RetrogeneDB ID: retro_cjac_2768

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:125247012..125247999(+)
• Located in intron of: None

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_2768
ACACAGCGCTTCTGTGAGGTGGTTCCAGGACTCAACGACACGGCCGAGAACCTGCTGCGCATTACTGAGCTTGGCCTGCA
GGTGTCTCCCTCCACGCTCTTCGCCGTCGCCAGCATCCTGGAGGGCTGTGCCTTCCTCAGTGGGTCCCCGCAGAACGCCC
TGCTGCCCGGAGCGCTGGAGCTCGCGTGTCAGCGCCAGGTTTTCCTGGGCGGAGATGACTTCAAGTCTGGCCAGACCAAA
GTCAAGTCCGTGTTCGTGGACTTCCTCATCAGCTCTGACCTCAAGACCATGTCCATCGTGAGTTACAACCACCTGGGCAA
CAAGGATGGGCAGAACCTGTCGGCGCCGTTGCAGTTCCGCTCTAAGGAGGTGTCCAAGAGCAACGTGGTGGATGACATGG
TGCAGAGCAACCCACTGCTCCATACGCCCGACGAGGAGCCCGACCCCTGCGTGGTCATCAAGTACATGCCGTAAGTGGGC
GACAGCAAGCTCCCGCTGGATGAGTATACCTCGGAGCTAATGCTGGGCGAGACCAACACAGTGGTGCTGCAGGACACGTG
CGAGGACTCGCTGCTGGCCGCACCCATCACGCTAGACCTGGCGCTGCTGACCGACCTGTGCCAGCGCATGAGCTTCTGTG
CGGATGCTGACCCCGAGCCGCAGACCATCCACCCGGTGCTGTCCCTGCTCAGCTTCCTATTCAAGGCGCCGCTGGTGCCG
CGGGACAGCCGGGTGATCAATGCGCTTTTCCGCCAGCGCAGCTGCATCGAGAGCATCCTCAGGGCCTGCGTGGGGCTCCC
GCCACAGAACCACATGCTCCTGGAGCACAAGATGGAGCGCCCAGGGCCCAGCCTCAAGCTAGCCGGACCCGTGGCTGCCG
CCTGCCCTGTGTCGAACAACAAAGGACCAAAACCCGCTTCCACCAACGGCTGCACCGCTGATGCCAATGGGCACCCACAA
GTGGAGGAACCCTAGATGCCCACCACC

Alignment

ORF - retro_cjac_2768 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.02 %
• Parental protein coverage: 92.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TERFCEVVPGLNDTAENLLRTIELGLEVSPSTLFAVASILEGCAFLNGSPQNTLVPGALELACQRRVFVG
          T.RFCEVVPGLNDTAENLLR..ELGL.VSPSTLFAVASILEGCAFL.GSPQN.L.PGALELACQR.VF.G
Retrocopy TQRFCEVVPGLNDTAENLLRITELGLQVSPSTLFAVASILEGCAFLSGSPQNALLPGALELACQRQVFLG

Parental  GDDFKSGQTKVKSVLVDFLISSGLKTMSIVSYNHLGNNDGQNLSAPLQFRSKEVSKSNVVDDMVQSNPVL
          GDDFKSGQTKVKSV.VDFLISS.LKTMSIVSYNHLGN.DGQNLSAPLQFRSKEVSKSNVVDDMVQSNP.L
Retrocopy GDDFKSGQTKVKSVFVDFLISSDLKTMSIVSYNHLGNKDGQNLSAPLQFRSKEVSKSNVVDDMVQSNPLL

Parental  YMPGEEPDHCVVIKYVPYVGDSKRALDEYTSELMLGGTNTLVLHNTCEDSLLAAPIMLDLALLTELCQRV
          ..P.EEPD.CVVIKY.P.VGDSK..LDEYTSELMLG.TNT.VL..TCEDSLLAAPI.LDLALLT.LCQR.
Retrocopy HTPDEEPDPCVVIKYMP*VGDSKLPLDEYTSELMLGETNTVVLQDTCEDSLLAAPITLDLALLTDLCQRM

Parental  SFCTDADPEPQTFHPVLSLLSFLFKAPLVPPGSPVINALFRQRSCIENILRACVGLPPQNHMLLEHKMER
          SFC.DADPEPQT.HPVLSLLSFLFKAPLVP..S.VINALFRQRSCIE.ILRACVGLPPQNHMLLEHKMER
Retrocopy SFCADADPEPQTIHPVLSLLSFLFKAPLVPRDSRVINALFRQRSCIESILRACVGLPPQNHMLLEHKMER

Parental  SGPSLKQVGPLTAACPVLNKKGPVPISTNGCTGDANGHPQVEEPSMLTT
          .GPSLK..GP..AACPV.N.KGP.P.STNGCT.DANGHPQVEEP.M.TT
Retrocopy PGPSLKLAGPVAAACPVSNNKGPKPASTNGCTADANGHPQVEEP*MPTT

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	0.00 RPM	2.49 RPM
SRP051959_kidney	0.00 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_2768 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2768 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2768 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,