RetrogeneDB ID: retro_cjac_2384

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:144019804..144020518(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PARL
• Ensembl ID: ENSCJAG00000021241
• Aliases: None
• Description: presenilin associated, rhomboid-like [Source:HGNC Symbol;Acc:18253]

Sequence

>retro_cjac_2384
ATGGGGTGGCATGGCTGAGCACAGAAAGGCTGGGGCTGTGGCTCAGTGTGGACTCAACTGGTGGGCAGCGGTAGCTGCGA
GGAACTCACTATGGCCCTAGTCCCGCCGCAGATGCTCGGACGCAACAGGTTTCACTCCTTTATTCAGGAAAAACGTGGAT
TCAGAAAAGCATCCAGTAAGATTGAACCTCGAAGATCAGACAGGGACAACTGGTGAAGCATATGAGAGAAGTGCTTTGAT
TCCTACTGTGGAAGCAACAGTCTTTTATCTTTCTCCTTATCCTCTAAGGAGGATGCTCATAAAACCTTTATTTTTTACTG
TTGGGTTTTCAGGCTGTGCATTTGGATCAGCTGCTGTTTGGGAATGTGAATCACTGAAATCCAGGGTCCGGAGCTATTTT
CATAGCATAAAAGCTGATTGGTTGGATAGCATAAGATGACAAAAGAAAGGAGACTTCAGAAAGGAGATTAAGAAGTGGTG
GAATAATCTAAGTGATGGCCAGCAGACAGTGACAGGTATCACAGCTGCAAATGTCCTTGTAGTCTGCTTATGGAGAGTAC
CTTCTCTGCACTGGACAGTGATCAGATATTTCACATCTAATCCAGCCTCAAAAGTCCTTGTTTTCCAATGTTGCTGTCAA
CATTCAATCACTTCTCCTTGTTTCACATGGCAGCAAATATGTAAGTTTTGTGGAGCTTCTCCTCCAGCATTGTA

Alignment

ORF - retro_cjac_2384 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.61 %
• Parental protein coverage: 62.53 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAWRGWSQRSWGCGPAWAAPVGGRGCEELTTALAPPRLFGR-RFTFVIQQKCGFRKA-PRKVELRRSDTG
          M.W.G..Q..WGCG..W...VG...CEELT.AL.PP...GR.RF...IQ.K.GFRKA.P....L....TG
Retrocopy MGWHG*AQKGWGCGSVWTQLVGSGSCEELTMALVPPQMLGRNRFHSFIQEKRGFRKA>PVRLNLE-DQTG

Parental  TSGKAHKRSALIPPVEETAFYPSPYPIRT-LIKPLFFTVGFTGCAFGSAAIWQYESLKSRVQSYFDGIKA
          T.G.A..RSALIP.VE.T.FY.SPYP.R..LIKPLFFTVGF.GCAFGSAA.W..ESLKSRV.SYF..IKA
Retrocopy TTGEAYERSALIPTVEATVFYLSPYPLRRMLIKPLFFTVGFSGCAFGSAAVWECESLKSRVRSYFHSIKA

Parental  DWLDSIRPQKKGDFRKEINKWWNNLSDGQRTVTGIIAANVLVFCLWRVPSLKRTMTRYFTSNPASKVL-C
          DWLDSIR.QKKGDFRKEI.KWWNNLSDGQ.TVTGI.AANVLV.CLWRVPSL..T..RYFTSNPASKVL.C
Retrocopy DWLDSIR*QKKGDFRKEIKKWWNNLSDGQQTVTGITAANVLVVCLWRVPSLHWTVIRYFTSNPASKVL<C

Parental  SPMLLSTFSHFSLIHMAANMYVLWSFSSSIV
          .PMLLSTF.HFSL.HMAANM.VLWSFSSSIV
Retrocopy FPMLLSTFNHFSLFHMAANM*VLWSFSSSIV

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	18.28 RPM
SRP051959_heart	0.14 RPM	17.61 RPM
SRP051959_kidney	0.07 RPM	15.93 RPM
SRP051959_liver	0.06 RPM	14.43 RPM
SRP051959_lung	0.05 RPM	14.58 RPM
SRP051959_lymph_node	0.02 RPM	19.54 RPM
SRP051959_skeletal_muscle	0.00 RPM	15.37 RPM
SRP051959_spleen	0.06 RPM	15.84 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2384 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2384 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2384 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021241	2 retrocopies	retro_cjac_1415, retro_cjac_2384 ,
Dipodomys ordii	ENSDORG00000014935	1 retrocopy	retro_dord_315,
Homo sapiens	ENSG00000175193	1 retrocopy	retro_hsap_3526,
Gorilla gorilla	ENSGGOG00000000416	1 retrocopy	retro_ggor_2384,
Mus musculus	ENSMUSG00000033918	2 retrocopies	retro_mmus_1882, retro_mmus_3526,
Nomascus leucogenys	ENSNLEG00000006072	1 retrocopy	retro_nleu_491,
Otolemur garnettii	ENSOGAG00000006126	1 retrocopy	retro_ogar_648,
Pan troglodytes	ENSPTRG00000015673	1 retrocopy	retro_ptro_2394,
Ictidomys tridecemlineatus	ENSSTOG00000023222	1 retrocopy	retro_itri_380,