RetrogeneDB ID: retro_cjac_2770

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:125948220..125949025(+)
• Located in intron of: ENSCJAG00000010773

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNAI1
• Ensembl ID: ENSCJAG00000000518
• Aliases: None
• Description: None

Sequence

>retro_cjac_2770
CATGCCGCGGTCTTTCCTTGTCAGGAGGCCCTTTGACCCCGATCGGAAGCCAAACTACAGCAAGCTCCAGGACTCTCATC
TAGAGTTTACCTTCCAGCAAGCCTACGAGCAGGCCCACTTGCTGGCAGCCACCATCCCACGTCCGGAGATCCTCAATCCC
ACCGCCTCGCTGCCAACGCTCATCTGGGACGCTTTCCTGGAGCTCCACGCCCAGCCAATTGCCCGGGCCTCCCTCCAGTT
TGGACTCTCCCAGGAGAGTGGCAAGGCAGCAGAGCTGACCTCGCTGTCGGATGAGGACAGCGGGAAAGGCTCCCAGCCCC
GCAGCCCACTCTCACAGGCTCCTTTGTCTTTCTTCTCCACTTCAGCCTCTTCCTTGGAGGCCGAGGCCGATGCCGCCTTG
CCAGGCTTGGGCCAAGTGCCCAAGCGGCTGGCCCAGCTCTCTGAGACCAGGGATTCCCAGTTTCGAAAAGCCTTCAACTG
CAGATACTGCAATAAGGAATGCCTCAGCCTGAGTGCCCTCAAGACGCACATCCGAACCCACACGCTACCCTTTGTCTGTG
AAATTTGCGGGAAGACCTTTTCCAGACCCTGGTTGCTGCAGTGCCATGTCCGGACCCACACCGGTGAGAAGCCCTTCTCC
TGTCCCCACTGCAGCCGCGCCTTCGCCGACCGCTCCAACCTGCGGGCCCACCTCCAGACCCACTTGGAGGTCAAGAAGTA
CCAGTGCCAGGCGTGCACTCAAACCTTCTCCCGAATGGCCTTGCTCCACAAGCACCAAGAGTCGAGCTGCTCAGGGGGCC
CCCGC

Alignment

ORF - retro_cjac_2770 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HAALFFLSEAL-DSNRRPNYSELQTLS-KFTFQQPYDQAHLLAA-IPPPEILNPTASLPTLIWDSVLAPQ
          HAA.F...EAL.D..R.PNYS.LQ.....FTFQQ.Y.QAHLLAA.IP.PEILNPTASLPTLIWD..L...
Retrocopy HAAVFPCQEAL>DPDRKPNYSKLQDSHLEFTFQQAYEQAHLLAATIPRPEILNPTASLPTLIWDAFLELH

Parental  AQPTAWASLR---AQESPRAAELTSLSDEDSGKGSQPPSPPSPASSSFSSTSASSLEAEAYAVFPGLVQV
          AQP.A.ASL.....QES..AAELTSLSDEDSGKGSQP.SP.S.A..SF.STSASSLEAEA.A..PGL.QV
Retrocopy AQPIARASLQFGLSQESGKAAELTSLSDEDSGKGSQPRSPLSQAPLSFFSTSASSLEAEADAALPGLGQV

Parental  PKQLAQLSEAKDLQSRKAFNCKYCNKEYLSLGALKMHIRSHTLPCVCGTCGKAFSRPWLLQGHVRTHTGE
          PK.LAQLSE..D.Q.RKAFNC.YCNKE.LSL.ALK.HIR.HTLP.VC..CGK.FSRPWLLQ.HVRTHTGE
Retrocopy PKRLAQLSETRDSQFRKAFNCRYCNKECLSLSALKTHIRTHTLPFVCEICGKTFSRPWLLQCHVRTHTGE

Parental  KPFSCPHCSRAFADRSNLRAHLQTHSDVKKYQCQACARTFSRMSLLHKHQESGCSGCPR
          KPFSCPHCSRAFADRSNLRAHLQTH..VKKYQCQAC..TFSRM.LLHKHQES.CSG.PR
Retrocopy KPFSCPHCSRAFADRSNLRAHLQTHLEVKKYQCQACTQTFSRMALLHKHQESSCSGGPR

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	0.49 RPM
SRP051959_heart	0.00 RPM	0.30 RPM
SRP051959_kidney	0.00 RPM	0.27 RPM
SRP051959_liver	0.00 RPM	0.13 RPM
SRP051959_lung	0.00 RPM	0.62 RPM
SRP051959_lymph_node	0.00 RPM	0.05 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.57 RPM
SRP051959_spleen	0.00 RPM	0.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2770 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2770 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2770 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000518	1 retrocopy	retro_cjac_2770 ,
Myotis lucifugus	ENSMLUG00000015053	2 retrocopies	retro_mluc_117, retro_mluc_726,
Macaca mulatta	ENSMMUG00000019719	1 retrocopy	retro_mmul_214,