRRLAAFVGFRFPILGVHLKDLVALQLALPDWLDPARTRLHEGKMKQVFSILEKLAIVTRLWSP

Parental  VQANPDLLSLLTVSLDQYQTEDELYQLSLQREPRSKSSPTSPTSCTPPPRPPVLDEWTSAAKPKLDQALV
          VQAN.DLL.LLT.SLDQ.Q.EDEL.QLS.QREPRSKS.PTSPTSCTPPPRP.VL.EWTSAAKPKLDQALV
Retrocopy VQANRDLLGLLTASLDQ*QMEDELHQLSQQREPRSKSLPTSPTSCTPPPRP*VLEEWTSAAKPKLDQALV

Parental  VEHIEKMVESVFRNFDVDGDGHISQEEFQIIRGNFPYLSAFGDLDQNQDGCISREEMVSYFLRSSSVLGG
          VEHIEKMVESVF.NFDVDGDGHISQEEFQIIRGNFPYLSAFGDLDQNQD..ISRE.MVSYFLRSSSVLG.
Retrocopy VEHIEKMVESVFWNFDVDGDGHISQEEFQIIRGNFPYLSAFGDLDQNQDCYISREKMVSYFLRSSSVLGD

Parental  RMGFVHNFQESNSLRPVACRHCKALILGIYKQGLKCRACGVNCHKQCKDHLSVECRRRAQSVSLEGCAPS
          R.G.VHNFQESNSLRPV.CRHCKA.ILGIYKQGLKCRACGVNCHKQCKD.LSVEC..R.QSVSLEG.APS
Retrocopy RVGVVHNFQESNSLRPVTCRHCKAPILGIYKQGLKCRACGVNCHKQCKDRLSVECWLRTQSVSLEGSAPS

Parental  PSPTHSHHHRAFSFSLPRPGRR
          P.PTHSHHH.AFSFSL.RP.RR
Retrocopy PLPTHSHHHGAFSFSLSRPARR

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	2.29 RPM
SRP051959_heart	0.04 RPM	7.81 RPM
SRP051959_kidney	0.00 RPM	3.04 RPM
SRP051959_liver	0.00 RPM	2.92 RPM
SRP051959_lung	0.08 RPM	24.94 RPM
SRP051959_lymph_node	0.02 RPM	59.43 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.99 RPM
SRP051959_spleen	0.02 RPM	19.47 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_845 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_845 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_845 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	ENSCJAG00000002861	1 retrocopy	retro_cjac_845 ,