RetrogeneDB ID: retro_cjac_3372

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01175663.1:27149..27618(-)
• Located in intron of: ENSCJAG00000019545

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_3372
GTTACCCAGGGTGAAGTGCAGTGGCGCAATCTTCACTCACTGCAACCTCCGCCTCCCAGGTTCAAGTGATTCTCCTGCCT
TAGCCTACTGGGTAGCTGGGACTATGGGAGTATGCCACCGTGTCTGACTAATTTTTGTATTTTTAGTAGAGATGGATTTT
CACCATGTTGGCTAGGCTGGTCTTGAACTCCTGGCCTCAAGTGATCCACCCTCCTGGGCCTCCCAAAGTGCTGGGATTTC
AGGTGTGAGCCACTGTGCCTGGACTTTTTTTTTTTTTTGAGATAGTCTTGCTCTATTACACAGGCTGGAGTGCAAAGGCA
CACTCTCAGCTCACTGCAACCTCCCAGGTCCAAGTGATTCTCCTGCCTCAGCCTCCTGAATAGCTGGGACTACAGATATG
CACCATCATGCCTGGCTAATTTCTGTATTTTTAGTAGGGATGATGTTTCACCATCTTGTCCAGGCTGGT

Alignment

ORF - retro_cjac_3372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.86 %
• Parental protein coverage: 86.67 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VVQTGVQWHDLGSLQPPPPGFKRFSCLSLPSSWDYRRTPPCPANFLVLLPTGFC-HVGKAGLKFLASSDP
          V.Q..VQW..L.SLQPPPP.FK.FSCLSL..SWDY...PPC..NF......GF..HVG.AGL..LASSDP
Retrocopy VTQGEVQWRNLHSLQPPPPRFK*FSCLSLLGSWDYGSMPPCLTNFCIFSRDGFS>HVG*AGLELLASSDP

Parental  PIFASQSAGITGVSHSAENRLNIRVSLPL-PRLERNGAILAHCNLHLLGSGNSPASASRVAGITGTRHHA
          P..ASQSAGI.GVSH.A........SL.L..RLE..G...AHCNL...G...SPASAS..AG.T...HHA
Retrocopy PSWASQSAGISGVSHCAWTFFFF*DSLALLHRLECKGTLSAHCNLP--GPSDSPASAS*IAGTTDMHHHA

Parental  QLI-FFLVETGFHHVDQDG
          .LI..FLV...FHH..Q.G
Retrocopy WLISVFLVGMMFHHLVQAG

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	0.07 RPM	13.16 RPM
SRP051959_heart	0.02 RPM	81.88 RPM
SRP051959_kidney	0.07 RPM	6.41 RPM
SRP051959_liver	0.13 RPM	1.04 RPM
SRP051959_lung	0.15 RPM	17.91 RPM
SRP051959_lymph_node	0.14 RPM	4.06 RPM
SRP051959_skeletal_muscle	0.00 RPM	8.63 RPM
SRP051959_spleen	0.15 RPM	13.36 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3372 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3372 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,