RetrogeneDB ID: retro_cjac_1273

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:37133290..37133935(-)
• Located in intron of: ENSCJAG00000019192

Retrocopy information

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

Parental gene information

• Parental gene symbol: MA_R322_JSMB1F6EF
• Ensembl ID: ENSCJAG00000006738
• Aliases: None
• Description: None

Sequence

>retro_cjac_1273
GAGGAGGAAGTAATGATTCTGGAGAGAATCTTACTGTAGACCGTCAAGTTTGATTTATGGGTGGAACATACATACCAGTT
CCTACTCAAATATGCAAAGCAATTCAAAGGTGATAAAAACAAAATTCAAAAGTTGGTTCAAATGGCATGGACATTTGTAA
ATGACAGTCTCTGCACCACCTTGTCACTGCAGTGGGAACCAGAGATCATAGCGGTAGCAGTGATGTATCTCGCAGGACGT
TTGTGCAAATTCGAAATACAAGAATGAACCTCCAAACCCATGTATAGGAGGTGGTGGGAACAGTTTGTTCAAGATGTCCC
AGTTGACGTTTTGGAAGACATGTGCCACCAAATCCTGGATCTTTACTCACAAGGAAAACAACAGATGCCTCATCACACCC
CCCATCAGCTGCAACAGCCCCCATCTCTTCAGCCTGCACCACAAGTGCCGCAAGTACAACAGTCACAACCGTCTCAAGGC
TCCGAACCATCCCAGCCCCAGCAGAAGGACCCCCAGCAACCAGCCCAGTAGCAGCAGCCAGCCCAGCAGCCCAAGAAACC
CTCTCTGCAGCCCAGTTCTCCCCAACAGATTAAGCGAGCCATGGTTGTTTCTCCCAAAGAAGAGAACAAAGCAGAACCAC
CTTCA

Alignment

ORF - retro_cjac_1273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.05 %
• Parental protein coverage: 60.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEII
          .EEVM.LERILL.T.KFDL.VEH.YQFLLKYAKQ.KGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEII
Retrocopy EEEVMILERILL*TVKFDLWVEHTYQFLLKYAKQFKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEII

Parental  AVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQFVQDVPVDVLEDICHQILDLYSQGKQQMPHHTPHQLQQP
          AVAVMYLAGRLCKFEIQE.TSKPMYRRWWEQFVQDVPVDVLED.CHQILDLYSQGKQQMPHHTPHQLQQP
Retrocopy AVAVMYLAGRLCKFEIQE*TSKPMYRRWWEQFVQDVPVDVLEDMCHQILDLYSQGKQQMPHHTPHQLQQP

Parental  PSLQPTPQVPQVQQSQPSQGSEPSQPQQKDPQQPAQQQQPAQQPKKPSPQPSSPRQVKRAVVVSPKEENK
          PSLQP.PQVPQVQQSQPSQGSEPSQPQQKDP.............KKPS.QPSSP.Q.KRA.VVSPKEENK
Retrocopy PSLQPAPQVPQVQQSQPSQGSEPSQPQQKDPXXXXXXXXXXXXXKKPSLQPSSPQQIKRAMVVSPKEENK

Parental  AAGPA
          A..P.
Retrocopy AEPPS

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	0.24 RPM	8.10 RPM
SRP051959_heart	0.21 RPM	6.58 RPM
SRP051959_kidney	0.27 RPM	6.86 RPM
SRP051959_liver	0.06 RPM	4.92 RPM
SRP051959_lung	0.23 RPM	6.39 RPM
SRP051959_lymph_node	0.09 RPM	6.89 RPM
SRP051959_skeletal_muscle	0.24 RPM	5.55 RPM
SRP051959_spleen	0.13 RPM	6.87 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1273 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1273 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1273 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001388	1 retrocopy	retro_cjac_780,
Callithrix jacchus	ENSCJAG00000006738	1 retrocopy	retro_cjac_1273 ,
Callithrix jacchus	ENSCJAG00000011407	1 retrocopy	retro_cjac_1814,
Myotis lucifugus	ENSMLUG00000012493	1 retrocopy	retro_mluc_313,