RetrogeneDB ID:

retro_cjac_1580

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:17:8215632..8216264(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000005535
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000009747
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1580
CGAGCTGAGCGCCTCCAGAGAGAAGTTGAGGGAGAAAGGCGGGCCCGGGAACAGGCTGAGGCTAAGGTGGCCTCCTTGAA
CCGTAGGATCCAGCTGGTTGAAGAGAAGCTGGACCATGCTCAGGAGCACCCGGCCACTGCCCTGCAAAAGCTGGAAGAAG
CTGAAAAAGCTGCTGATGAGAGTGAGAGAGGTATGAAGGTTATTGAAAACCGGGCCTTAAAAGATGAAGAGAAGATGGAA
CTCCAGGAAATCCAACTCAAAGAAGCTAAGCACATTGCAGGAAAGGCAGATAGGAAGTATGAAGAGGTGGTCATAAGTTG
GTGATCATTGAAGGAGACTTGGAACGCACAGAGGAACGAGCTGAGCTGGCAGAGTCCCGTTGCCGAGAGATGGATGAGCA
GATCAGACTGATGGACCAGAACCTGAAGTTTCTGAGTGCTGCTGAAGAAAAGTACTCTCAAAAAGAAGACAAATATGAGG
AAAAGATCAAGATTCTTACTGACAAACTCAGGGAGGCAGAGACCCGTGCTGAGTTTGCTGAGAGATCGGTAGCCAAGCTG
GAAAAGGCAATTGATGACTTGGAAGATAAACTGAAATGTACCAAAGAGGAGCACCTCTGTACACAAAGGATG

ORF - retro_cjac_1580 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.4 %
Parental protein coverage: 85.08 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalRAERLQREVEGERRAREQAEAEVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIEN
RAERLQREVEGERRAREQAEA.VASLNRRIQLVEE.LD.AQE..ATALQKLEEAEKAADESERGMKVIEN
RetrocopyRAERLQREVEGERRAREQAEAKVASLNRRIQLVEEKLDHAQEHPATALQKLEEAEKAADESERGMKVIEN
ParentalRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVA-RKLVIIEGDLERTEERAELAESRCREMDEQIRLMD
RALKDEEKMELQEIQLKEAKHIA..ADRKYEEV...KLVIIEGDLERTEERAELAESRCREMDEQIRLMD
RetrocopyRALKDEEKMELQEIQLKEAKHIAGKADRKYEEVV<HKLVIIEGDLERTEERAELAESRCREMDEQIRLMD
ParentalQNLKCLSAAEEKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSVAKLEKTIDDLEDKLKCTKEEHLCTQ
QNLK.LSAAEEKYSQKEDKYEE.IKILTDKL.EAETRAEFAERSVAKLEK.IDDLEDKLKCTKEEHLCTQ
RetrocopyQNLKFLSAAEEKYSQKEDKYEEKIKILTDKLREAETRAEFAERSVAKLEKAIDDLEDKLKCTKEEHLCTQ
ParentalRM
RM
RetrocopyRM

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP051959_colon 0 .07 RPM 68 .16 RPM
SRP051959_heart 0 .00 RPM 20 .50 RPM
SRP051959_kidney 0 .07 RPM 33 .86 RPM
SRP051959_liver 0 .02 RPM 34 .29 RPM
SRP051959_lung 0 .16 RPM 91 .80 RPM
SRP051959_lymph_node 0 .16 RPM 96 .96 RPM
SRP051959_skeletal_muscle 0 .00 RPM 20 .29 RPM
SRP051959_spleen 0 .06 RPM 93 .74 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1580 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1580 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1580 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 10 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000043552 retrocopies
Callithrix jacchus ENSCJAG000000096272 retrocopies
Callithrix jacchus ENSCJAG00000009747 9 retrocopies
Callithrix jacchus ENSCJAG000000141351 retrocopy
Gorilla gorilla ENSGGOG000000126683 retrocopies
Nomascus leucogenys ENSNLEG000000109908 retrocopies
Pongo abelii ENSPPYG000000007872 retrocopies
Rattus norvegicus ENSRNOG000000174411 retrocopy
Sus scrofa ENSSSCG000000065563 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000235256 retrocopies



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