RetrogeneDB ID: retro_cjac_500

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:4620929..4621280(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000003196
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TXNDC9
• Ensembl ID: ENSCJAG00000009936
• Aliases: None
• Description: thioredoxin domain containing 9 [Source:HGNC Symbol;Acc:24110]

Sequence

>retro_cjac_500
ATGGAAGCTGATGCATCCGTTGATATGTTTTCCAAAGTCCTAGAGAATCAGCTGCTTCAGACTACCAAACTAGTGAAAGA
ACATTTGGATTCTGAAATTCAGAAACTGGATCAGATGGATGAGGATGAATTGGAATGGCTTAAAGAAAAGAGACTTGAGG
CACTAAGGAAAGCTCAACAACAGAAACAAGAATGGCTTTCTAAAGGACATGGGGAATACAGAGAAATCCCTAGTGAAAGA
GACTTTTTTGAAGAAGTCAAGGAAAGCAAAAAAGTGGTTTGCCATTTCTATAGAGACTCCACATTCAGGTGTAAAACACT
AGACAGACATCTGGTGATATTGTCCTCGAGA

Alignment

ORF - retro_cjac_500 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.16 %
• Parental protein coverage: 51.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEADASVDMFSKVLENQLLQTTKIVEEHLDSEIQKLDQMDEDELERLKEKRLQALRKAQQQKQEWLSKGH
          MEADASVDMFSKVLENQLLQTTK.V.EHLDSEIQKLDQMDEDELE.LKEKRL.ALRKAQQQKQEWLSKGH
Retrocopy MEADASVDMFSKVLENQLLQTTKLVKEHLDSEIQKLDQMDEDELEWLKEKRLEALRKAQQQKQEWLSKGH

Parental  GEYREIPSERDFFQEVKESKKVVCHFYRDSTFRCKILDRHLVILSKK
          GEYREIPSERDFF.EVKESKKVVCHFYRDSTFRCK.LDRHLVILS..
Retrocopy GEYREIPSERDFFEEVKESKKVVCHFYRDSTFRCKTLDRHLVILSSR

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	10.23 RPM
SRP051959_heart	0.00 RPM	8.56 RPM
SRP051959_kidney	0.00 RPM	11.20 RPM
SRP051959_liver	0.02 RPM	7.17 RPM
SRP051959_lung	0.00 RPM	10.18 RPM
SRP051959_lymph_node	0.00 RPM	13.15 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.76 RPM
SRP051959_spleen	0.00 RPM	11.91 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_500 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_500 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_500 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009936	1 retrocopy	retro_cjac_500 ,
Dipodomys ordii	ENSDORG00000013557	1 retrocopy	retro_dord_141,
Homo sapiens	ENSG00000115514	1 retrocopy	retro_hsap_3042,
Gorilla gorilla	ENSGGOG00000024615	1 retrocopy	retro_ggor_2096,
Myotis lucifugus	ENSMLUG00000008110	1 retrocopy	retro_mluc_717,
Mus musculus	ENSMUSG00000058407	2 retrocopies	retro_mmus_2791, retro_mmus_873,
Pan troglodytes	ENSPTRG00000012278	1 retrocopy	retro_ptro_1996,