RetrogeneDB ID: retro_cjac_1254

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:13145969..13147620(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R12A
• Ensembl ID: ENSCJAG00000019271
• Aliases: None
• Description: None

Sequence

>retro_cjac_1254
GCAGCAGCTCGAAAGGAAGAACGGATCGTGCTTAGAGATGCCAGGCAGTGGCTAAATAGTGGTCATATAAATGATGTCCG
ACATGCAGAATCTGGAGGTACAGCACTTCACGTTGCAGCTGCTAAAGGCTATACGGAAGTTTTAAAACTTTTAATACAGG
CAGGATATGATACTAATATTAAAGACTATGATGGCTGGACACCTCTTCATGCTGCAGCTCATTGGGGTAAAGAAGAAGCA
TGTCGAATTTTAGTGGACAATCTCTGTGATGAGATGGTCAACAAAGTGGGCCAAACAGCCTTTGATGTAGCAGATGAAGA
CATTTTAGGATATTTAGAAGAGCTGCAAAAGAAACAAAATCTGCTCCATAGTGAAAAACGGGATAAGAAATCTCCACTAA
TTGAATCTACAGCAAATATGGACAATAATCAGTCACAGAAGACCTTTAAAAACAAAGAGACATTGATTATTGAGCCAGAG
AAAAATGCATCCCATATTGAATCTCTGGAACAAGAAAATGTTGATGAAGAAGAAGAACGAAAGAAAGATGAGTCTAGCTG
CTCTAGGGAAGAAGATGAGGAAGATGACTTGGAATCAGAAGCTGAAACAGATAAGACAAAACCCTGACTTCTGTAACTAA
TGTCAACACTTCTAGTACACAAGCAGCTACTGTAGCTGTTACAACACCTACTGTGTTATCAGGTCAAGCAACACCTACAT
CGCCTATTAAAAAGTTTCCAACTACAGCTACAAAAATTTCTCCCAAAGAAGAAGAGAGAAAAGATGAGTCTCCTGCCACT
TGGAGGTTAGGACTTAGAAAGGCCGGCAGTTATGGCACACTTGCTGAAATCACAGCATCAAAAGAGGGTCAGAAAGAAAA
AGATACTGCAGGTGTTACACGTTCAGCTTCGAGTCCCAGACTTTCCTCCTCTTTGGATAATAAAGAAAAGGAGAAAGATA
GTAAAGGAACTAGGCTTGCATATGTCGCGCCTACAATACCAAGATGACTAGTCAGTACATCTGACGTTGAAGAGAAAGAA
AACAGAGATTCTTCAAGTTTGCGAACAAGTAGTTCATATACAAGGAGAAAATGGGAAGATGATCTTAAAAAAATAGCTCA
ATTAATGAAGGATCAACTTATCATAAAAGTTGCTCCTTTGGTAGAAGACAAGATGATTTGATTAGTTCCAGTGTTCCAAG
CACCACGTCAACACCAACAGTTACCTCTGCAGCTGGGCTTCAGAAAAGTCTGCTTTCCAGCACAAGCACTGCTACAAAGA
TTACAATCAGTTCTTCCTCAGCAGGCACACAAAGCAGTACCTCAAATCGTTTGTGGGCTGAGGATAGTATAGAAAAAGAA
AAGGACAGTGTTCCTACATCAGTGACCATTCCCATTGCTCCAACTGTTGTAAATGCTGCAGCTTCTACCACAACCCTGAC
TACAACTACTGCTGGCACTGTCTCCTCCACAACAGAGGTCAGGGAGAGACACAGATCATACCCTACTCCTGTTAGGGATG
AAGAGTCTGAATCCCAAAGAGAAGCAAGATCTAGACAAGCAAGGCAATCTAGAAGATCAACACAGGGAGTGACATTAACT
GATCTTCAAGAAGCTGGGAAAACTATAGGAAGAAGTCGTTCTACCAGAACC

Alignment

ORF - retro_cjac_1254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.4 %
• Parental protein coverage: 53.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AARKEEERIMLRDARQWLNSGHINDVRHAKSGGTALHVAAAKGYTEVLKLLIQAGYDVNIKDYDGWTPLH
          AA...EERI.LRDARQWLNSGHINDVRHA.SGGTALHVAAAKGYTEVLKLLIQAGYD.NIKDYDGWTPLH
Retrocopy AAARKEERIVLRDARQWLNSGHINDVRHAESGGTALHVAAAKGYTEVLKLLIQAGYDTNIKDYDGWTPLH

Parental  AAAHWGKEEACRILVDNLCDMEMVNKVGQTAFDVADEDILGYLEELQKKQNLLHSEKRDKKSPLIESTAN
          AAAHWGKEEACRILVDNLCD.EMVNKVGQTAFDVADEDILGYLEELQKKQNLLHSEKRDKKSPLIESTAN
Retrocopy AAAHWGKEEACRILVDNLCD-EMVNKVGQTAFDVADEDILGYLEELQKKQNLLHSEKRDKKSPLIESTAN

Parental  MDNNQSQKTFKNKETLIIEPEKNASRIESLEQEKVDEEEEGKKDESSCSSEEDEEDDSESEAETDKTKP-
          MDNNQSQKTFKNKETLIIEPEKNAS.IESLEQE.VDEEEE.KKDESSCS.EEDEEDD.ESEAETDKTKP.
Retrocopy MDNNQSQKTFKNKETLIIEPEKNASHIESLEQENVDEEEERKKDESSCSREEDEEDDLESEAETDKTKP<

Parental  LASVTNVNTSSTQAATVAVTTPTVSSGQATPTSPIKKFPTTATKISPKEEERKDESPATWRLGLRKTGSY
          L.SVTNVNTSSTQAATVAVTTPTV.SGQATPTSPIKKFPTTATKISPKEEERKDESPATWRLGLRK.GSY
Retrocopy LTSVTNVNTSSTQAATVAVTTPTVLSGQATPTSPIKKFPTTATKISPKEEERKDESPATWRLGLRKAGSY

Parental  GALAEITASKEGQKEKDTAGVTRSASSPRLSSSLDNKEKEKDSKGTRLAYVAPTIPRRLASTSDIEEKEN
          G.LAEITASKEGQKEKDTAGVTRSASSPRLSSSLDNKEKEKDSKGTRLAYVAPTIPR.L.STSD.EEKEN
Retrocopy GTLAEITASKEGQKEKDTAGVTRSASSPRLSSSLDNKEKEKDSKGTRLAYVAPTIPR*LVSTSDVEEKEN

Parental  RDSSSLRTSSSYTRRKWEDDLK-KNSSINEGSTYHKSCSFGRRQDDLISSSVPSTTSTPTVTSAAGLQKS
          RDSSSLRTSSSYTRRKWEDDLK.KNSSINEGSTYHKSCSFGRRQDDLISSSVPSTTSTPTVTSAAGLQKS
Retrocopy RDSSSLRTSSSYTRRKWEDDLK<KNSSINEGSTYHKSCSFGRRQDDLISSSVPSTTSTPTVTSAAGLQKS

Parental  LLSSTSTTTKITTGSSSAGTQSSTSNRLWAEDSTEKEKDNVPTSVTIPVAPTVVNAAASTTTLTTTTAGT
          LLSSTST.TKIT..SSSAGTQSSTSNRLWAEDS.EKEKD.VPTSVTIP.APTVVNAAASTTTLTTTTAGT
Retrocopy LLSSTSTATKITISSSSAGTQSSTSNRLWAEDSIEKEKDSVPTSVTIPIAPTVVNAAASTTTLTTTTAGT

Parental  VSSTTEVRERRRSYLTPVRDEESESQRKARSRQARQSRRSTQGVTLTDLQEAEKTIGRSRSTRT
          VSSTTEVRER.RSY.TPVRDEESESQR.ARSRQARQSRRSTQGVTLTDLQEA.KTIGRSRSTRT
Retrocopy VSSTTEVRERHRSYPTPVRDEESESQREARSRQARQSRRSTQGVTLTDLQEAGKTIGRSRSTRT

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	0.09 RPM	84.82 RPM
SRP051959_heart	0.09 RPM	127.17 RPM
SRP051959_kidney	0.04 RPM	63.72 RPM
SRP051959_liver	0.02 RPM	26.86 RPM
SRP051959_lung	0.07 RPM	113.74 RPM
SRP051959_lymph_node	0.11 RPM	101.53 RPM
SRP051959_skeletal_muscle	0.04 RPM	40.09 RPM
SRP051959_spleen	0.06 RPM	99.24 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1254 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1254 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1254 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019271	1 retrocopy	retro_cjac_1254 ,