RetrogeneDB ID: retro_cjac_2831

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:95644521..95645507(-)
• Located in intron of: ENSCJAG00000013398

Retrocopy information

• Ensembl ID: ENSCJAG00000013531
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_2831
ACACAGCGCTTCTGTGAGGTGGTTCCAGGCCTCAACTACACGGCCGAGAACCTGCTGCGCACCACTGAGCTTGGCCTGCA
GGTGTCTCCCTCCACGCTCTTCGCCGTTGCCAGCATCCTGGAGGGCTGTGCTTTCCACAATGAGTCCCCGCAGAACACCC
TGCTACCCGGAGCTCTTGAGCTCGCGTGTCAGTGCCGGGTTTTCGTGGGTGGATATGACTTCATGTCTGGCCAGACCAAA
GTCAAGTCCGTGCTGTGGACTTTCTCATCAGCTCTGGCCTCAAGACCATGTCCATCGTGAGTTACAACAACCTGGGCAAC
AACGACGGGCACAACCTGTCGGCGCCGTTGCAGTTCCGCTCTAAGGAGGTGTCCAAGAACAACGTGGTGGACGACATGGT
GCAGAGCAACACACTGCTCTATACGCCCGGCGAGGAGCCCGACCGCTGCGTGGTCATGAAGTACGTGCCGTACGTGGGTG
ACAGCAAGGGCGCGCTGGATGAGTATACCTCGGAGCTAATGCTGGGCGGGACCAACACAGTGGGGCTGCACAACAGATGC
AAGAACTTGCTGCTGGCCGCACCCATCACGCTAGACCTGGCGCTGCTGACCGAGCTGTCCCAGCGCATGAGCTTCTGCGT
GGACGCTGACCCCGAGCCGCAGACTATCCACCCCGTGCTGTCCCTGCTCAGCTTCCTATTCAAGGCGCCGCTGGTACCGC
CGGACAGTCCGGTGATCAATGTGCTTCTCCACCAGCGCAGCTGCATCGAGAACATCCTCAGGGCCTGCGTGGGGCTCCCG
CCACAGAATCACATACTCCTGGAGCACAAGATGGAGCGCCCAGGGCCCGGACTCAAGCAAGTTGGACTTGTGGCTGCCGC
CAGCCCTGTGTCCAACAAGAAAGGTCCGGTACCTGCTTCCACCGACGGCTGCACCGGTGATGCCAATGGGAACCCACAAG
TGGAGGAACCCCAGGTGCCCAACACC

Alignment

ORF - retro_cjac_2831 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.85 %
• Parental protein coverage: 92.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TERFCEVVPGLNDTAENLLRTIELGLEVSPSTLFAVASILEGCAFLNGSPQNTLVPGALELACQRRVFVG
          T.RFCEVVPGLN.TAENLLRT.ELGL.VSPSTLFAVASILEGCAF.N.SPQNTL.PGALELACQ.RVFVG
Retrocopy TQRFCEVVPGLNYTAENLLRTTELGLQVSPSTLFAVASILEGCAFHNESPQNTLLPGALELACQCRVFVG

Parental  GDDFKSGQTKVKSVL-VDFLISSGLKTMSIVSYNHLGNNDGQNLSAPLQFRSKEVSKSNVVDDMVQSNPV
          G.DF.SGQTKVKSVL.VDFLISSGLKTMSIVSYN.LGNNDG.NLSAPLQFRSKEVSK.NVVDDMVQSN..
Retrocopy GYDFMSGQTKVKSVL<VDFLISSGLKTMSIVSYNNLGNNDGHNLSAPLQFRSKEVSKNNVVDDMVQSNTL

Parental  LYMPGEEPDHCVVIKYVPYVGDSKRALDEYTSELMLGGTNTLVLHNTCEDSLLAAPIMLDLALLTELCQR
          LY.PGEEPD.CVV.KYVPYVGDSK.ALDEYTSELMLGGTNT..LHN.C...LLAAPI.LDLALLTEL.QR
Retrocopy LYTPGEEPDRCVVMKYVPYVGDSKGALDEYTSELMLGGTNTVGLHNRCKNLLLAAPITLDLALLTELSQR

Parental  VSFCTDADPEPQTFHPVLSLLSFLFKAPLVPPGSPVINALFRQRSCIENILRACVGLPPQNHMLLEHKME
          .SFC.DADPEPQT.HPVLSLLSFLFKAPLVPP.SPVIN.L..QRSCIENILRACVGLPPQNH.LLEHKME
Retrocopy MSFCVDADPEPQTIHPVLSLLSFLFKAPLVPPDSPVINVLLHQRSCIENILRACVGLPPQNHILLEHKME

Parental  RSGPSLKQVGPLTAACPVLNKKGPVPISTNGCTGDANGHPQVEEPSMLTT
          R.GP.LKQVG...AA.PV.NKKGPVP.ST.GCTGDANG.PQVEEP....T
Retrocopy RPGPGLKQVGLVAAASPVSNKKGPVPASTDGCTGDANGNPQVEEPQVPNT

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	0.60 RPM	0.55 RPM
SRP051959_heart	0.44 RPM	2.49 RPM
SRP051959_kidney	0.44 RPM	2.64 RPM
SRP051959_liver	0.39 RPM	0.93 RPM
SRP051959_lung	0.67 RPM	7.01 RPM
SRP051959_lymph_node	0.75 RPM	11.21 RPM
SRP051959_skeletal_muscle	0.39 RPM	0.76 RPM
SRP051959_spleen	0.57 RPM	5.17 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2831 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2831 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2831 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,