RetrogeneDB ID: retro_cjac_435

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:81957066..81958055(+)
• 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_435
ACGGCCAACACAGAGGGCCTTCTGTGAGGTGGTTCCAGGCCTCAACGACACGCTGAGAACCTGCTGCGCACCATCGAGCT
TGGCCTGGAGGTATCTCCCTCTACGCTCTTCACCTTCGCCAGCATCCTGGAGGGCTGTGCCTTCCTCATTGGGTCCCTGC
CGAACACCCTGGTGCCCGGAGCTCTTGAGCTCGCGTGTCAGCGCCTGTTTTCGTGGGTAGAGATGACTTTAAGTCTGGCC
AGACTAAAGTCGAGTCCGTGCTTGTGGACTTCCTCATCAGCTCTGCCCTCAAGACCATGTCCATCGTGAGTTACAACCAC
CTGGGCAACAACTGGCAGAACCTGTCGGCGCCGTTGCAGTTCCGCTCTAAGGAGGTGTCCAAGAGCAACGTGGTGGACGA
CATGGTGCAGAGTAACCCAGTGCTCTATACACCCAGCGAGGAGCCCGGCCACTGAGTGGTCATCAAGTACATGCCGTACG
TGGGCGACAGCAAGCGCGCGCTGGATGAGTATACCTTGGAGCTAATGCTGGGTGGGACCAACTCACTGGTGCTGCACAAA
ACGTGCGAGGACTCCCTGCCGGCCGCACCCATTCTAGACCTGGCGCTGCTGACCGAGCTGTGCCAGCGCGTGAGCTTCTG
CACTGACGCCGACCCTGAGCCTCAGACCTTCCATCCCATTCTGTCCTTGCTCAGCTTCCTCTTCAAGGCGCCGCTAGTGC
TGCCGGGCAGCCCAGTGATCAATGCGCTTTTCCGCAAGTGCAGCTGCATCGAGAACATCCTCAGGGCCTGCGAGGGGCTC
CCGCCACAGAACCACATGCTCCTGGATCATAAGATGGAGTGCCCAGGGCCCAGACTCAAGCAAGTCGGACCCCTGGCTGC
TGCCCACCCTGTGTCGAACAAGAAAGGACTGGTACCCGTTTCCACCAACGGCTGTACCGGTGATGCCAATGGGTACCCAC
AAGTGGAGGAACCCCAGATGCCCACCACC

Alignment

ORF - retro_cjac_435 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.46 %
• Parental protein coverage: 93. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TANTE-RFCEVVPGLNDT-AENLLRTIELGLEVSPSTLFAVASILEGCAFLNGSPQNTLVPGALELACQR
          TANTE..FCEVVPGLNDT.AENLLRTIELGLEVSPSTLF..ASILEGCAFL.GS..NTLVPGALELACQR
Retrocopy TANTE>AFCEVVPGLNDT<AENLLRTIELGLEVSPSTLFTFASILEGCAFLIGSLPNTLVPGALELACQR

Parental  R-VFVGGDDFKSGQTKVKSVLVDFLISSGLKTMSIVSYNHLGNNDGQNLSAPLQFRSKEVSKSNVVDDMV
          ..VFVG.DDFKSGQTKV.SVLVDFLISS.LKTMSIVSYNHLGNN..QNLSAPLQFRSKEVSKSNVVDDMV
Retrocopy L<VFVGRDDFKSGQTKVESVLVDFLISSALKTMSIVSYNHLGNN-WQNLSAPLQFRSKEVSKSNVVDDMV

Parental  QSNPVLYMPGEEPDHCVVIKYVPYVGDSKRALDEYTSELMLGGTNTLVLHNTCEDSLLAAPIMLDLALLT
          QSNPVLY.P.EEP.H.VVIKY.PYVGDSKRALDEYT.ELMLGGTN.LVLH.TCEDSL.AAPI.LDLALLT
Retrocopy QSNPVLYTPSEEPGH*VVIKYMPYVGDSKRALDEYTLELMLGGTNSLVLHKTCEDSLPAAPI-LDLALLT

Parental  ELCQRVSFCTDADPEPQTFHPVLSLLSFLFKAPLVPPGSPVINALFRQRSCIENILRACVGLPPQNHMLL
          ELCQRVSFCTDADPEPQTFHP.LSLLSFLFKAPLV.PGSPVINALFR..SCIENILRAC.GLPPQNHMLL
Retrocopy ELCQRVSFCTDADPEPQTFHPILSLLSFLFKAPLVLPGSPVINALFRKCSCIENILRACEGLPPQNHMLL

Parental  EHKMERSGPSLKQVGPLTAACPVLNKKGPVPISTNGCTGDANGHPQVEEPSMLTT
          .HKME..GP.LKQVGPL.AA.PV.NKKG.VP.STNGCTGDANG.PQVEEP.M.TT
Retrocopy DHKMECPGPRLKQVGPLAAAHPVSNKKGLVPVSTNGCTGDANGYPQVEEPQMPTT

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	0.02 RPM	2.64 RPM
SRP051959_liver	0.00 RPM	0.93 RPM
SRP051959_lung	0.00 RPM	7.01 RPM
SRP051959_lymph_node	0.05 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_435 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_435 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_435 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,