RetrogeneDB ID: retro_cjac_2428

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:33021394..33022412(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GRAMD2
• Ensembl ID: ENSCJAG00000018524
• Aliases: None
• Description: GRAM domain containing 2 [Source:HGNC Symbol;Acc:27287]

Sequence

>retro_cjac_2428
GAGGACAGCAACCAACAAATGCACGGAAAGATTTCTCTGAATGGTCCTGTGTCCTACAAAGAGAAACCAGACAGAGTTCA
GGAGCCCCAGGACTGCAGTCCGCACTGCCTGGAAGACTTGAAGGGTAAAGATAAAGAAGTGTGGCCGAGAAGGGATACCA
CTGAATACATACAACCAGCAATACCACAAGCTGTTTAAGGATGTTCCCTTGGAGAAAGTGGTTCTCAAAGTGTGCTCCTG
AGCCCTCCAAAGGGACCTCCTTCTTCAGGGCCGGCTCTACATCTCCCCCAACTGACTCTGCTTCCACACCAGCCTCTTTG
GCAAGGATATTAAGGTGGTCATTCCTGTGGTGTCTGTACAAATGATCAAAAACACAAGCTGGCATAGCTCCTTCCTAACG
GACTGGCCATCACCACCAACACCACCAGAAGTGTATCTTCGTGTCACTGCTGTCCCGGGACAGGGTATACGAACTGCTGA
GGAGAGTCTGCACCCACCTGCAGCCTTCCAGCAACAAGAGTCTAAGCGTAAGAGAATTTCCAGAGGAACCTGAGTCTCTG
GAAGTCCTCATCCCTGAGATGAAGTGGAGAAAGGTATGCCCTTCCTCCAGGTCCCTGTCTCTCCTGGACAACATGCCTCA
TACCCCTCCAGCATTTGTGGACTCCACAGTTTCTTCCCCTCCAGGAAGCCTCCAGGGCCTGAAAAGTCAAGAGCCCAAGT
AGCCTCTGAAAATGGCAGGAGGTGGCCATGGCCCATGCCGGGCTGGGGTCCTGCCTGCCCTGAGAAGATGCAGAACTGCT
CTCCCACTGCAGAGAATGCTGTCTGTGAGGAAGATGAGCTGGAGGAGGAGTCTGGAAGCACCGGGTAGCTGAGGCCCTGG
GATTATCGGCTCCTGAAGGTCTTCTTTGTGCTGATCTGCATCCTGGTCGAGTCCTCATCTTAACTGGCATTCTGGATTTC
ACAGCCAGAGCAGCAGCTATGCTCCTTGAGTTGGGACAGCCCAGTCCCTGGGTACAGG

Alignment

ORF - retro_cjac_2428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.73 %
• Parental protein coverage: 96.88 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QGDNQQMHGKTSLNSPVSCKEKPDSVQEPLDCSLHC-PEGLKG-EEIKKCGREGIPLNKYNQQYHKLFKD
          ...NQQMHGK.SLN.PVS.KEKPD.VQEP.DCS.HC.P..L.G...IKKCGREGIPLN.YNQQYHKLFKD
Retrocopy EDSNQQMHGKISLNGPVSYKEKPDRVQEPQDCSPHC<PGRLEG<VKIKKCGREGIPLNTYNQQYHKLFKD

Parental  VPLEEVVLKVCSCALQRDLLLQGRLYISPNWLCFHASLFGKDIKVVIPVVSVQMIK-KHKLARLLPNGLA
          VPLE.VVLKVCS.ALQRDLLLQGRLYISPN.LCFH.SLFGKDIKVVIPVVSVQMIK.KHKLA.LLPNGLA
Retrocopy VPLEKVVLKVCS*ALQRDLLLQGRLYISPN*LCFHTSLFGKDIKVVIPVVSVQMIK<KHKLA*LLPNGLA

Parental  ITTNTS-QKYIFVSLLSRDSVYELLRRVCTHLQPSSKKSLSVRQFPEEPESLEVLIPEMKWRKVCPSSRS
          ITTNT..QK.IFVSLLSRD.VYELLRRVCTHLQPSS.KSLSVR.FPEEPESLEVLIPEMKWRKVCPSSRS
Retrocopy ITTNTT<QKCIFVSLLSRDRVYELLRRVCTHLQPSSNKSLSVREFPEEPESLEVLIPEMKWRKVCPSSRS

Parental  LSLPDNMPRTPAASVDSTDSFFPS-RTPPGPEKSRAQVASENGRRWAWPMPGWGPACPKKMPNCSPTAEN
          LSL.DNMP.TP.A.VDST.S..P....P.GPEKSRAQVASENGRRW.WPMPGWGPACP.KM.NCSPTAEN
Retrocopy LSLLDNMPHTPPAFVDSTVSSPPG<KPP-GPEKSRAQVASENGRRWPWPMPGWGPACPEKMQNCSPTAEN

Parental  AVCEEDELEEETGSTGELRLWDYQLLKVFFVLICILVVSSSYLAFRISQLEQQLCSLSWDSPVPGHR
          AVCEEDELEEE.GSTG.LR.WDY.LLKVFFVLICILV.SSS.LAF.ISQ.EQQLCSLSWDSPVPG.R
Retrocopy AVCEEDELEEESGSTG*LRPWDYRLLKVFFVLICILVESSS*LAFWISQPEQQLCSLSWDSPVPGYR

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	0.62 RPM
SRP051959_heart	0.00 RPM	1.25 RPM
SRP051959_kidney	0.00 RPM	8.34 RPM
SRP051959_liver	0.00 RPM	0.30 RPM
SRP051959_lung	0.02 RPM	12.85 RPM
SRP051959_lymph_node	0.00 RPM	0.30 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.44 RPM
SRP051959_spleen	0.00 RPM	0.15 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2428 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2428 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2428 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018524	3 retrocopies	retro_cjac_1618, retro_cjac_2061, retro_cjac_2428 ,