RetrogeneDB ID: retro_cjac_2250

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:83499477..83499867(-)
• Located in intron of: ENSCJAG00000003975

Retrocopy information

• Ensembl ID: ENSCJAG00000022862
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LY6E
• Ensembl ID: ENSCJAG00000021460
• Aliases: None
• Description: lymphocyte antigen 6 complex, locus E [Source:HGNC Symbol;Acc:6727]

Sequence

>retro_cjac_2250
ATGAAGACCTTGCTGGTGCTGCTGGCTGCCCTTCTGGGTGTTGAGCGAGCCGGCTCGCTGATGTGCTTCTCCTGCCAGAA
CCAGAAGAGCAATCTGTACTGCCTGAAGCCCACCATCTGCTCCGACCAGGACAGCTACTGCCTGACGGTGACTGCGTCTG
CCGGCATCGGAAAGATCGTCACATTTGGCCACACCCTGAGCAAGTCCTGTTCCTCGGTCTGTCCCCTCCCAGGAAACGTC
AATGCTGGCATAGCTTCCATGGGCATCCGCTGCTGCCAGGGCTTCCTGTGCAATTTCAGCGCGGCCGATGGCGGGCTGCG
GGCCAGCGCCACCCTGCTGGGTGCCGGACTGCTGCTGAGCCTGTTGCCTGCCCTGCTGCGTTTTGGCCCC

Alignment

ORF - retro_cjac_2250 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.46 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKTLLVLLAALLGVERAGSLMCFSCQNQKSNLYCLKPTICSDQDSYCLTVTASAGIGKIVTFGHTLSKSC
          MKTLLVLLAALLGVERAGSLMCFSCQNQKSNLYCLKPTICSDQDSYCLTVTASAGIGKIVTFGHTLSKSC
Retrocopy MKTLLVLLAALLGVERAGSLMCFSCQNQKSNLYCLKPTICSDQDSYCLTVTASAGIGKIVTFGHTLSKSC

Parental  SPVCPLPGNVNAGIASMGIRCCQGFLCNFSAANGGLRASATLLGAGLLLSLLPALLRFGP
          S.VCPLPGNVNAGIASMGIRCCQGFLCNFSAA.GGLRASATLLGAGLLLSLLPALLRFGP
Retrocopy SSVCPLPGNVNAGIASMGIRCCQGFLCNFSAADGGLRASATLLGAGLLLSLLPALLRFGP

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	0.29 RPM	2.95 RPM
SRP051959_heart	0.12 RPM	3.17 RPM
SRP051959_kidney	0.11 RPM	2.17 RPM
SRP051959_liver	3.08 RPM	5.59 RPM
SRP051959_lung	0.42 RPM	10.80 RPM
SRP051959_lymph_node	0.37 RPM	7.03 RPM
SRP051959_skeletal_muscle	0.02 RPM	1.46 RPM
SRP051959_spleen	0.99 RPM	26.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2250 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2250 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2250 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021460	2 retrocopies	retro_cjac_2250 , retro_cjac_808,
Mus musculus	ENSMUSG00000022587	1 retrocopy	retro_mmus_724,
Pongo abelii	ENSPPYG00000018927	1 retrocopy	retro_pabe_2122,
Tursiops truncatus	ENSTTRG00000001986	2 retrocopies	retro_ttru_1323, retro_ttru_742,