RetrogeneDB ID: retro_ptro_308

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:66167236..66168533(-)
• Located in intron of: ENSPTRG00000034314

Retrocopy information

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

Parental gene information

• Parental gene symbol: GALNT11
• Ensembl ID: ENSPTRG00000019891
• Aliases: None
• Description: None

Sequence

>retro_ptro_308
TTATCAGTAACTGCAGGCTACCACAGAGATGTGCCAGGGACAAAGAATACAGCATGTAAAGTCCTACCTCCTGACCTGCC
AGTTGCTTACATAATTGTTATCTGTTTCCACAATGAAGCTTTTTCTGCCCTGTCTCCAGACGCTGCACATTGTCACAAAT
TGCATGCCAGCAAACCTGCTTCATGAAATCATCTTTATGGATGTTGTTAGCGACCTTGATGACTTGAAAGGAGGACGAGA
TGAATATGTCCAAAAATACCTCCTTGGAAAAATTAAGGTATAAGAAACATAAAGTGTGAGGGATTGATTCAAGGAAGAAT
GAGTGTAGCAGTCCACACAACAGAAGTCCTTGTGTTCCTAGACAGCCAATTGAAGTGAATGTGATGTGGCAGCAGCCCTT
GCTGGCTGTCATCTGTGTGGACTAGCAGACCATGATGTTCTCAGTGATTGATATCATTAGTGCCAACACGCTAGCCTACA
GCTCATCCTCTGTTGTCCGTGGAGGATTCAACTGAGGGCTGCACTTCAAATAGGAGCTTGTTCCCCTTTCTGAGCTAGGA
TGAGCAGAAAAAGCCACAGCACCAACAAAGTCACCGATAATGGCTGGAGGATTGTTTGCCAGGAACAGACAGTATTTCCA
GGAACTTGGACAGTATGATACTGGCATGGATATCTGGAGAGGAGAAAACTTGGAAATATCATTTCAGATCTGGGTGTGTG
GAGGTAAGTTCTTCATCATGCCTTGCTCTACAGTAGGACACATTTTCCAAAAAAAGGGGACCATATGGATCTCCTGAAGG
CCGGGATGCCATGAACACAACTTTTTGCAGCTGGCACATGTCTGGCTGGATGAATAAAGGCGCAGTATTTTTCCTTAAGA
CTTAATCTGGAGAGGAAAAGCTTTGGAACCATCAGTGAGCATGTTGAATTGAGAAAGAAGTTAGGATGCAAATCATTTGA
ATGGTATTTGGGTAATATTTACCCAAAGATGCAGATATCTGGGACCCATGACAAATCCCAGCAACCCACTTTTATCAGTA
GAGGGCCAAAATGCCCCAAAGTCCTTCAACTTGGAAGGCTCTATCACCTCCAGACCAACAAATGTCTGGTGGCTCAGGGC
TGCCCAAGTTGGAAAGGAGGCCTACTAGTGCTTAAGACTTGTGAGCATGGGGACCCAAATCAGATCTGGATTTATAATGA
AGAGCATGAATTGGTTTTAAACCATCTTCTTTGTCTAGGTATGACAGAAACTAGCTCATCAGACCCACCACAACTCGTGG
AGTGCCATGGGTCAGGC

Alignment

ORF - retro_ptro_308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.53 %
• Parental protein coverage: 71.55 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  ISNRLGYHRDVPDTRNAACKEKFYPPDLPAASI-VICFYNEAFSAL-LRTVHSVIDRTPAHLLHEIILVD
          .S...GYHRDVP.T.N.ACK....PPDLP.A.I.VICF.NEAFSAL.L.T.H.V....PA.LLHEII..D
Retrocopy LSVTAGYHRDVPGTKNTACK--VLPPDLPVAYIIVICFHNEAFSAL>LQTLHIVTNCMPANLLHEIIFMD

Parental  DDSDFDDLKGELDEYVQKYLPGKIKV-IRNTKREGLIRGRMIGAAHATGEVLVFLDSHC-EVNVMWLQPL
          ..SD.DDLKG..DEYVQKYL.GKIKV.IRN.K.EGLI.GRM..A.H.T.EVLVFLDS...EVNVMW.QPL
Retrocopy VVSDLDDLKGGRDEYVQKYLLGKIKV<IRNIKCEGLIQGRMSVAVHTT-EVLVFLDSQL<EVNVMWQQPL

Parental  LAAIREDRHTVVCPVIDIISADTLAYSSSPVVRGGFNWGLHFKWDLVPLSELGGAEGATAPIKSPTMAGG
          LA.I..D..T....VIDIISA.TLAYSSS.VVRGGFN.GLHFK..LVPLSELG.AE.ATAP.KSP.MAGG
Retrocopy LAVICVD*QTMMFSVIDIISANTLAYSSSSVVRGGFN*GLHFK*ELVPLSELG*AEKATAPTKSPIMAGG

Parental  LFAMNRQYFHELGQYDSGMDIWGGENLEISFRIWMCGGKLFIIPCSRVGHIF-RKRRPYGSPEGQDTMT-
          LFA.NRQYF.ELGQYD.GMDIW.GENLEISF.IW.CGGK.FI.PCS.VGHIF..KR.PYGSPEG.D.M..
Retrocopy LFARNRQYFQELGQYDTGMDIWRGENLEISFQIWVCGGKFFIMPCSTVGHIF>KKRGPYGSPEGRDAMN<

Parental  HNSLRLAHVWLDE-YKEQYFSLRPDLKTKSYGNISERVELRKKLGCKSFKWYLDNVYPEMQISGSHAKPQ
          HN.L.LAHVWLDE..K.QYFSLR..L..KS.G.ISE.VELRKKLGCKSF.WYL.N.YP.MQISG.H.K.Q
Retrocopy HNFLQLAHVWLDE<IKAQYFSLRLNLERKSFGTISEHVELRKKLGCKSFEWYLGNIYPKMQISGTHDKSQ

Parental  QPIFVNRGPKRPKVLQRGRLYHLQTNKCLVAQGRPSQKGGLVVLKACDYSDPNQIWIYNEEHELVLNSLL
          QP.F..RGPK.PKVLQ.GRLYHLQTNKCLVAQG.PS.KGGL.VLK.C...DPNQIWIYNEEHELVLN.LL
Retrocopy QPTFISRGPKCPKVLQLGRLYHLQTNKCLVAQGCPSWKGGLLVLKTCEHGDPNQIWIYNEEHELVLNHLL

Parental  CLDMSETRSSDPPRLMKCHGSG
          CL.M.ET.SSDPP.L..CHGSG
Retrocopy CLGMTETSSSDPPQLVECHGSG

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
SRP007412_brain_prefrontal_cortex	0.02 RPM	56.45 RPM
SRP007412_cerebellum	0.00 RPM	49.83 RPM
SRP007412_heart	0.00 RPM	13.87 RPM
SRP007412_kidney	0.00 RPM	257.10 RPM
SRP007412_liver	0.07 RPM	14.47 RPM
SRP007412_testis	0.00 RPM	8.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_308 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_308 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_308 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_402
Gorilla gorilla	retro_ggor_399

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001121	1 retrocopy	retro_chof_1535,
Homo sapiens	ENSG00000178234	1 retrocopy	retro_hsap_402,
Gorilla gorilla	ENSGGOG00000008784	1 retrocopy	retro_ggor_399,
Nomascus leucogenys	ENSNLEG00000004613	1 retrocopy	retro_nleu_1573,
Pan troglodytes	ENSPTRG00000019891	1 retrocopy	retro_ptro_308 ,
Pan troglodytes	ENSPTRG00000021180	1 retrocopy	retro_ptro_777,