RetrogeneDB ID: retro_cjac_1369

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:98452587..98452963(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TXNDC12
• Ensembl ID: ENSCJAG00000021581
• Aliases: None
• Description: thioredoxin domain containing 12 (endoplasmic reticulum) [Source:HGNC Symbol;Acc:24626]

Sequence

>retro_cjac_1369
AAGATGCAGTCAGTTCCTAGCAGTTTGCCCCTGATGGTGATTATTCATAAGTCATGGTGTGGAGCTTGCAATGCTTGAAA
GCCCAAATTTGCAGAACCTCTAGAAATTTCAGAACTTTCTCATAGTTTTGTTACGGTAAACCTTGAGGATGAAGGAGGAC
GCAAGGATGAGGATTTTGCCCTGATAGAGTTATATTTCACACATCGTTTGTTTGGATCCCAGTGGTAAGGCGCATCCTGA
AATCATCAATGAGAATGGAAACTCCAGCTGCAAGTATTTCTACATCAGTGCCGAGCAAGTTGTTCAGGGGATGAAGGAAG
CTCAGGAAAGGCTGATGGGTGATGCCTTTAGAAAGAAACGTCTTGATAATGATTTG

Alignment

ORF - retro_cjac_1369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.44 %
• Parental protein coverage: 73.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKEAAASGLPLMVIIHKSWCGACKALKPKFAESTEISELSHNFVMVNLEDEEEPKDEDFS-PDG-GYIPR
          K.....S.LPLMVIIHKSWCGAC.A.KPKFAE..EISELSH.FV.VNLEDE...KDEDF..PD...YI..
Retrocopy KMQSVPSSLPLMVIIHKSWCGACNA*KPKFAEPLEISELSHSFVTVNLEDEGGRKDEDFA<PDR<SYISH

Parental  ILFLDPSGKVHPEIINENGNPSYKYFYVSAEQVVQGMKEAQERLTGDAFREKHLEDEL
          I..LDPSGK.HPEIINENGN.S.KYFY.SAEQVVQGMKEAQERL.GDAFR.K.L...L
Retrocopy IVCLDPSGKAHPEIINENGNSSCKYFYISAEQVVQGMKEAQERLMGDAFRKKRLDNDL

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	0.04 RPM	10.96 RPM
SRP051959_heart	0.02 RPM	7.40 RPM
SRP051959_kidney	0.00 RPM	13.38 RPM
SRP051959_liver	0.00 RPM	20.10 RPM
SRP051959_lung	0.02 RPM	9.84 RPM
SRP051959_lymph_node	0.02 RPM	8.15 RPM
SRP051959_skeletal_muscle	0.07 RPM	8.34 RPM
SRP051959_spleen	0.02 RPM	10.88 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1369 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1369 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1369 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021581	2 retrocopies	retro_cjac_1369 , retro_cjac_1440,