RetrogeneDB ID: retro_cjac_3823

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL284790.1:29690..30649(+)
• 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_3823
GAGTGTACAACAGATTCCCACCAGTGCAACTCTACCCAGATCTGCACTCATATCACTGAAGGCAGGTACCCCTGCTCCTG
CACCGATGGATACTGGCTACTGGAAGGCCAGTGCTTAGATATTGATGAGTGTCACTATGGTACTGCCAGCAGCTCTGTGC
GAATGTTCCTGGATCCTACTCTTGTACATGCAACCCTGGTTTTATCCTCAATGAGGATGGAAGCTCTTGCCAAGATGTGA
ACGAGTGTGTAACTGAGGACCCCTGCGTGCAAACCTGCATCAATACCTATGGCTCTTTCGTCTGCCACTGTGACCTAGGA
TATGAACTTGAGGAAGATGGTGTTCACTGCAGTGATGTGGATGAGTGCAGCTTCTCTGAGTTCCTCTGCCAACATGAATG
TGTGAACCAGCCCAGCATGTACTTCTGCTCCTGCCCTTCAGGCTACATCCTACTGGATGACAACCGAAGCCGCCAGGACA
TCAATGAATGTGAGCACAGAAAGCACACATGAAACCTGCAGCAGACTTGCTACAATTTACAAGGGGGTTTCAAACGCATT
GACCCCATCCGATGTGAGGAGTCTTATCTGAGGATCAGCGATAACTGCTGTATGTGTCCTGCTGAGAACCCTGGCTGCAG
AGACAAGCCCTTTACCATCTTGTACCTGGACGTGGATGTGGTGTCAGGACACTTCGTTCCTGCTGACATCTTCCAAATGC
AAGCCACGACCTGCTACCCTGGGGCCTATTACCTTTTCCAGATCAAATCTGGGAACAAGGACAGAGAATTTTATGTGCAG
CAAATGGGCCCCATCAGCGCCATCCTAGTGATGACGCGCCCCCTCAAAGGGCCCCGGGAAATCCAGCTGGACTTGGAAAT
GATCACTGTCAACACTGTCATCAACTTCAGAGGCAGCTCTGTGGTCCCACTGTGGATATATGTGTCTCAGTGCCCATTC

Alignment

ORF - retro_cjac_3823 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.67 %
• Parental protein coverage: 58.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ECATDSHQCNPTQICIN-TEGGYTCSCTDGYWLLEGQCLDIDECRYG-YCQQLCANVPGSYSCTCNPGFT
          EC.TDSHQCN.TQIC...TEG.Y.CSCTDGYWLLEGQCLDIDEC.YG.YCQQLCANVPGSYSCTCNPGF.
Retrocopy ECTTDSHQCNSTQICTHITEGRYPCSCTDGYWLLEGQCLDIDECHYG<YCQQLCANVPGSYSCTCNPGFI

Parental  LNEDGRSCQDVNECATENPCVQTCVNTYGSFICRCDPGYEPEEDGVHCSDMDECSFSEFLCQHECVNQPG
          LNEDG.SCQDVNEC.TE.PCVQTC.NTYGSF.C.CD.GYE.EEDGVHCSD.DECSFSEFLCQHECVNQP.
Retrocopy LNEDGSSCQDVNECVTEDPCVQTCINTYGSFVCHCDLGYELEEDGVHCSDVDECSFSEFLCQHECVNQPS

Parental  TYFCSCPPGYILLDDNRSCQDINECEHRNHTCNLQQTCYNLQGGFKCIDPIRCEEPYLRISDNRCMCPAE
          .YFCSCP.GYILLDDNRS.QDINECEHR.HT.NLQQTCYNLQGGFK.IDPIRCEE.YLRISDN.CMCPAE
Retrocopy MYFCSCPSGYILLDDNRSRQDINECEHRKHT*NLQQTCYNLQGGFKRIDPIRCEESYLRISDNCCMCPAE

Parental  NPGCRDQPFTILYRDMDVVSGRSVPADIFQMQATTRYPGAYYIFQIKSGNEGREFYMRQTGPISATLVMT
          NPGCRD.PFTILY.D.DVVSG..VPADIFQMQATT.YPGAYY.FQIKSGN..REFY..Q.GPISA.LVMT
Retrocopy NPGCRDKPFTILYLDVDVVSGHFVPADIFQMQATTCYPGAYYLFQIKSGNKDREFYVQQMGPISAILVMT

Parental  RPIKGPREIQLDLEMITVNTVINFRGSSVIRLRIYVSQYPF
          RP.KGPREIQLDLEMITVNTVINFRGSSV..L.IYVSQ.PF
Retrocopy RPLKGPREIQLDLEMITVNTVINFRGSSVVPLWIYVSQCPF

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_3823 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3823 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3823 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,