RetrogeneDB ID: retro_cjac_3226

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:64031590..64032100(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023388
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TESC
• Ensembl ID: ENSCJAG00000009509
• Aliases: None
• Description: tescalcin [Source:HGNC Symbol;Acc:26065]

Sequence

>retro_cjac_3226
AAGGAGAACTTCAACAATGTCCCGGACCTGGAGCTCAACCCCATCCGTTCCAAAATTGTTCGTGCCTTCTTCGACCACAG
GAACCTGCGCAAGGGACCCAGCGGCCTGGCTGATGAGATCAATTTCGAGGACTTCCTGACTATCATGTCCTACTTCCGGC
CCATCGACACCAACACGGGCGAGGAGCAGGTGGCGCAGTCCCGGAAGGAGAAGCTGAGATTTCTGTTCCACATGTATGAC
GCCGACAGCGACGGCCGCATCACCCTGGAAGAATACCGAAATGTGGTCGAGGAGCTGCTGTTGGAAAACCAGCACATGGA
GGAGTCCGCTGGCTCCATCGCCGAGGGGGCCATGATGGAGGCGGCCAGCGTGTGCTTGGGGCAAATGGAGCCTGATCAGG
TGTACGAAGGGATCACCTTCGAGGACTTCCTGAAGATCTTGCAGGGGATCGACATTGAGTCCAAGATGCACATCTGCTTC
CTTAACATGGAAACCATGGCCCTCTGCCAC

Alignment

ORF - retro_cjac_3226 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.47 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KENFNNVPDLELNPIRSKIVRAFFDNRNLRKGPSGLADEINFEDFLTIMSYFRPIDTTMGEEQVELSRKE
          KENFNNVPDLELNPIRSKIVRAFFD.RNLRKGPSGLADEINFEDFLTIMSYFRPIDT..GEEQV..SRKE
Retrocopy KENFNNVPDLELNPIRSKIVRAFFDHRNLRKGPSGLADEINFEDFLTIMSYFRPIDTNTGEEQVAQSRKE

Parental  KLRFLFHMYDSDSDGRITLEEYRNVVEELLSGNPHIEKESARSIADGAMMEAASVCVGQMEPDQVYEGIT
          KLRFLFHMYD.DSDGRITLEEYRNVVEELL..N.H.E.ESA.SIA.GAMMEAASVC.GQMEPDQVYEGIT
Retrocopy KLRFLFHMYDADSDGRITLEEYRNVVEELLLENQHME-ESAGSIAEGAMMEAASVCLGQMEPDQVYEGIT

Parental  FEDFLKIWQGIDIETKMHVRFLNMETMALCH
          FEDFLKI.QGIDIE.KMH..FLNMETMALCH
Retrocopy FEDFLKILQGIDIESKMHICFLNMETMALCH

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	0.78 RPM
SRP051959_heart	0.28 RPM	5.77 RPM
SRP051959_kidney	0.04 RPM	0.64 RPM
SRP051959_liver	0.09 RPM	0.35 RPM
SRP051959_lung	0.13 RPM	0.78 RPM
SRP051959_lymph_node	0.00 RPM	0.27 RPM
SRP051959_skeletal_muscle	0.02 RPM	0.59 RPM
SRP051959_spleen	0.04 RPM	1.60 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3226 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3226 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3226 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009509	1 retrocopy	retro_cjac_3226 ,
Mus musculus	ENSMUSG00000029359	1 retrocopy	retro_mmus_212,
Rattus norvegicus	ENSRNOG00000001128	1 retrocopy	retro_rnor_244,