RetrogeneDB ID: retro_cjac_2803

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:32303607..32304540(-)
• Located in intron of: ENSCJAG00000010218

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISYNA1
• Ensembl ID: ENSCJAG00000014230
• Aliases: None
• Description: None

Sequence

>retro_cjac_2803
ACACACCGCTTCTGTGAGGTGGTTCCAGGCCTCAAGGACGCGGCCGAGAACCTGCTGCGCACCACTGAGCTTGGCCTGCG
GGTGTCTCCCTCCACGCTCTTCGCCGTCGCCAGCATCCTGGAGGGCTGTGCCTTCCTCAGTGGGTCCCCGCAGAACACCC
TGCTGCCCGGAGCTCTGGAGCTCGCGTGTCAGCGCCGGGTTTTCGTGGGCGGAGATGACTTCAAGTCTGGACAGACCAAA
GTCAAGTTCGTGCTCGTGGACTTCCTCATCAGCTCTAGCCTCAAGACCATGTCCATCGTGAGTTACAACCACCTGGGCAA
CAACGAAGGGCAGAACCTGTCGGCGCCGTTGCAGTTCCGCTCTAAGGAGGTGTCCAAGAGCAACGTGGTGGACGACATGG
TGCAGAGCAACCCACTGCTCTATACGCCCGGCGAGGAGCCCGACCCCTGCGTGGTCATCAAGTACATGCCGTAAGTGGGC
GACAGCAAGCGCGCGCTGGATGAGTATACCTCGGAGCTAATGCTGGGCGGGACCAACACAGTGGTGCTGCAGGACACGTG
CGAGGACTCGCTGCTGGCCGCACCCATCACGCTAGACCTGGCGCAGCTGACCGAGCTGTGCCAGAGCCTGAGCTTCTGCG
CGGACGCTGACCCCAAGCCGCAGACCATCCACCCCTTGCTGTCCCTGCTCATCTTCCTATTCAAGGCGCCGCTGGTGCCG
CCGGGCAGCCGGGTGATCAATGCGCTTTTCCGCCAGAGCAGCTGCATCGAGAACATCCTCAGGGCCTGCATGGGGCTCCC
GCCACAGAACCACATGCTCCTGGAGCACAAGATGGAGCGCCCAGGGCCCGGCCTCAAGGAAGTCGGACCCGTGGCTTCCG
CCTGCCCTGTGTCGAACAAGAAAGGACCGATGGTACTCATCATCTCTCCATGC

Alignment

ORF - retro_cjac_2803 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.85 %
• Parental protein coverage: 55.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TERFCEVVPGLNDTAENLLRTIELGLEVSPSTLFAVASILEGCAFLNGSPQNTLVPGALELACQRRVFVG
          T.RFCEVVPGL.D.AENLLRT.ELGL.VSPSTLFAVASILEGCAFL.GSPQNTL.PGALELACQRRVFVG
Retrocopy THRFCEVVPGLKDAAENLLRTTELGLRVSPSTLFAVASILEGCAFLSGSPQNTLLPGALELACQRRVFVG

Parental  GDDFKSGQTKVKSVLVDFLISSGLKTMSIVSYNHLGNNDGQNLSAPLQFRSKEVSKSNVVDDMVQSNPVL
          GDDFKSGQTKVK.VLVDFLISS.LKTMSIVSYNHLGNN.GQNLSAPLQFRSKEVSKSNVVDDMVQSNP.L
Retrocopy GDDFKSGQTKVKFVLVDFLISSSLKTMSIVSYNHLGNNEGQNLSAPLQFRSKEVSKSNVVDDMVQSNPLL

Parental  YMPGEEPDHCVVIKYVPYVGDSKRALDEYTSELMLGGTNTLVLHNTCEDSLLAAPIMLDLALLTELCQRV
          Y.PGEEPD.CVVIKY.P.VGDSKRALDEYTSELMLGGTNT.VL..TCEDSLLAAPI.LDLA.LTELCQ..
Retrocopy YTPGEEPDPCVVIKYMP*VGDSKRALDEYTSELMLGGTNTVVLQDTCEDSLLAAPITLDLAQLTELCQSL

Parental  SFCTDADPEPQTFHPVLSLLSFLFKAPLVPPGSPVINALFRQRSCIENILRACVGLPPQNHMLLEHKMER
          SFC.DADP.PQT.HP.LSLL.FLFKAPLVPPGS.VINALFRQ.SCIENILRAC.GLPPQNHMLLEHKMER
Retrocopy SFCADADPKPQTIHPLLSLLIFLFKAPLVPPGSRVINALFRQSSCIENILRACMGLPPQNHMLLEHKMER

Parental  SGPSLKQVGPLTAACPVLNKKGPVPISTNGC
          .GP.LK.VGP...ACPV.NKKGP.......C
Retrocopy PGPGLKEVGPVASACPVSNKKGPMVLIISPC

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	0.55 RPM
SRP051959_heart	0.02 RPM	2.49 RPM
SRP051959_kidney	0.02 RPM	2.64 RPM
SRP051959_liver	0.00 RPM	0.93 RPM
SRP051959_lung	0.00 RPM	7.01 RPM
SRP051959_lymph_node	0.00 RPM	11.21 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.76 RPM
SRP051959_spleen	0.00 RPM	5.17 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2803 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2803 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2803 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014230	6 retrocopies	retro_cjac_2768, retro_cjac_2803 , retro_cjac_2809, retro_cjac_2831, retro_cjac_3817, retro_cjac_435,
Homo sapiens	ENSG00000105655	1 retrocopy	retro_hsap_2918,
Gorilla gorilla	ENSGGOG00000016939	1 retrocopy	retro_ggor_2019,
Nomascus leucogenys	ENSNLEG00000006026	1 retrocopy	retro_nleu_826,