RetrogeneDB ID: retro_cjac_3024

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:128373198..128374190(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STRADA
• Ensembl ID: ENSCJAG00000019701
• Aliases: None
• Description: None

Sequence

>retro_cjac_3024
AAGATTAACCTGGAAGCTTGTTCCAGTGCGATGGTAGCATTATTGCAGGGCAAGCTGCATATCTCTAGACTCTTCAAACA
TCCCAATATTGTGCCATATCGAGCCAACTTTATTGCAGACAATGACAATGAGCTGTGGGTTGTCACATCATTAATGGCGT
ATGGTTCTGCAAAGGATCTCATCTGTACACACTTTATGGATGGCATGAATGAGCTGGCAATCACTTACATCCTGCAGGGG
TGCTGAAGGCCCTCGACTACATCCACCACATCGGATATGTACACAGGAGTGTCAAAACGAGCCACATCCTCATCTCTGTG
GATGGGAAGGTCTACCTGTCTGGTTTGTGCAGCAACCTCAGCATGATAAGCCACCAGCAGTGGCAGTGAGTGGTCCACGA
CTTTCCCGAGTACAGTGTCAAGGTTCTGCTGTGGCTCGGCCCTGAGGTCCCCAGAAGAATCTCCAGGGTTATGATGCCAA
GGCTGACATCTACAGTGTGGGAATCACAGTGTGTGAACTGGCCAATGGCCACGTCCCCTTTTAAGAATATGCCTACTACC
CAGATGCTGCAGAGAAATTGAATGGCACAGTGCCCTGCCTGTTGGATACCAGCACCATCTTCTCCAAGGAGCTGACCATG
AGCCCTTCATGCTCAGTGGCCAACTCAGGCCTGAATGAAAGCCTGACCACCAGCAACCCCTGGCCTCCAATGGCAACTCG
CCTACTCACCCTTACCACCGAACCTTCTCCCACTTCCACCACTTTGTGGAGCAGTGCCTTCAGTGCAACCCAGATGCCTG
GCAGAACACCAGCACCCTCCTGAACCACTCTTTTTCAAGCAGATCAAGCGACGTGCCTCAGAGGCTTTGCCTGAATTGCT
TTGTCCTGTCACCCCCATCACCAGTTTTGAAGGCAGCCAGTCTCAGGACTGCAGTGGAATCTTTGGCTGAGTAACAAACC
TGGAAGAGCTAGAGGTGGACGATTGGGAGTTC

Alignment

ORF - retro_cjac_3024 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.89 %
• Parental protein coverage: 88.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  RINLEACSNEMVTFLQGELHVSKLFSHPNIVPYRATFIADN--ELWVVTSFMAYGSAKDLICTHFMDGMN
          .INLEACS..MV..LQG.LH.S.LF.HPNIVPYRA.FIADN..ELWVVTS.MAYGSAKDLICTHFMDGMN
Retrocopy KINLEACSSAMVALLQGKLHISRLFKHPNIVPYRANFIADNDNELWVVTSLMAYGSAKDLICTHFMDGMN

Parental  ELAIAYILQG-VLKALDYIHHMGYVHRSVKASHILISVDGKVYLSGLRSNLSMISHGQRQRVVHDFPKYS
          ELAI.YILQG.VLKALDYIHH.GYVHRSVK.SHILISVDGKVYLSGL.SNLSMISH.Q.Q.VVHDFP.YS
Retrocopy ELAITYILQG<VLKALDYIHHIGYVHRSVKTSHILISVDGKVYLSGLCSNLSMISHQQWQ*VVHDFPEYS

Parental  VKVLPWLSPEVL-QQNLQGYDAKSDIYSVGITACELANGHVPF-KDMPATQML-LEKLNGTVPCLLDTST
          VKVL.WL.PEV..Q.NLQGYDAK.DIYSVGIT.CELANGHVPF.K.MP.TQML..EKLNGTVPCLLDTST
Retrocopy VKVLLWLGPEVP<QKNLQGYDAKADIYSVGITVCELANGHVPF>KNMPTTQML<AEKLNGTVPCLLDTST

Parental  IPTEELTMSPSRSVANSGLSDSLTTSTPRP-SNGDSPSHPYHRTFSPHFHHFVEQCLQRNPDSRPSASTL
          I...ELTMSPS.SVANSGL..SLTTS.P.P.SNG.SP.HPYHRTFS.HFHHFVEQCLQ.NPD.....STL
Retrocopy IFSKELTMSPSCSVANSGLNESLTTSNPWP<SNGNSPTHPYHRTFS-HFHHFVEQCLQCNPDAWQNTSTL

Parental  LNHS-FFKQIKRRASEALPELLRPVTPITNFEGSQSQDHSGIFGLITNLEELEVDDWEF
          LNHS.FFKQIKRRASEALPELL.PVTPIT.FEGSQSQD.SGIFG..TNLEELEVDDWEF
Retrocopy LNHS<FFKQIKRRASEALPELLCPVTPITSFEGSQSQDCSGIFG*VTNLEELEVDDWEF

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	6.70 RPM
SRP051959_heart	0.00 RPM	10.19 RPM
SRP051959_kidney	0.02 RPM	10.25 RPM
SRP051959_liver	0.00 RPM	6.95 RPM
SRP051959_lung	0.00 RPM	12.90 RPM
SRP051959_lymph_node	0.02 RPM	22.74 RPM
SRP051959_skeletal_muscle	0.02 RPM	10.18 RPM
SRP051959_spleen	0.04 RPM	13.51 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3024 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3024 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3024 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019701	1 retrocopy	retro_cjac_3024 ,