RetrogeneDB ID: retro_cjac_3949

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286374.1:7177..7583(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FHAD1
• Ensembl ID: ENSCJAG00000008888
• Aliases: None
• Description: forkhead-associated (FHA) phosphopeptide binding domain 1 [Source:HGNC Symbol;Acc:29408]

Sequence

>retro_cjac_3949
TATGATGCCGGGCGGGATGGCTTCATCGACCTGATGGAGCTAAAGCTCATGATGGAGAAACTTGGGGCCCCCCCAGACCC
ACCTGGGCCTAAAAAGCATGATCAAGGAGGTGGATGAGGACTTTGACAGCAAGCTGAGCTTCCAGGAGTTCCTCCTGATC
TTCTGAAAGGCGGCAGCCAGGGAGCTTGAGGAGGACAGTGCGCTGTGCGTGCTGGCCCACCTCTCCGAGATCAACATCCC
CAGTGAGGGCATCGAGGGGGCCAAGACCTTCTTTGAGGCCAAGGTCCAGGCCATCAACGTGTCCAGCCGCTTTAAGGAGG
AGATCAAGTCGGAGCAGGAGGAAAGGAAGCATGCGGAGATGAAGCAGCGGAAAGCGGCCTTCAAGGAGCTGCAGTCCACC
TTTAAG

Alignment

ORF - retro_cjac_3949 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.51 %
• Parental protein coverage: 91.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YDAGRDGFIDLMELKLMMEKLGAP-QTHLGLKNMIKEVDEDFDSKLSFREFLLIFRKAAAGELQEDSGLC
          YDAGRDGFIDLMELKLMMEKLGAP.QTHLGLK.MIKEVDEDFDSKLSF.EFLLIF.KAAA.EL.EDS.LC
Retrocopy YDAGRDGFIDLMELKLMMEKLGAP>QTHLGLKSMIKEVDEDFDSKLSFQEFLLIF*KAAARELEEDSALC

Parental  VLARLSEIDVSSEGVKGAKSFFEAKVQAINVSSRFEEEIKAEQEERKKQAEEMKQRKAAFKELQSTFK
          VLA.LSEI...SEG..GAK.FFEAKVQAINVSSRF.EEIK.EQEERK....EMKQRKAAFKELQSTFK
Retrocopy VLAHLSEINIPSEGIEGAKTFFEAKVQAINVSSRFKEEIKSEQEERKH--AEMKQRKAAFKELQSTFK

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	0.22 RPM	8.65 RPM
SRP051959_heart	0.18 RPM	1.68 RPM
SRP051959_kidney	0.02 RPM	12.38 RPM
SRP051959_liver	0.06 RPM	5.61 RPM
SRP051959_lung	0.33 RPM	14.01 RPM
SRP051959_lymph_node	0.48 RPM	9.41 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.86 RPM
SRP051959_spleen	0.32 RPM	15.25 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3949 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3949 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3949 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008888	1 retrocopy	retro_cjac_3949 ,