RetrogeneDB ID: retro_cjac_1415

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:76891112..76891786(-)
• Located in intron of: ENSCJAG00000008783

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_1415
TCTATCTGGCAATAAGAATCACTGAAATCCAGGGTCCAGAGTTATTTTGATGATATACAAGTTGACTGGTTGGATAGCAT
AAGACCACAAAAAGGAGACTTCAGAAAGGAGATAAATAAGTGGTGGAATAACCTAAGTGACGGCCAGCAGACTGAGACAG
ATTATCACAGCTGCAAATGAATGTCTTTGTATTCTGTTTATAGGAGCACCTTCTCTACAGTGGGACAATGATCAGATATT
TTGCATCTAATCCAGCCTCAGAAGTCCTTTCTCCAATGTTGCTGTCAATATTCAATCATTTCTCCTTATTTCACATGGCA
CCAAATATGTATGTTTTGTGGAGTTCCTCCTCTGACACAGTGAACATTCTGGGTCAAGAGTAGTCCATGGCAGTGTACCT
ATAGGCAGGTATTATTTCCAAATGTGTCAATTGTGTGTGTAAAGTTGCCACAGGAAGATATGGACCATCACTTGATGCAT
CTGGCACCATCATGACAGTCCTTGCAGCTGTCTGCACTAAGATCCCAGAAGGGACGCTTGCCATTATTTCCCTTCAGATG
TTCATATTCCCAGCAGGGAATATCCTAAAAGCTACTATTGCCATGGATACAGCAGGAATGATCCTGGGATAGAAATTTTT
TAATCATGCAGCACATCTTGGGGGGGTTCTTTGG

Alignment

ORF - retro_cjac_1415 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.81 %
• Parental protein coverage: 59.37 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AIWQYESLKSRVQSYFDGIKADWLDSIRPQKKGDFRKEINKWWNNLSDGQRTVTG-IIAANVLVFCLW-R
          .IWQ.ESLKSRVQSYFD.I..DWLDSIRPQ.KGDFRKEINKWWNNLSDGQ.T.T..I.AAN.....L...
Retrocopy SIWQ*ESLKSRVQSYFDDIQVDWLDSIRPQ-KGDFRKEINKWWNNLSDGQQTETD>ITAANECLCILFIG

Parental  VPSLK-RTMTRYFTSNPASKVLCSPMLLSTFSHFSLIHMAANMYVLWSFSSSIVNLLGQEQFMAMYLSAG
          .PSL...TM.RYF.SNPAS.VL.SPMLLS.F.HFSL.HMA.NMYVLWS.SS..VN.LGQE..MA.YL.AG
Retrocopy APSLQ>GTMIRYFASNPASEVL-SPMLLSIFNHFSLFHMAPNMYVLWSSSSDTVNILGQE*SMAVYL*AG

Parental  VISNFVSYVCKVATGRYGPSLGASGAIMTVLAAVCTKMPEGRLAIIFLPILTFTAGNALKAIIAMDTAGL
          .IS..V..VCKVATGRYGPSL.ASG.IMTVLAAVCTK.PEG.LAII.L....F.AGN.LKA.IAMDTAG.
Retrocopy IISKCVNCVCKVATGRYGPSLDASGTIMTVLAAVCTKIPEGTLAIISLQMFIFPAGNILKATIAMDTAGM

Parental  ILGWKVFDHAAHLGGALF
          ILG.K.F.HAAHLGG.L.
Retrocopy ILG*KFFNHAAHLGGVLW

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	0.93 RPM	18.28 RPM
SRP051959_heart	0.61 RPM	17.61 RPM
SRP051959_kidney	0.69 RPM	15.93 RPM
SRP051959_liver	0.41 RPM	14.43 RPM
SRP051959_lung	1.12 RPM	14.58 RPM
SRP051959_lymph_node	1.44 RPM	19.54 RPM
SRP051959_skeletal_muscle	0.79 RPM	15.37 RPM
SRP051959_spleen	0.67 RPM	15.84 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1415 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1415 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1415 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2290

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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,