RetrogeneDB ID: retro_cjac_3813

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL284763.1:347249..348502(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTR3
• Ensembl ID: ENSCJAG00000014091
• Aliases: None
• Description: None

Sequence

>retro_cjac_3813
ATGGCGAGATGGCTGCCGGCCTGTGTAGTGGACTGTGGCACGGGGTATGCAAAACTAGGATATGCTGGAAATACAGAACT
GCAGTTTAACATCCCTTCTTGTATTGCTATAAAGGAGTCGGTAAAAGTGGGTGATCAAGCTCAAAGGAGGGTGATGAAAG
CTGCTGATGACCTAGACTTCTTCAATGGTGATGAAGCAATAGGAAAACCTACATATGCAACAAAGTGGCCAATCTGCCAT
GGTACAGTTGAATATTGGGACTTGATGGAAAGGTTTATGGAGCAAGTGATCGTTAAATATTTAAGGGAAAAACCTGAAGA
CTATTATTTTCTCTTGACTGAACTTCCATTGAATACTCCAGAAAACAGGGAATATACTGCTGAAATAATGTTTGAATCTT
TCAATGTTCCAGGCTTGTACATTGCTGTGCAGGCTGTTCTTGCCTTAGCTACATCTTGGACCTCAAGAAAAGTAGGAGAA
CGGACATTGACTGGTATGGTAATAGATAGTGGAGATGGTGTCACTCATGTCATTCCTGTGGCTGAAGGGTATGTGAAGGG
TTATATTAAACACATTCCAATCACAGGATGAGATATAACATATTTTAATCAGGAACTGCTGAGAGACCAATAAGTAGGAA
TCCCTCCAGAACAATCTTTGGAAACTGGCAAGGCAGTAAAGGAGTGCTATAGTTACGTCTGCCCAGATTTAGTGAAAGAA
TTTAACAAGTATGATACAGATGGGTCAAAACGGATTAAACCGTATACTGGAATCAATGCTATCTCAAAGAAAGAATTTTT
CAGTTGATGTTGGTTATGAGAGATTTTTTGGACCTGAAATCTTTTTTTCATCCAGAGTTTTGTAATCCAGACTTTACACA
ACCTATCTCAGAAGTTGTAGATGAAGTAATTTAGAATTGTCCTGTTGATGTCAGACATCATCTCTACAAAAATATTGTCC
TCTCTGGAGGTTCAACCATGTTCAGGGAATTTGCACATCACTTGCAAAGAGATTTAAAAAGAACTGTAGATGCCCGGCTG
AAATTAAGTGAGGAATTTAGTGGTGGTAAATTAAAGCCATAACCTATTGATGTACAAGTCATTACACACCACATGCAGAA
ATATGCAGTTTGGTTTGGAGGATTAGTTCTGGCTTCCACACCTGAGTTCTACCAATTATGCCACACCAAAAAGGATTATA
AAAAAATTGGACCTAGCATTTGTCGTCACAATCCAGTGTTTGGAGTCATGTCA

Alignment

ORF - retro_cjac_3813 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEKP
          MA..LPACVVDCGTGY.KLGYAGNTE.QF.IPSCIAIKES.KVGDQAQRRVMK..DDLDFF.GDEAI.KP
Retrocopy MARWLPACVVDCGTGYAKLGYAGNTELQFNIPSCIAIKESVKVGDQAQRRVMKAADDLDFFNGDEAIGKP

Parental  TYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFESFNVPGLY
          TYATKWPI.HG.VE.WDLMERFMEQVI.KYLR..PED.YFLLTE.PLNTPENREYTAEIMFESFNVPGLY
Retrocopy TYATKWPICHGTVEYWDLMERFMEQVIVKYLREKPEDYYFLLTELPLNTPENREYTAEIMFESFNVPGLY

Parental  IAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLLRD
          IAVQAVLALA.SWTSR.VGERTLTG.VIDSGDGVTHVIPVAEGYV.G..IKHIPI.G.DITYF.Q.LLRD
Retrocopy IAVQAVLALATSWTSRKVGERTLTGMVIDSGDGVTHVIPVAEGYVKG-YIKHIPITG*DITYFNQELLRD

Parental  REVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWIKQYTGINAISKKE-FSIDVGYERFLGP
          ..VGIPPEQSLET.KAVKE.YSYVCPDLVKEFNKYDTDGSK.IK.YTGINAISKKE.FS.DVGYERF.GP
Retrocopy Q*VGIPPEQSLETGKAVKECYSYVCPDLVKEFNKYDTDGSKRIKPYTGINAISKKE>FSVDVGYERFFGP

Parental  EI-FFHPEFANPDFTQPISEVVDEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLK
          EI.FFHPEF.NPDFTQPISEVVDEVI.NCP.DVR..LYKNIVLSGGSTMFR.F...LQRDLKRTVDARLK
Retrocopy EI>FFHPEFCNPDFTQPISEVVDEVI*NCPVDVRHHLYKNIVLSGGSTMFREFAHHLQRDLKRTVDARLK

Parental  LSEELSGGRLKPKPIDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS
          LSEE.SGG.LKP.PIDVQVITHHMQ.YAVWFGG..LASTPEFYQ.CHTKKDY..IGPSICRHNPVFGVMS
Retrocopy LSEEFSGGKLKP*PIDVQVITHHMQKYAVWFGGLVLASTPEFYQLCHTKKDYKKIGPSICRHNPVFGVMS

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	183.47 RPM
SRP051959_heart	0.00 RPM	46.78 RPM
SRP051959_kidney	0.00 RPM	67.07 RPM
SRP051959_liver	0.00 RPM	47.96 RPM
SRP051959_lung	0.00 RPM	112.70 RPM
SRP051959_lymph_node	0.02 RPM	176.02 RPM
SRP051959_skeletal_muscle	0.00 RPM	24.63 RPM
SRP051959_spleen	0.00 RPM	146.91 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3813 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3813 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3813 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003401	1 retrocopy	retro_btau_672,
Callithrix jacchus	ENSCJAG00000014091	4 retrocopies	retro_cjac_3602, retro_cjac_3813 , retro_cjac_385, retro_cjac_4005,
Homo sapiens	ENSG00000115091	2 retrocopies	retro_hsap_1391, retro_hsap_4694,
Gorilla gorilla	ENSGGOG00000011346	1 retrocopy	retro_ggor_2921,
Mustela putorius furo	ENSMPUG00000010717	1 retrocopy	retro_mputfur_1275,
Mus musculus	ENSMUSG00000026341	1 retrocopy	retro_mmus_3653,
Nomascus leucogenys	ENSNLEG00000011619	2 retrocopies	retro_nleu_1077, retro_nleu_2364,
Pongo abelii	ENSPPYG00000012798	1 retrocopy	retro_pabe_3647,
Pan troglodytes	ENSPTRG00000012388	2 retrocopies	retro_ptro_3118, retro_ptro_955,
Vicugna pacos	ENSVPAG00000009479	1 retrocopy	retro_vpac_468,