RetrogeneDB ID: retro_cjac_3609

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01188362.1:3886..4326(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LTBP4
• Ensembl ID: ENSCJAG00000037941
• Aliases: None
• Description: None

Sequence

>retro_cjac_3609
GAGTTTTGCTGTTGTTACCCAGACTGGAGTGCAATGGCACAATCTCGGCTCACCGCAACCTCCGCCTCCTGGGTTCAAGC
AATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCACACACCACCATGCCCAGCTAATTTTTGTATTTTTAGT
AAAGACAGGGTTTCACCTCATTGACCAGGATGGCAGGATGATCTCGATCGCTTGACCTCGTGATCCACCCACTTCAGCCT
CCCAAAGTGCTGGGATTATAGGCATGAGCCACCACGCCCGGTCTCCTTTTTTTTTTGAGCTGGAATCCTGCTCTGTCGCT
AGGCTGGAGTGCAGTGGCACTATTTCAGCTCACTGCAACCTCCGTCTCCTGGGTTCAAGTGATTCCCCTGTCAGAGCCTC
CTGAGTAGCCGGGATTATAGATGCCCTCCACCATGCCCAG

Alignment

ORF - retro_cjac_3609 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.14 %
• Parental protein coverage: 79.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ESCC-VVQTGVQWHDLGSLQPPPPGFKRFSCLSLPSSWDYRRTPPCPANFLV-LLPTGFCHVGKAG--LK
          E.CC.V.QTGVQWH.LGS.QPPPPGFK.FSCLSLPSSWDYR.TPPCPANF...L..TGF......G....
Retrocopy EFCC>VTQTGVQWHNLGSPQPPPPGFKQFSCLSLPSSWDYRHTPPCPANFCI>LVKTGFHLIDQDGRMIS

Parental  FLASSDPPIFASQSAGITGVSHSAENRLNIRV-SLPLPRLERNGAILAHCNLHLLGSGNSPASASRVAGI
          .....DPP..ASQSAGI.G.SH.A.........S....RLE..G.I.AHCNL.LLGS..SP..AS.VAGI
Retrocopy IA*PRDPPTSASQSAGIIGMSHHARSPFFFELESCSVARLECSGTISAHCNLRLLGSSDSPVRAS*VAGI

Parental  TGTRHHAQ
          ....HHAQ
Retrocopy IDALHHAQ

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	13.16 RPM
SRP051959_heart	0.00 RPM	81.88 RPM
SRP051959_kidney	0.00 RPM	6.41 RPM
SRP051959_liver	0.00 RPM	1.04 RPM
SRP051959_lung	0.02 RPM	17.91 RPM
SRP051959_lymph_node	0.00 RPM	4.06 RPM
SRP051959_skeletal_muscle	0.00 RPM	8.63 RPM
SRP051959_spleen	0.00 RPM	13.36 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3609 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3609 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3609 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,