RetrogeneDB ID: retro_cjac_1799

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:59849236..59849791(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000010288
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000000128
• Aliases: D4S234E, NSG1
• Description: None

Sequence

>retro_cjac_1799
ATGGTGAAGTTGGGGAACAATTTCGCGGAAACGGGCACCAAGCAGCCGCTGCTGGAGGATGGCTTCGACACCATGCCCCT
GATGACGCCCCTCGATGTCAACCACCTGCAGTTACCGCCCCCGGATAAGGTGGTCGTGAAAACTAAGACCGAGTATAAAC
CTGACCGCAAGAAAGGGAAAGCACGTCCTCCCCAAATTGCTGAGTTCAGTGTCAGCATCACGGAGGGTGTCACCGAGAGG
TTTAAGGTCTCTGTGCTGGTCCTCTTCGCCCTGGCCTTCCTCACCTGTGTCATCTTCCTGGTCGTCTACAAGGTGTACAA
GTATGACCGCGCCTGCCCCGATGGCTTCGTCCTCAAGAACACCCAGTGCATCCCAGAAGGCTTGGAGAGCTACTACGCGG
AGCAAGACTCCAGTGTCCGGGAGAAATTTTACACAGTCATAAAGCACTATAACCTGGCGAAGCAGAGCATCACGCGCTCC
GTATCGCCCAGGATGTCAGTTCTGTCGGAAGGGAGGCTGTCGGAGCAGGAGACTGAGGCGGCTGAGAAGTCAGCT

Alignment

ORF - retro_cjac_1799 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVKLGNNFAEKGTKQPLLEDGFDTIPLMTPLDVNQLQFPPPDKVVVKTKTEYEPDRKKGKARPPQIAEFT
          MVKLGNNFAE.GTKQPLLEDGFDT.PLMTPLDVN.LQ.PPPDKVVVKTKTEY.PDRKKGKARPPQIAEF.
Retrocopy MVKLGNNFAETGTKQPLLEDGFDTMPLMTPLDVNHLQLPPPDKVVVKTKTEYKPDRKKGKARPPQIAEFS

Parental  VSITEGVTERFKVSVLVLFALAFLTCVVFLVVYKVYKYDRACPDGFVLKNTQCIPEGLESYYAEQDSSAR
          VSITEGVTERFKVSVLVLFALAFLTCV.FLVVYKVYKYDRACPDGFVLKNTQCIPEGLESYYAEQDSS.R
Retrocopy VSITEGVTERFKVSVLVLFALAFLTCVIFLVVYKVYKYDRACPDGFVLKNTQCIPEGLESYYAEQDSSVR

Parental  EKFYTVINHYNLAKQSITRSVSPWMSVLSEEKLSEQETEAAEKSA
          EKFYTVI.HYNLAKQSITRSVSP.MSVLSE..LSEQETEAAEKSA
Retrocopy EKFYTVIKHYNLAKQSITRSVSPRMSVLSEGRLSEQETEAAEKSA

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	0.02 RPM	1.60 RPM
SRP051959_heart	0.11 RPM	2.96 RPM
SRP051959_kidney	0.02 RPM	1.20 RPM
SRP051959_liver	0.02 RPM	0.48 RPM
SRP051959_lung	0.02 RPM	1.61 RPM
SRP051959_lymph_node	0.00 RPM	1.83 RPM
SRP051959_skeletal_muscle	0.02 RPM	0.39 RPM
SRP051959_spleen	0.13 RPM	1.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1799 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1799 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1799 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000128	1 retrocopy	retro_cjac_1799 ,
Tursiops truncatus	ENSTTRG00000012823	1 retrocopy	retro_ttru_1031,