RetrogeneDB ID: retro_cjac_486

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:176753009..176753704(+)
• Located in intron of: ENSCJAG00000018173

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000001431
• Aliases: None
• Description: None

Sequence

>retro_cjac_486
AAGGAGAGAGAAACCTCTCCTCGTTTTGCCCAGTGTGGCATGTTGGAGTATGAATATTCTCAGCGATGGAAGTGTTTGGA
CATGAAATGGAACAACAGCAAAGAGAACAAGCTGAAAAGAAACAGGAAGGATGCAAAAGACAAACTGGAAAATGAAATGG
AAGATGCCTACCATGAACATCAGGCAAATCTTTTGCACCAAGATCTGAAGAGACGACAGGAGGACTTAAGACACATGGAA
GAACTTCACAATCAAGAAATGCAGAAATGTTAAGAAATACAATTGAGGCAAGAGGAGGAACGATGTAGAAGCGAGGAAGA
GATGATGATTTGTCAACGTGAGATGGAAGAACAAATGAGGCACCAAAGAGAGGAAAGTTACAGCTGAATAGGCTACACGG
ATCAAAGAGACATGAGAACGGATGGCAGAGGAGAAACAAACATGGGAGGCTGTGGTTCAGGAGGCCAGAAAGCTCCACCT
TTAGGTGGTGGTGGCGGCATAGGTTCTGAAGCTAATCCTGGAGTTCCACCAGCAACCATGAGTGGTTCCAGGATGGGAAT
TGACTTGTGTACTGAGCGCCTTGGGCAGGGAGGTGCGGGGCCTGTAGGTGGCCAGGGTCTTAGAGGAATGGGCCTGGAAC
TCCAGCAGGCTACGACAAAGAGAGAGGAGTACAAAGGCCCAAACAAAAAACCCCA

Alignment

ORF - retro_cjac_486 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.03 %
• Parental protein coverage: 50.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KERETPPRFAQHGTFEYEYSQRWKSLD-EMEKQQREQVEKNMKDAKDKLESEMEDAYHEHQANLLRQDLM
          KERET.PRFAQ.G..EYEYSQRWK.LD.............N.KDAKDKLE.EMEDAYHEHQANLL.QDL.
Retrocopy KERETSPRFAQCGMLEYEYSQRWKCLDMKWNNSKENKLKRNRKDAKDKLENEMEDAYHEHQANLLHQDLK

Parental  RRQEELRRMEELHNQEMQKRKEMQLRQEEERRRREEEMMIRQREMEEQMRRQREESYSRMGYMDPRERDM
          RRQE.LR.MEELHNQEMQK..E.QLRQEEER.R.EEEMMI.QREMEEQMR.QREESYS..GY.D...RDM
Retrocopy RRQEDLRHMEELHNQEMQKC*EIQLRQEEERCRSEEEMMICQREMEEQMRHQREESYS*IGYTD--QRDM

Parental  TMGGGGAMNMGDPYGSGGQKFPPLGGGGGIGYEANPGVPPATMSGSMMGSDMRTERFGQGGAGPVGGQGP
          ...G.G..NMG...GSGGQK.PPLGGGGGIG.EANPGVPPATMSGS.MG.D..TER.GQGGAGPVGGQG.
Retrocopy RTDGRGETNMGG-CGSGGQKAPPLGGGGGIGSEANPGVPPATMSGSRMGIDLCTERLGQGGAGPVGGQGL

Parental  RGM-GPGTPAGYGRGREEYEGPNKKP
          RGM.GPGTPAGY...R.......K.P
Retrocopy RGM<GPGTPAGYDKERGVQRPKQKTP

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	0.40 RPM	53.03 RPM
SRP051959_heart	0.21 RPM	57.15 RPM
SRP051959_kidney	0.27 RPM	64.63 RPM
SRP051959_liver	0.17 RPM	35.29 RPM
SRP051959_lung	0.29 RPM	64.50 RPM
SRP051959_lymph_node	0.50 RPM	74.06 RPM
SRP051959_skeletal_muscle	0.15 RPM	38.28 RPM
SRP051959_spleen	0.34 RPM	63.68 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_486 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_486 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_486 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003595	1 retrocopy	retro_cfam_198,
Callithrix jacchus	ENSCJAG00000001431	4 retrocopies	retro_cjac_1073, retro_cjac_2542, retro_cjac_2697, retro_cjac_486 ,
Callithrix jacchus	ENSCJAG00000036744	1 retrocopy	retro_cjac_3990,
Felis catus	ENSFCAG00000031287	1 retrocopy	retro_fcat_1989,
Gasterosteus aculeatus	ENSGACG00000002034	1 retrocopy	retro_gacu_13,
Gadus morhua	ENSGMOG00000011950	1 retrocopy	retro_gmor_20,
Macropus eugenii	ENSMEUG00000014082	1 retrocopy	retro_meug_164,
Oryctolagus cuniculus	ENSOCUG00000001877	1 retrocopy	retro_ocun_1834,
Oreochromis niloticus	ENSONIG00000017737	1 retrocopy	retro_onil_21,
Sarcophilus harrisii	ENSSHAG00000016107	1 retrocopy	retro_shar_36,
Tetraodon nigroviridis	ENSTNIG00000011331	1 retrocopy	retro_tnig_32,
Takifugu rubripes	ENSTRUG00000003783	1 retrocopy	retro_trub_8,
Drosophila melanogaster	FBgn0004227	1 retrocopy	retro_dmel_11,