RetrogeneDB ID: retro_cjac_1346

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:61052599..61053363(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CA
• Ensembl ID: ENSCJAG00000013634
• Aliases: None
• Description: protein phosphatase 2, catalytic subunit, alpha isozyme [Source:HGNC Symbol;Acc:9299]

Sequence

>retro_cjac_1346
TGTGGAGATGTGCATGGGCAATTTCATGATCTCATGGAACTGTTTAGAATTGGTGGCAAATCACCAGATACAAATTATTG
TTTATGGGAGATTATGTTGACAGAGGATATTATTCAGTTGAAACAGTTACACTGCCTGTAGCTCTTAAGGTTCGTTACCG
TGAACGCATCACCATTCTTCGAGGGAATCATGACAGCAGACACATCACACAAGTTTATGGTTTCTATGATGAGTGTTTCA
GAAAATACGGAAATGCAAATGTTTGGAAATATTTTACAGATCTTTTTGACTATCTTCCTCTCACTGCCTTGGTGGATGGG
CAAATCTTCTGTCTACATGGTGGTCTCTCGCCATCTGTAGATACACTGGATCATATCAGAGCACTTGCTCGCCTACAAGA
AGTTCCCCATGAGGGTCCAATGTGTGACTTGCTGTGGTCAGATCCAGATGACCATGGTGGTTGGGGTATATCTCCTCAGG
GAGCTGGTTACACCTTTGGACAAGATATTTCTGAGACATTTAATCATGCCAATGGCCTCACGTTGGTGTCTAGAGCTCAC
CAGCTAGTGATGGAGGGATATAACTGGTGCCATGACCAGAATGTAGTAACGATTTTCAGTGCTCCAAACTATTGTTATTG
TTGAGGTAACCAAGCTGCAATCATGGAACTTGACGATACTCTAAAATACTCTTTCTTGCAGTTTGACCCAGCACCTCGTA
GAGGCGAGCCACATGTTACTCGTGGTACCCCAGACTACTTCCTG

Alignment

ORF - retro_cjac_1346 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.92 %
• Parental protein coverage: 82.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CGDVHGQFHDLMELFRIGGKSPDTNY-LFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNHESRQI
          CGDVHGQFHDLMELFRIGGKSPDTNY.LFMGDYVDRGYYSVETVTL.VALKVRYRERITILRGNH.SR.I
Retrocopy CGDVHGQFHDLMELFRIGGKSPDTNY<LFMGDYVDRGYYSVETVTLPVALKVRYRERITILRGNHDSRHI

Parental  TQVYGFYDECLRKYGNANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEG
          TQVYGFYDEC.RKYGNANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPS.DTLDHIRAL.RLQEVPHEG
Retrocopy TQVYGFYDECFRKYGNANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSVDTLDHIRALARLQEVPHEG

Parental  PMCDLLWSDPDDRGGWGISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAP
          PMCDLLWSDPDD.GGWGISP.GAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHD.NVVTIFSAP
Retrocopy PMCDLLWSDPDDHGGWGISPQGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDQNVVTIFSAP

Parental  NYCYRCGNQAAIMELDDTLKYSFLQFDPAPRRGEPHVTRRTPDYFL
          NYCY..GNQAAIMELDDTLKYSFLQFDPAPRRGEPHVTR.TPDYFL
Retrocopy NYCYC*GNQAAIMELDDTLKYSFLQFDPAPRRGEPHVTRGTPDYFL

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	0.07 RPM	47.90 RPM
SRP051959_heart	0.16 RPM	54.08 RPM
SRP051959_kidney	0.16 RPM	40.98 RPM
SRP051959_liver	0.09 RPM	30.37 RPM
SRP051959_lung	0.07 RPM	40.75 RPM
SRP051959_lymph_node	0.09 RPM	43.29 RPM
SRP051959_skeletal_muscle	0.37 RPM	60.86 RPM
SRP051959_spleen	0.36 RPM	43.07 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1346 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1346 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1346 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002653	1 retrocopy	retro_acar_69,
Callithrix jacchus	ENSCJAG00000012460	1 retrocopy	retro_cjac_985,
Callithrix jacchus	ENSCJAG00000013634	2 retrocopies	retro_cjac_1346 , retro_cjac_4113,
Homo sapiens	ENSG00000113575	1 retrocopy	retro_hsap_369,
Nomascus leucogenys	ENSNLEG00000026729	1 retrocopy	retro_nleu_2441,
Otolemur garnettii	ENSOGAG00000009695	2 retrocopies	retro_ogar_3414, retro_ogar_921,
Rattus norvegicus	ENSRNOG00000005389	5 retrocopies	retro_rnor_1263, retro_rnor_1264, retro_rnor_1265, retro_rnor_1266, retro_rnor_817,
Sarcophilus harrisii	ENSSHAG00000016632	3 retrocopies	retro_shar_313, retro_shar_428, retro_shar_471,
Ictidomys tridecemlineatus	ENSSTOG00000010560	1 retrocopy	retro_itri_258,