RetrogeneDB ID: retro_cjac_445

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:90407479..90408613(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTOV1
• Ensembl ID: ENSCJAG00000004105
• Aliases: None
• Description: prostate tumor overexpressed 1 [Source:HGNC Symbol;Acc:9632]

Sequence

>retro_cjac_445
GCTCCTGGCCGGCCACAGCCTCCGCGGATCCGGGCCCGTTCGGCCCCTCCCATGGAAGGTGCTCGGGTCTTCGGGACGCT
GGGTCCCATCGGTCCCTCCTCGCCTGGGCTCACCCTCGGGGGTCTGGCAGTGAGCGAGCACCGGCTCAGCAACAAGCTGC
TTGCCTGGATCGGCGTCCTGGAGTGGCAGGAGAAGCGCAGACCCTACTCTGACTCCACCGCGAAACTGAAGCGGACCTTG
CCCTGCCAAGCCTGTGTGAACCAAGGGGAGAACCTGGAGACTGACCAGTGGCCGCAGAAGCTGATCATGCAGCTGATCCC
ACAGCAGCTGCTGACCACGCTGGGCCCACTGTTCCGCAACTCCCAGCTGGCACAGTTCCACTTCACCAACAGAGACTGTG
ACTCGCTCAAGGGGCTCTGCCGAGTCATGGGCAACGGCTTCGCGGACTGCATGCTGTTCCCCCACATCTTCCCCTGTGAG
GTGCGCGTGCTCATGCTCCTGTACTCGTCCAAGAAGAAGATCTTCATGGGCCTCATCCCCTACGACCAGAGCGGTTTCGT
CAGCGCCATCCGGCAGGTCATCACCACCCGCAAGCAGGCAGTGGGACCTGGTGGCGTCAACGCAGGCCCAGTGCAGATCG
TCAACAACAAGTTCCTGGCGTGGCGCGGTGTCATGGAGTGGCAGGAGCCCAGGCCTGAGCCCAACAGCCGGTCCAAGAGG
TGGCTGCCGTCCCACGTCTACGTGAACCAGGGAGAGATCCTGAGGACCGAGCAGTGGCCAAGAAAGCTGTGCATGCAGCT
CATCCCGCAGCAGCTGCTGACCACGCTGGTGCCGCAGTTTTGAAACTCACTCCTGGTGCAATTCCACTTCACCAAGGACC
TGGAGACGCTGAAGAGCCTGTGCCGCATCATGGACAATGGCTTCGCTGGCTGCGTGCACTTTTCCTACAAAGCGTCGTGT
GAGATCCGCGTGCTCATGCTCCTGTACTCTTCAGAGAAGAAAATCTTCATCGGCCTCATCCCCCATGACCAGGGCAACTT
TGTCAACGGCATCCGGCGCGTCATTGCCAACCAACAGCAGGTCCTACACCGGAACCTGGAGCAGGAGCAGCAGCAGCAGC
GAGGGATGGGGGGG

Alignment

ORF - retro_cjac_445 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.3 %
• Parental protein coverage: 90.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPRGPQPPRIRARSAPPMEGARVFGALGPIGPSSPGLTLGGLAVSEHRLSNKLLAWSGVLEWQEKRRPYS
          .P..PQPPRIRARSAPPMEGARVFG.LGPIGPSSPGLTLGGLAVSEHRLSNKLLAW.GVLEWQEKRRPYS
Retrocopy APGRPQPPRIRARSAPPMEGARVFGTLGPIGPSSPGLTLGGLAVSEHRLSNKLLAWIGVLEWQEKRRPYS

Parental  DSTAKLKRTLPCQAYVNQGENLETDQWPQKLIMQLIPQQLLTTLGPLFRNSQLAQFHFTNRDCDSLKGLC
          DSTAKLKRTLPCQA.VNQGENLETDQWPQKLIMQLIPQQLLTTLGPLFRNSQLAQFHFTNRDCDSLKGLC
Retrocopy DSTAKLKRTLPCQACVNQGENLETDQWPQKLIMQLIPQQLLTTLGPLFRNSQLAQFHFTNRDCDSLKGLC

Parental  RVMGNGFAGCMLFPHISPCEVRVLMLLYSSKKKIFMGLIPYDQSGFVSAIRQVITTRKQAVGPGGVNAGP
          RVMGNGFA.CMLFPHI.PCEVRVLMLLYSSKKKIFMGLIPYDQSGFVSAIRQVITTRKQAVGPGGVNAGP
Retrocopy RVMGNGFADCMLFPHIFPCEVRVLMLLYSSKKKIFMGLIPYDQSGFVSAIRQVITTRKQAVGPGGVNAGP

Parental  VQIVNNKFLAWSGVMEWQEPRPEPNSRSKRWLPSHVYVNQGEILRTEQWPRKLCMQLIPQQLLTTLVPLF
          VQIVNNKFLAW.GVMEWQEPRPEPNSRSKRWLPSHVYVNQGEILRTEQWPRKLCMQLIPQQLLTTLVP.F
Retrocopy VQIVNNKFLAWRGVMEWQEPRPEPNSRSKRWLPSHVYVNQGEILRTEQWPRKLCMQLIPQQLLTTLVPQF

Parental  RNSRLVQFHFTKDLETLKSLCRIMDNGFAGCVHFSYKASCEIRVLMLLYSSEKKIFIGLIPHDQGNFVNG
          .NS.LVQFHFTKDLETLKSLCRIMDNGFAGCVHFSYKASCEIRVLMLLYSSEKKIFIGLIPHDQGNFVNG
Retrocopy *NSLLVQFHFTKDLETLKSLCRIMDNGFAGCVHFSYKASCEIRVLMLLYSSEKKIFIGLIPHDQGNFVNG

Parental  IRRVIANQQQVLQRNLEQE-QQQRGMGG
          IRRVIANQQQVL.RNLEQE.QQQRGMGG
Retrocopy IRRVIANQQQVLHRNLEQEQQQQRGMGG

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	4.90 RPM
SRP051959_heart	0.02 RPM	10.93 RPM
SRP051959_kidney	0.00 RPM	9.38 RPM
SRP051959_liver	0.00 RPM	6.17 RPM
SRP051959_lung	0.00 RPM	9.21 RPM
SRP051959_lymph_node	0.00 RPM	7.90 RPM
SRP051959_skeletal_muscle	0.02 RPM	9.15 RPM
SRP051959_spleen	0.00 RPM	8.17 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_445 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_445 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_445 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003495	1 retrocopy	retro_cfam_289,
Callithrix jacchus	ENSCJAG00000004105	1 retrocopy	retro_cjac_445 ,
Homo sapiens	ENSG00000104960	1 retrocopy	retro_hsap_2694,
Gorilla gorilla	ENSGGOG00000010182	1 retrocopy	retro_ggor_1877,
Macaca mulatta	ENSMMUG00000011618	1 retrocopy	retro_mmul_1426,
Nomascus leucogenys	ENSNLEG00000005374	1 retrocopy	retro_nleu_1191,
Pongo abelii	ENSPPYG00000010265	1 retrocopy	retro_pabe_2288,
Pan troglodytes	ENSPTRG00000011321	1 retrocopy	retro_ptro_1818,