RetrogeneDB ID: retro_cjac_2311

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:17867058..17867687(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000001100
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000012712
• Aliases: None
• Description: None

Sequence

>retro_cjac_2311
CTGAAGGTGAAGAAGGGCGGCGGCGGGGCCGGTACGGGGGCGGAGCCCGCTCCAGGGCCCTCGGGCCGAGCGTGGCCCCC
ATACCAGAGCCGCAGGCTGAATCCGAATCTGGGTCCGAGTCGGAACCGGACGCAGGCCCAGGGCCCATGCCGGGGCCGCT
GCAGAGGAAGCAGCCGATCGGGCCGGAGGACGTGCTGGGGCTGCAGCGGATCACGGGTGACTACCTCTGCTCCCCTGAGG
AGAATATCTACAAGATCGACTTCGTCAGGTTTAAGATTCGGGACATGGACTCAGGCACTGTCCTCTTTGAAATCAAGAAG
CCCCCAGCTTCAGAGCGGTTGCCCATCAGCCGGCGGGACCTGGACCCCAATGCTGGGCGCTTTGTCCGCTACCAGTTCAC
ACCTGCCTTCCTCCGTCTGAGGCAGGTGGGAGCCACGGTGGAGTTCACCGTGGGAGACAAGCCTGTCAACAACTTCCGAA
TGATCGAGAGACACTACTTCCGCAACCAGCTACTCAAAAGCTTTGACTTCCACTTTGGCTTCTGCATCCCCAGCAGCAGA
ACACCTGCGAACACATCTATGACTTACCCCCTCTCTCCGAGGAGCTGATCAAGCGAGATGATCCGCCAC

Alignment

ORF - retro_cjac_2311 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.18 %
• Parental protein coverage: 87.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKVKKGGGGAGTGAEPAPGPS-GPSVAPIPEPQAESESGSESEPDAGPGPMPGPLQRKQPIGPEDVLGLQ
          .KVKKGGGGAGTGAEPAPGPS.GPSVAPIPEPQAESESGSESEPDAGPGPMPGPLQRKQPIGPEDVLGLQ
Retrocopy LKVKKGGGGAGTGAEPAPGPS<GPSVAPIPEPQAESESGSESEPDAGPGPMPGPLQRKQPIGPEDVLGLQ

Parental  RITGDYLCSPEENIYKIDFVRFKIRDMDSGTVLFEIKKPPASERLPISRRDLDPNAGRFVRYQFTPAFLR
          RITGDYLCSPEENIYKIDFVRFKIRDMDSGTVLFEIKKPPASERLPISRRDLDPNAGRFVRYQFTPAFLR
Retrocopy RITGDYLCSPEENIYKIDFVRFKIRDMDSGTVLFEIKKPPASERLPISRRDLDPNAGRFVRYQFTPAFLR

Parental  LRQVGATVEFTVGDKPVNNFRMIERHYFRNQLLKSFDFHFGFCIPSSK-NTCEHIYDFPPLSEELI-SEM
          LRQVGATVEFTVGDKPVNNFRMIERHYFRNQLLKSFDFHFGFCIPSS..NTCEHIYD.PPLSEELI.SEM
Retrocopy LRQVGATVEFTVGDKPVNNFRMIERHYFRNQLLKSFDFHFGFCIPSSR<NTCEHIYDLPPLSEELI>SEM

Parental  IRH
          IRH
Retrocopy IRH

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	1.51 RPM
SRP051959_heart	0.00 RPM	4.07 RPM
SRP051959_kidney	0.00 RPM	3.08 RPM
SRP051959_liver	0.04 RPM	2.17 RPM
SRP051959_lung	0.03 RPM	2.13 RPM
SRP051959_lymph_node	0.05 RPM	2.47 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.65 RPM
SRP051959_spleen	0.02 RPM	3.72 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2311 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2311 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2311 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004930	1 retrocopy	retro_amel_1529,
Callithrix jacchus	ENSCJAG00000012712	1 retrocopy	retro_cjac_2311 ,
Cavia porcellus	ENSCPOG00000002937	1 retrocopy	retro_cpor_939,
Felis catus	ENSFCAG00000024212	1 retrocopy	retro_fcat_923,
Myotis lucifugus	ENSMLUG00000012359	1 retrocopy	retro_mluc_2325,
Vicugna pacos	ENSVPAG00000004356	1 retrocopy	retro_vpac_402,