RetrogeneDB ID: retro_cjac_3993

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286683.1:5507..6494(-)
• 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_3993
GATGAAGGCAACCAGTGTGTGGATGTGGACAAGTGTGCAACAGATTCCCACCAGTGCAACTCTACCCAGATCTGTATCAA
CAATGAAGGCGGGTACACCTGCTCCTGCACCGATGGATACTGGCTACTGGAAGGCCAGTGCTTAGATATTGATGAATGTC
ACTATGGTTACTGCCAGCAGCTCTGTGTGAATGTTCCTTGATCCTACTCTTGTACATGCAACCCTGGTTTTACCCTCAAT
GAGGATGGAAGGTCTTGCCAAGATGTGAACGAGTGTGTAACTGAGAGCCCCTGTGTGCAAACCTGCGTCAACACCTATGC
CTCTTTCGTCTGCCACTGTGACCCGGGATATGAACTTGAGGAAGATGGTGTTCACTGCAGTGATGTGGACGAGTGTAGCT
TCTCTGAGTTCCTCTGCCAACATGAATGTGTGAACCAGCCTGGCACATATTTCTGCTCCTGCCCTTCAGGCTACATCCTA
CTGGATGACAACCAAAGCTGCCAGGATATCAATGAATGTGAGCACAGAAACCACACATGCAACCTGCAGCAGACTTGCTA
CAATTTACAAGGGGGCTTCAAATGCATTGACCCCATCCGCTGTGAGGAGCCTTATCTGAGGATCAATGATAACCGCTGTA
TGTGTCCTGCTGAGAACCCTGGCTGCAGAGACCAGCCCTTTACCATCTTGTACCTGGACGTGGATGTGGTGTCAGGACAC
TCTGTTCCCGCTGACATCTTCCAAATGCAAGCCACGACCTGCTACCCTGGGGCCTATTACATTTTCCAGATCAACTCTGG
GAATGAGGGCAGAGAATTTTATGTGCAGCAAACGGGCCCCATCAGCACCACCCTAGTGATGACGCGCCCCATCAAAGGGC
CCCAGGAAATCCAGTTGGACTTGGAAATGATCACTGTCAACACTGTCATCAACTTCAGAGGCAGCTCTGTGATCCGACTG
TGGATATATGTGTCGCAATACCCATTC

Alignment

ORF - retro_cjac_3993 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.1 %
• Parental protein coverage: 60.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DEGNQCVDVDECATDSHQCNPTQICINTEGGYTCSCTDGYWLLEGQCLDIDECRYGYCQQLCANVPGSYS
          DEGNQCVDVD.CATDSHQCN.TQICIN.EGGYTCSCTDGYWLLEGQCLDIDEC.YGYCQQLC.NVP.SYS
Retrocopy DEGNQCVDVDKCATDSHQCNSTQICINNEGGYTCSCTDGYWLLEGQCLDIDECHYGYCQQLCVNVP*SYS

Parental  CTCNPGFTLNEDGRSCQDVNECATENPCVQTCVNTYGSFICRCDPGYEPEEDGVHCSDMDECSFSEFLCQ
          CTCNPGFTLNEDGRSCQDVNEC.TE.PCVQTCVNTY.SF.C.CDPGYE.EEDGVHCSD.DECSFSEFLCQ
Retrocopy CTCNPGFTLNEDGRSCQDVNECVTESPCVQTCVNTYASFVCHCDPGYELEEDGVHCSDVDECSFSEFLCQ

Parental  HECVNQPGTYFCSCPPGYILLDDNRSCQDINECEHRNHTCNLQQTCYNLQGGFKCIDPIRCEEPYLRISD
          HECVNQPGTYFCSCP.GYILLDDN.SCQDINECEHRNHTCNLQQTCYNLQGGFKCIDPIRCEEPYLRI.D
Retrocopy HECVNQPGTYFCSCPSGYILLDDNQSCQDINECEHRNHTCNLQQTCYNLQGGFKCIDPIRCEEPYLRIND

Parental  NRCMCPAENPGCRDQPFTILYRDMDVVSGRSVPADIFQMQATTRYPGAYYIFQIKSGNEGREFYMRQTGP
          NRCMCPAENPGCRDQPFTILY.D.DVVSG.SVPADIFQMQATT.YPGAYYIFQI.SGNEGREFY..QTGP
Retrocopy NRCMCPAENPGCRDQPFTILYLDVDVVSGHSVPADIFQMQATTCYPGAYYIFQINSGNEGREFYVQQTGP

Parental  ISATLVMTRPIKGPREIQLDLEMITVNTVINFRGSSVIRLRIYVSQYPF
          IS.TLVMTRPIKGP.EIQLDLEMITVNTVINFRGSSVIRL.IYVSQYPF
Retrocopy ISTTLVMTRPIKGPQEIQLDLEMITVNTVINFRGSSVIRLWIYVSQYPF

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	0.02 RPM	52.32 RPM
SRP051959_kidney	0.27 RPM	30.11 RPM
SRP051959_liver	0.09 RPM	0.50 RPM
SRP051959_lung	0.02 RPM	14.67 RPM
SRP051959_lymph_node	0.00 RPM	2.35 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.98 RPM
SRP051959_spleen	0.02 RPM	23.84 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3993 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3993 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3993 has 0 orthologous retrocopies within eutheria group .

---

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,