RetrogeneDB ID: retro_cjac_3822

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL284790.1:26139..27125(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBLN5
• Ensembl ID: ENSCJAG00000017963
• Aliases: None
• Description: None

Sequence

>retro_cjac_3822
GATGAAGGCAACCAGTGTGTGGATGTGGACGAGTGTACAACAGATTCCCACCAGTGCAACTCTACCCAGATCTGCATCAA
CACTGAAGGCAGGTACCCCTGCTCCTGCACCGATGGATACTGGCTACTGGAAGGCCAGTGCTTAGATATTGATGAGTGTC
ACTATGGTACTGCCAGCAGCTCTGTGCGAATGTTCCTGGATCCTACTCTTGTACATGCAACCCTGGTTTTACCCTCAATG
AGGATGGAAGCTCTTGCCAAGATGTGAACGAGTGTGTAACTGAGGACCCCTGCGTGCAAACCTGCATCAATACCTACGGC
TCTTTCGTCTGCCACTGTGACCTAGGATATGAACTTGAGGAAGATGGTGTTCACTGCAGTGATGTGGATGAGTGCAGCTT
CTCTGAGTTCCTCTGCCAACATGAATGTGTGAACCAGCCCAGCATGTACTTCTGCTCCTGCCCTTCATGCTACATCCTAC
TGGATGACAACCGAAGCCGCCAGGACATCAATGAATGTGAGCACAGAAAGCACACATGAAACCTGCAGCAGACTTGCTAC
AATTTACAAGGGGGGTTCAAACGCATTGACCCCATCCGATGTGAGGAGCCTTATCTGAGGATCAGTGATAACTGCTGTAT
GTGTCCTGCTGAGAACCCTGGCTGCAGAGACAAGCCCTTTACCATCTTGTACCTGGACGTGGATGTGGTGTCAGGACACT
TCGTTCCTGCTGACATCTTCCAAATGCAAGCCACGACCTGCTACCCTGGGGCCTATTACCTTTTCCAGATCAAATCTGGG
AACAAGGACAGAGAATTTTATGTGCAGCAAATGGGCCCCATCAGCGCCATCCTAGTGATGACGCGCCCCCTCAAAGGGCC
CCGGGAAATCCAGCTGGACTTGGAAATGATCACTGTCAACACTGTCATCAACTTCAGAGGCAGCTCTGTGGTCCCACTGT
GGATATATTTGTCTCAGTACCCATTC

Alignment

ORF - retro_cjac_3822 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.27 %
• Parental protein coverage: 60.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DEGNQCVDVDECATDSHQCNPTQICINTEGGYTCSCTDGYWLLEGQCLDIDECRYG-YCQQLCANVPGSY
          DEGNQCVDVDEC.TDSHQCN.TQICINTEG.Y.CSCTDGYWLLEGQCLDIDEC.YG.YCQQLCANVPGSY
Retrocopy DEGNQCVDVDECTTDSHQCNSTQICINTEGRYPCSCTDGYWLLEGQCLDIDECHYG<YCQQLCANVPGSY

Parental  SCTCNPGFTLNEDGRSCQDVNECATENPCVQTCVNTYGSFICRCDPGYEPEEDGVHCSDMDECSFSEFLC
          SCTCNPGFTLNEDG.SCQDVNEC.TE.PCVQTC.NTYGSF.C.CD.GYE.EEDGVHCSD.DECSFSEFLC
Retrocopy SCTCNPGFTLNEDGSSCQDVNECVTEDPCVQTCINTYGSFVCHCDLGYELEEDGVHCSDVDECSFSEFLC

Parental  QHECVNQPGTYFCSCPPGYILLDDNRSCQDINECEHRNHTCNLQQTCYNLQGGFKCIDPIRCEEPYLRIS
          QHECVNQP..YFCSCP..YILLDDNRS.QDINECEHR.HT.NLQQTCYNLQGGFK.IDPIRCEEPYLRIS
Retrocopy QHECVNQPSMYFCSCPSCYILLDDNRSRQDINECEHRKHT*NLQQTCYNLQGGFKRIDPIRCEEPYLRIS

Parental  DNRCMCPAENPGCRDQPFTILYRDMDVVSGRSVPADIFQMQATTRYPGAYYIFQIKSGNEGREFYMRQTG
          DN.CMCPAENPGCRD.PFTILY.D.DVVSG..VPADIFQMQATT.YPGAYY.FQIKSGN..REFY..Q.G
Retrocopy DNCCMCPAENPGCRDKPFTILYLDVDVVSGHFVPADIFQMQATTCYPGAYYLFQIKSGNKDREFYVQQMG

Parental  PISATLVMTRPIKGPREIQLDLEMITVNTVINFRGSSVIRLRIYVSQYPF
          PISA.LVMTRP.KGPREIQLDLEMITVNTVINFRGSSV..L.IY.SQYPF
Retrocopy PISAILVMTRPLKGPREIQLDLEMITVNTVINFRGSSVVPLWIYLSQYPF

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	2.20 RPM
SRP051959_heart	0.00 RPM	52.32 RPM
SRP051959_kidney	0.00 RPM	30.11 RPM
SRP051959_liver	0.00 RPM	0.50 RPM
SRP051959_lung	0.00 RPM	14.67 RPM
SRP051959_lymph_node	0.00 RPM	2.35 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.98 RPM
SRP051959_spleen	0.00 RPM	23.84 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3822 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3822 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3822 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017963	3 retrocopies	retro_cjac_3822 , retro_cjac_3823, retro_cjac_3993,
Callithrix jacchus	ENSCJAG00000037941	35 retrocopies	retro_cjac_3343, retro_cjac_3355, retro_cjac_3369, retro_cjac_3372, retro_cjac_3389, retro_cjac_3391, retro_cjac_3423, retro_cjac_3425, retro_cjac_3430, retro_cjac_3445, retro_cjac_3456, retro_cjac_3474, retro_cjac_3476, retro_cjac_3477, retro_cjac_3487, retro_cjac_3491, retro_cjac_3543, retro_cjac_3545, retro_cjac_3547, retro_cjac_3549, retro_cjac_3566, retro_cjac_3583, retro_cjac_3598, retro_cjac_3609, retro_cjac_3616, retro_cjac_3622, retro_cjac_3633, retro_cjac_3641, retro_cjac_3656, retro_cjac_3672, retro_cjac_3674, retro_cjac_3677, retro_cjac_3682, retro_cjac_3733, retro_cjac_3736,