RetrogeneDB ID: retro_cjac_837

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:23559799..23560800(+)
• Located in intron of: None

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_837
TCCTATGTTCCATGTGGAAAGTGGATAAAATTCAGCAAACTATCTCTGAAGTGTCGAGACTGTTGTGTGGTGTCTCATCC
AGGATGTTGGGACCGCTGTCCCGTTCCCTTCATTTCTACCCTGATAGGAACACCTGTCAAGACTGGAGAGAGAATGCTGG
CAGATTTTGTGTCCCAGACTTCTCCAATGATCCCCCGCCACTGGTGTGCATTGTGTAAATGAGAGTGAGCAGAGATGTGA
CTGAGACAGGCCCGTATAGGATCTCTGGCTGTGACTGCACAGTAAAAGAGCCGAAAGAGAAATTCCTCAGAGTGAAAACT
GTACCCCTCCTCAGCAAAGTAGATGGTATCTTTGTGATCTGTAGCCTTCTGAAAGACTTTCTTCAAAACCTCAAAGAACC
TCTTCTGACCTTTCGCCTAAACAAAGCCTTTATGGAGGCAGCAGAAATCACAGATGAAGTCAATAGCATAGCTGCCAAGT
ACCAGGGTGTTGGTGAACTGCCCCAGGCCAACAGGGACACATTAGCTTTCCTCATGATTCACTTGCAGAGAGTGGTTCAG
AGTCCACATACTAAAATGGATGTTGCCAATCTGGCTATAATCTTTGGCTCTACAATAGTGGCCCATGCTGTGCCCAATCC
AGACCCAGTGACAATGTTACAGGACATCAAGTGTCAACCCAAGGTAGTTGAGCACCTGCTTTCCTTGTCCCTGGAGTATT
GGAATCAGTTCATCATGATGGAACAAGAGAACATTGACGCCCTACATGTCATCGAAAACTCAAATGCCTTTTCAACACCA
CAAACACCAGATATTAAAGTGAGTTTACTGGGACCTGTGACCACTCCCAAATGTCAGCTTCTCAAGACTCCTTCATCTGG
TTCCCTGTCATAGAGAATTCATTCTACCCTCAACAAGAACACTCCCAGATTTGGGCGCAAAAGCAAGTCTGCCACCAACC
TAGGATGACAAGGCAACTTTTTTGCTTCTCCAATGCTCAAG

Alignment

ORF - retro_cjac_837 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.9 %
• Parental protein coverage: 52.36 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AFVPFDVLIKIQAXSLKCRDCRVVSHPECRDRCP-PCNPTLIGTPVKIGEGMLADFVSQTSPMI-PSIVV
          ..VP....IK....SLKCRDC.VVSHP.C.DRCP.P...TLIGTPVK.GE.MLADFVSQTSPMI.P...V
Retrocopy SYVPCGKWIKFSKLSLKCRDCCVVSHPGCWDRCPVPFISTLIGTPVKTGERMLADFVSQTSPMI<PPPLV

Parental  HCVNEIEQRGLTETGLYRISGCDRTVKELKEKFLRVKTVPLLSKVDDIHAICSLLKDFLRNLKEPLLTFR
          ..V.....R..TETG.YRISGCD.TVKE.KEKFLRVKTVPLLSKVD.I..ICSLLKDFL.NLKEPLLTFR
Retrocopy CIV*MRVSRDVTETGPYRISGCDCTVKEPKEKFLRVKTVPLLSKVDGIFVICSLLKDFLQNLKEPLLTFR

Parental  LNKAFMEAAEIADEDNSIAAMYQAVGELPQANRDTLAFLMIHMQRVAQSPHTKMDVANLAKVFGPTIVAH
          LNKAFMEAAEI.DE.NSIAA.YQ.VGELPQANRDTLAFLMIH.QRV.QSPHTKMDVANLA..FG.TIVAH
Retrocopy LNKAFMEAAEITDEVNSIAAKYQGVGELPQANRDTLAFLMIHLQRVVQSPHTKMDVANLAIIFGSTIVAH

Parental  AVPNPDPVTMLQDIKRQPKVVERLLSLPLEYWSQFMMVEQENIDPLHVIENSNAFSTPQTPDIKVSLLGP
          AVPNPDPVTMLQDIK.QPKVVE.LLSL.LEYW.QF.M.EQENID.LHVIENSNAFSTPQTPDIKVSLLGP
Retrocopy AVPNPDPVTMLQDIKCQPKVVEHLLSLSLEYWNQFIMMEQENIDALHVIENSNAFSTPQTPDIKVSLLGP

Parental  VTTPEHQLLKTPSSSSLSQRVRSTLTKNTPRFGSKSKSATNLGRQGNFFASPMLK
          VTTP..QLLKTPSS.SLS.R..STL.KNTPRFG.KSKSATNLG.QGNFFASPMLK
Retrocopy VTTPKCQLLKTPSSGSLS*RIHSTLNKNTPRFGRKSKSATNLG*QGNFFASPMLK

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	19.28 RPM
SRP051959_heart	0.02 RPM	2.32 RPM
SRP051959_kidney	0.00 RPM	2.53 RPM
SRP051959_liver	0.00 RPM	1.49 RPM
SRP051959_lung	0.03 RPM	8.83 RPM
SRP051959_lymph_node	0.00 RPM	17.05 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.59 RPM
SRP051959_spleen	0.02 RPM	9.94 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_837 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_837 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_837 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 ,