RetrogeneDB ID: retro_cjac_3269

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:16418079..16419848(-)
• Located in intron of: ENSCJAG00000020407

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLEKHA5
• Ensembl ID: ENSCJAG00000001320
• Aliases: None
• Description: None

Sequence

>retro_cjac_3269
ATGCGGATCTATTATTTCTGCACTGATACAGGAAAGGAAACGGAGTTGTGGATGAAAGCTGTGTTAGACGCTGCCCTAGT
ACAGACAGAACCTGCGAAAAGAGTGGACAAGATTACATCTGAAAATGCACCAACTAAAGAAACCAATAACCTTCCCAACC
ATAGAGTGCTGATTAAACCAGAGATCCAAAACAATCAAAAAAACAAGGAAATGAGCAAAATCAAAGAAGAAAAGGCATTA
GAAGCTGAAAAATATGGACTTCAGCAGGATGGTCAAGATAGACCCTTAACAAAATTGATAGTGTAAAGTTGAATTCTCTG
CCTTCTGAGTATGAGAGTGGGTCAGCCTGCCCTGCTTAGACTGCACACTACAGACCAGTCAACTTAAACAGTTCCGAGAA
CAAAATAGTCAGTGTTAGCCTGGCAGATCTTAGAGGTGAAAATCACCCCAGTACAGGGCCCTTATACAGAGGCTGATGGA
GTCATACAGGGAACAAATTCAGTGCAGCAATTGGAAGAGTGGATTAACATCCAGAAGGGGAGGAGTCATGAAGAAGAAAG
CAGGGGAGTAATTTCTTACCAAACATTACCAAGAAATATGCCAAGCCGCAGAGCTCAGATTATGGCCCACTACCCTGAAG
GTTACAGAACACTCCCAAGAAACAGCAAGACAAGGCCTGAAAGTATCTGCAGTGTAAACCCTTCCACTCATAACAAGACA
TCAGGACCTGGAGCAGAAGAGAAATGAGGTTCATGAGAGATGACACAATGTGGCAGCTGTACGAGTGGCAGCAGCATCAG
TTTTATAACAAACAGAGCACCCTCCCTCGACACAGTTCTTAACCCAAAACCATGGTTAATATTTCTGACCAGACAATGCA
CTCTATTCCCACATCACCTTCCCACGGGTCAATAGCTGCTTATCAGGAAGACTCCCCTCAACGAACTTACAGATCGGAAG
CATCTTCACCAATTCAGAGAGGAGATGTGACAATAGACCTCAGACACAGGGCCCATCACCCTAAGCATGTCTATGTGCCT
GACAGAGGATCAGTGCCAGCTGGACTGAACTTTATAGTCTGTTAGTCCCCAGAGCCTCCAAGGGAAAACGCTGTCACAAG
ATGAAGGCAGAGGCACATTATACAAATACAGACCCGAAGAAGTAAATATTGATGCCAAGTTAAGCCAATTATGTGAACAA
GATAAAGTGGCGCGTGCTCTGGAAGAGCAACTTCAGCAGCTCCACGAGGAGAAATACACGCTTGAGCAAGCTTTACTATA
AGCCAGCCAAGAGATAGAAATGCAGGCAGATAACCCAGCAGCCATTCAGACAGTGGTGTTACAAAGGGACGATTTACAAA
ATGGACTGCTTAGTACATCAAGAAGTTCTCCAGCCACTGCCGAATTGGAACGAGCATGGAGAGAATATGATGAGTTAGAA
CACGACGTGACTATTACCAGGAAGCAGATGCAAGAGCAGCTAGATCACCTTGGTGAAGTTCAGACGGAATCAGCAGGAAT
TCAGCGAGCACAGATTCAGAAAGAACTTTGGCGAATTCAAGATGTCATGGAAGGACTGAGTAAACACAGCAGCAAAGAGG
TACTACAGCAATAGGTATGGTAGGACCAAAGCCTTTCTCAACAGTTAAGTACAAAAATGAGGGTCCAGATTATAGACTCT
ACAAGAGCGAACCAGAGTTAACAACAGTGGCAGAAGTTGATGAATCTAATGGAGAAGAAAAATCAGAACCTGTTTTGGAG
ATAGAAACA

Alignment

ORF - retro_cjac_3269 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.81 %
• Parental protein coverage: 67.81 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MRTYYFCTDTGKEMELWMKAMLDAALVQTEPVKRVDKITSENAPTKETNNIPNHRVLIKPEIQNNQKNKE
          MR.YYFCTDTGKE.ELWMKA.LDAALVQTEP.KRVDKITSENAPTKETNN.PNHRVLIKPEIQNNQKNKE
Retrocopy MRIYYFCTDTGKETELWMKAVLDAALVQTEPAKRVDKITSENAPTKETNNLPNHRVLIKPEIQNNQKNKE

Parental  MSKIEEKKALEAEKYGFQKDGQDRPLTK-INSVKLNSLPSEYESGSVCPVQTAHYRPVSLNSSENRIVNV
          MSKI.E.KALEAEKYG.Q.DGQDRPLTK.I.SVKLNSLPSEYESGS.CP..TAHYRPV.LNSSEN.IV.V
Retrocopy MSKIKEEKALEAEKYGLQQDGQDRPLTK<IDSVKLNSLPSEYESGSACPA*TAHYRPVNLNSSENKIVSV

Parental  SLADLRGGNHPST-GPLYTEADRVIQRTNSMQQLEQWIKIQKGRSHEEESRGVISYQTLPRNMPSHRAQI
          SLADLRG.NHPST.GP.YTEAD.VIQ.TNS.QQLE.WI.IQKGRSHEEESRGVISYQTLPRNMPS.RAQI
Retrocopy SLADLRGENHPST>GP-YTEADGVIQGTNSVQQLEEWINIQKGRSHEEESRGVISYQTLPRNMPSRRAQI

Parental  MARYPEGYRTLPRNSKTRPESICSVTPSTHDKTLAPGAEEK-RRSMRDDTMWQLYEWQQRQFYNKQSTLP
          MA.YPEGYRTLPRNSKTRPESICSV.PSTH.KT..PGAEEK..R.MRDDTMWQLYEWQQ.QFYNKQSTLP
Retrocopy MAHYPEGYRTLPRNSKTRPESICSVNPSTHNKTSGPGAEEK<MRFMRDDTMWQLYEWQQHQFYNKQSTLP

Parental  RHGSLSSPKTMVNISDQTMHSIPTSPSHGSIAAYQGYSPQRTYRSEVSSPIQRGDVTIDRRHRAHHPKHV
          RH.S...PKTMVNISDQTMHSIPTSPSHGSIAAYQ..SPQRTYRSE.SSPIQRGDVTID.RHRAHHPKHV
Retrocopy RHSS*--PKTMVNISDQTMHSIPTSPSHGSIAAYQEDSPQRTYRSEASSPIQRGDVTIDLRHRAHHPKHV

Parental  YVPDRRSVPAGL-TLQPVSPQSLQGKTLSQDEGRATLYKYRPEEVDIDAKLSRLCEQDKVVHALEEKLQQ
          YVPDR.SVPAGL.TL..VSPQSLQGKTLSQDEGR.TLYKYRPEEV.IDAKLS.LCEQDKV..ALEE.LQQ
Retrocopy YVPDRGSVPAGL>TL*SVSPQSLQGKTLSQDEGRGTLYKYRPEEVNIDAKLSQLCEQDKVARALEEQLQQ

Parental  LHKEKYMLEQALLSASQEIEMHADDPAAIQTVVLQRDDLQNGLLSTCRELSRATAELERAWREYDKLEYD
          LH.EKY.LEQALL.ASQEIEM.AD.PAAIQTVVLQRDDLQNGLLST.R..S.ATAELERAWREYD.LE.D
Retrocopy LHEEKYTLEQALL*ASQEIEMQADNPAAIQTVVLQRDDLQNGLLSTSRS-SPATAELERAWREYDELEHD

Parental  VTVTRNQMQEQLDHLGEVQTESAGIQRAQIQKELWRIQDVMEGLSKH-KQQRGTTEIGMLASKPFSTVKY
          VT.TR.QMQEQLDHLGEVQTESAGIQRAQIQKELWRIQDVMEGLSKH..QQRGTT.IGM...KPFSTVKY
Retrocopy VTITRKQMQEQLDHLGEVQTESAGIQRAQIQKELWRIQDVMEGLSKH<QQQRGTTAIGMVGPKPFSTVKY

Parental  KNEGPDYRLYKSEPELTTVAEVDESNGEEKSEPVSEIET
          KNEGPDYRLYKSEPELTTVAEVDESNGEEKSEPV.EIET
Retrocopy KNEGPDYRLYKSEPELTTVAEVDESNGEEKSEPVLEIET

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	0.02 RPM	18.55 RPM
SRP051959_heart	0.14 RPM	32.36 RPM
SRP051959_kidney	0.02 RPM	55.04 RPM
SRP051959_liver	0.00 RPM	18.65 RPM
SRP051959_lung	0.07 RPM	32.31 RPM
SRP051959_lymph_node	0.00 RPM	7.79 RPM
SRP051959_skeletal_muscle	0.00 RPM	8.06 RPM
SRP051959_spleen	0.02 RPM	25.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3269 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3269 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3269 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	ENSCJAG00000001320	1 retrocopy	retro_cjac_3269 ,