RetrogeneDB ID: retro_cjac_2794

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:28403752..28404399(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PIGX
• Ensembl ID: ENSCJAG00000013676
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class X [Source:HGNC Symbol;Acc:26046]

Sequence

>retro_cjac_2794
ACGTGTTCTGAAATTACTTTGAGACAAGAAGTTTTGAAAGAAGGTTTCCCCAGAGACCTTTTAATAAAAGTGAAGTTTGG
AGAAGGCATCGAGGAATAACAGAGGTGCCGAGTCTTAATGAAACAGAATATTCCTACAGGACATTTTGTGGATCCATATG
AGTTGGCTTCATTAGGAGAGAGAAACTTAACAGAAGCAATGATGGTTTTGGAAAATTTTGATACAGATGCCCCTATTTGT
CCAAGGAATCTGAAGTTCTCATTTATGTCAGACAAGATTCACAGTGCATTGATCGTTTTCAAGCCTTTTTGCCTGTGCAC
TACCACTATCATCGGCCACAGAGTAAAGATGGAGAAACCTTTACTGTGGTCAGTAACCTAGATTTGTTGATGTATTGTGA
CCAAGAGTTCCCGATTTTGAAATGCTGGGCCCACCCAGAAGTGGCAGCTCCCTGTGCTTTGGAGAATGAGAATATCTGCC
AGTGGAACAAGATGAAGCATAAATCAGTATACAAGAATGTGGTTCTGCAGGTTCCAGTGGGACTGACTGTACATTACCTC
TTTGTATGTTCTGTGACTCTGCTCACTACAATCCTGTGCTCTACTTTGATCCTCGTAACAGTTTTCAAATATGGCCATTT
TTCCCTG

Alignment

ORF - retro_cjac_2794 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TCSEITLRQEVLKDGFHRDLLIKVKFGEGIEDLQRCRLLIKQNIPTGLFVDPYELASLRERNITEAMMVS
          TCSEITLRQEVLK.GF.RDLLIKVKFGEGIE..QRCR.L.KQNIPTG.FVDPYELASL.ERN.TEAMMV.
Retrocopy TCSEITLRQEVLKEGFPRDLLIKVKFGEGIEE*QRCRVLMKQNIPTGHFVDPYELASLGERNLTEAMMVL

Parental  EN-FDVEAPNYLSKESEVLIYARRDSQCIDCFQAFLPVHYRYHRPHSKDGETFTVVSNPDLLMYCDQEFS
          EN.F....P.YLSKESEVLIY.R.DSQCID.FQAFLPVHY.YHRP.SKDGETFTVVSN.DLLMYCDQEF.
Retrocopy EN<F*YRCP-YLSKESEVLIYVRQDSQCIDRFQAFLPVHYHYHRPQSKDGETFTVVSNLDLLMYCDQEFP

Parental  ILKCWAHSEVAAPCALENEDICQWNKMKYKSVYKNVILQVPVGLTIHTSLVCSVTLLITILCCTLILVTV
          ILKCWAH.EVAAPCALENE.ICQWNKMK.KSVYKNV.LQVPVGLT.H...VCSVTLL.TILC.TLILVTV
Retrocopy ILKCWAHPEVAAPCALENENICQWNKMKHKSVYKNVVLQVPVGLTVHYLFVCSVTLLTTILCSTLILVTV

Parental  FKYGHFSL
          FKYGHFSL
Retrocopy FKYGHFSL

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	10.38 RPM
SRP051959_heart	0.00 RPM	8.75 RPM
SRP051959_kidney	0.00 RPM	11.34 RPM
SRP051959_liver	0.00 RPM	16.68 RPM
SRP051959_lung	0.00 RPM	14.67 RPM
SRP051959_lymph_node	0.00 RPM	13.38 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.41 RPM
SRP051959_spleen	0.00 RPM	14.68 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2794 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2794 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2794 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003759	1 retrocopy	retro_amel_386,
Callithrix jacchus	ENSCJAG00000013676	1 retrocopy	retro_cjac_2794 ,
Monodelphis domestica	ENSMODG00000018455	1 retrocopy	retro_mdom_1758,
Mustela putorius furo	ENSMPUG00000003841	1 retrocopy	retro_mputfur_1090,
Mus musculus	ENSMUSG00000023791	1 retrocopy	retro_mmus_943,
Oryctolagus cuniculus	ENSOCUG00000012329	1 retrocopy	retro_ocun_977,
Rattus norvegicus	ENSRNOG00000033623	2 retrocopies	retro_rnor_1998, retro_rnor_2555,