RetrogeneDB ID: retro_cjac_1325

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:18391042..18392036(+)
• Located in intron of: ENSCJAG00000001685

Retrocopy information

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

Parental gene information

• Parental gene symbol: RACGAP1
• Ensembl ID: ENSCJAG00000021058
• Aliases: None
• Description: Rac GTPase activating protein 1 [Source:HGNC Symbol;Acc:9804]

Sequence

>retro_cjac_1325
GTTCCACGTGGAAAGCAGATAAAATTTGGCAAACTATCTCTGAAGCGTCAAGACTGTCATGTGGTCTCTCATCCAGAATG
TCGGGACCGCTTTCCCATTCCCTGCATTCCTACCCTGATAGGAACACCTGTCAAGATTGGAGAGGGAATGCTGGCAGACT
TTGTGTCCCAGACTTCTCCAATGATCCTCTCCATTGTTGTGATGGTGTTAATGAGATTGAGCAGAGAGGTCTGACTGAGA
CAGGCCTGTATAGGATCTCTGGCTGTGACTGCACAGTAAAAGAGCTGAAAGAGAAATTCCTCAGAGTGAAAACTGTACCC
TTCCTCAGCAAAGTGGATGATATCCATGCTATCTGTAGCCTTCTAAAAGACTTTCTTTGAAACCTCAAAGAACCTCTTCT
GACCTTTCGCCTAAACAAAGCCTTTATGGAAGCAGCAGAAATCACAGATGAAGACAACAGCATAGCTGCCATGTACCAGG
CTGTTGGTGAACTGCCCCAGGCCAACAGGGACACATTAGCTTTCCTCATGATTCACTTGTAACAGTGGCACAGAGTCCAC
ATACTAAAATGGATTTTGCCAATCTGGCTAAAGTTTTTAGCCCTACAATAGTGGCCCATGCTGTGCCCAATCCAGACCCA
GTGACAATGTTACAGGACATCAAGCGTCAACCCAAGGTGGTTGAGCGCCTGCTTTCCTTGTCCCTGGAGTATTGGAGTCA
GTTCATGATGGTAGAACAACAGAACACTGACCCCCTACATGTCATTGAAAACTCAAATGCCTTTTCAACGCCACAGACAC
CAGATATTCAAGTGAGTTTACAGGGACCTGTGACCACTCCTGAACATCAGCTTCTCAAGACTCCTTCATCTAGTTCTCTG
TCACAGAGAGTTCGTTCCACCCTCACCAAGAACACTCCCAGATTTAGGAGCAAAAGCAAGTCTGCCACCAACCTAGGATG
ACAAGGCAAATTTTTTGCTTCTCCAATGCTCAAG

Alignment

ORF - retro_cjac_1325 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.22 %
• Parental protein coverage: 52.04 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VPFDVLIKIQAXSLKCRDCRVVSHPECRDRCP-PCNPTLIGTPVKIGEGMLADFVSQTSPMIPSIVVHC-
          VP....IK....SLK..DC.VVSHPECRDR.P.PC.PTLIGTPVKIGEGMLADFVSQTSPMI.SIVV...
Retrocopy VPRGKQIKFGKLSLKRQDCHVVSHPECRDRFPIPCIPTLIGTPVKIGEGMLADFVSQTSPMILSIVVMV<

Parental  VNEIEQRGLTETGLYRISGCDRTVKELKEKFLRVKTVPLLSKVDDIHAICSLLKDFLRNLKEPLLTFRLN
          VNEIEQRGLTETGLYRISGCD.TVKELKEKFLRVKTVP.LSKVDDIHAICSLLKDFL.NLKEPLLTFRLN
Retrocopy VNEIEQRGLTETGLYRISGCDCTVKELKEKFLRVKTVPFLSKVDDIHAICSLLKDFL*NLKEPLLTFRLN

Parental  KAFMEAAEIADEDNSIAAMYQAVGELPQANRDTLAFLMIHMQR-VAQSPHTKMDVANLAKVFGPTIVAHA
          KAFMEAAEI.DEDNSIAAMYQAVGELPQANRDTLAFLMIH....VAQSPHTKMD.ANLAKVF.PTIVAHA
Retrocopy KAFMEAAEITDEDNSIAAMYQAVGELPQANRDTLAFLMIHL*Q<VAQSPHTKMDFANLAKVFSPTIVAHA

Parental  VPNPDPVTMLQDIKRQPKVVERLLSLPLEYWSQFMMVEQENIDPLHVIENSNAFSTPQTPDIKVSLLGPV
          VPNPDPVTMLQDIKRQPKVVERLLSL.LEYWSQFMMVEQ.N.DPLHVIENSNAFSTPQTPDI.VSL.GPV
Retrocopy VPNPDPVTMLQDIKRQPKVVERLLSLSLEYWSQFMMVEQQNTDPLHVIENSNAFSTPQTPDIQVSLQGPV

Parental  TTPEHQLLKTPSSSSLSQRVRSTLTKNTPRFGSKSKSATNLGRQGNFFASPMLK
          TTPEHQLLKTPSSSSLSQRVRSTLTKNTPRF.SKSKSATNLG.QG.FFASPMLK
Retrocopy TTPEHQLLKTPSSSSLSQRVRSTLTKNTPRFRSKSKSATNLG*QGKFFASPMLK

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	0.67 RPM	19.28 RPM
SRP051959_heart	0.28 RPM	2.32 RPM
SRP051959_kidney	0.31 RPM	2.53 RPM
SRP051959_liver	0.19 RPM	1.49 RPM
SRP051959_lung	0.23 RPM	8.83 RPM
SRP051959_lymph_node	0.82 RPM	17.05 RPM
SRP051959_skeletal_muscle	0.13 RPM	1.59 RPM
SRP051959_spleen	0.36 RPM	9.94 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1325 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1325 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1325 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001701	1 retrocopy	retro_chof_1331,
Callithrix jacchus	ENSCJAG00000021058	2 retrocopies	retro_cjac_1325 , retro_cjac_837,