RetrogeneDB ID: retro_cjac_4199

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:85304953..85305622(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000006356
• Aliases: None
• Description: None

Sequence

>retro_cjac_4199
ATGTGTAATACTCCAACGTATGCTAAATTAGAAAAAAAAAAACCAGTTACATTGGTGGTTTTAATAAAAAATAATCTTGA
ATATATAGAATGAGAAGAATCTGGAGGCAAATATGATGAGATTGGATATAAAAAGAAAAAATACAGAGGGAAGCTAGTCA
GTCATGCATCTATATGAAAGGAGGTTGAAGATAAAGAATCAGAGGGAGAAGAGGATGAGAATGAAGATCTTTCTAAATAT
AAATTAGATGAAGATGAGGATGAAGATGATGCTGATCTATCAAAATATAATCTTGATGTCAGTGAAGAAGAAGATAATAA
TAAAAAGAAATCTAATAGAAAAAGTCCTCAACATCTCAATCTTCACTTTCACTATCTTTAACGTGTTCATTCTCCCTTTC
AAGTTCAAGATCTAGTTCCAGGTTTCTTTCAAGAAGTTCTAGTTCGCAGTCAAGATCTCATTCCAGTTTCAGAGAATATT
TAAGATGTTCTCGGTTGAAATCAAGATCTGACTCCAGGTCCCACAGGGGCTCTTCCACGCCCCCTCTCCAAAGAAAATGA
TGTTATTCAAGTTCATCACTTTCTCCTAAGTGGAATAGAAAGAGAAGTCATTTTAGATCTTCATCTGGTGATCACAGAAA
AGGATGAATAAGATTATGGTCACCTGAAA

Alignment

ORF - retro_cjac_4199 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.91 %
• Parental protein coverage: 66.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MCNTPKYAKLEERTGYGGGFNERENVEYIEREESDGEYDEFGRKKKKYRGKAVGPASILKEVEDKESEGE
          MCNTP.YAKLE.............N.EYIE.EES.G.YDE.G.KKKKYRGK.V..ASI.KEVEDKESEGE
Retrocopy MCNTPTYAKLEKKKPVTLVVLIKNNLEYIE*EESGGKYDEIGYKKKKYRGKLVSHASI*KEVEDKESEGE

Parental  EEDEDEDLSKYKLDEDEDEDDADLSKYNLDASEEEDSNKKKSNRRS-RSKSRSSHSRSSSRSSSPSSSRS
          E.DE.EDLSKYK.........ADLSKYNLD.SEEED.NKKKSNR.S..S.S.SS.S.S...S.S.SSSRS
Retrocopy E-DENEDLSKYKXXXXXXXXXADLSKYNLDVSEEEDNNKKKSNRKS<SSTSQSSLSLSLTCSFSLSSSRS

Parental  RSRSRSRSTSSSQSRSRSSSRERSRSRGSKSRSSSRS-TGAL---LPHEKDLIQVHHLLLRGTEREVVLD
          .SR..SRS.SSSQSRS.SS.RE..R....KSRS.SRS.TGAL...L..E.D.IQVHH.LL.G.EREV.LD
Retrocopy SSRFLSRS-SSSQSRSHSSFREYLRCSRLKSRSDSRS>TGALPRPLSKENDVIQVHHFLLSGIEREVILD

Parental  LLHLVIAKKDEQDHGHPK
          .LHLVI..KDE.D.GH.K
Retrocopy -LHLVITEKDE*DYGHLK

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	0.13 RPM	39.65 RPM
SRP051959_heart	0.02 RPM	60.48 RPM
SRP051959_kidney	0.00 RPM	60.66 RPM
SRP051959_liver	0.00 RPM	44.97 RPM
SRP051959_lung	0.00 RPM	64.92 RPM
SRP051959_lymph_node	0.00 RPM	81.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	54.22 RPM
SRP051959_spleen	0.00 RPM	66.83 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4199 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4199 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4199 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006356	2 retrocopies	retro_cjac_2350, retro_cjac_4199 ,
Macaca mulatta	ENSMMUG00000017312	2 retrocopies	retro_mmul_2602, retro_mmul_2618,
Monodelphis domestica	ENSMODG00000000504	2 retrocopies	retro_mdom_1975, retro_mdom_443,
Oryctolagus cuniculus	ENSOCUG00000004640	2 retrocopies	retro_ocun_1170, retro_ocun_776,
Otolemur garnettii	ENSOGAG00000000485	4 retrocopies	retro_ogar_1274, retro_ogar_1841, retro_ogar_2843, retro_ogar_976,
Pan troglodytes	ENSPTRG00000000856	1 retrocopy	retro_ptro_3251,
Tupaia belangeri	ENSTBEG00000002316	3 retrocopies	retro_tbel_122, retro_tbel_3653, retro_tbel_4007,