RetrogeneDB ID: retro_ptro_2767

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:77621953..77623106(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL3L
• Ensembl ID: ENSPTRG00000007617
• Aliases: None
• Description: ribosomal protein L3-like [Source:HGNC Symbol;Acc:10351]

Sequence

>retro_ptro_2767
CCCAGACATGGGTCCCTCAGCTTCCTGCCTCAGAAGTGCAGCAGGAGGCATCACAGGAAGGTGAAGAGCTTCCCTAAAGA
GGACCCTTCCAAGCCGGTCCACCTCATAGCCTTCCTGGGATACAAGGCAGGCATGACCCACATCGTGCGGGAAGTCGACA
GGCCAGGATCCAAGGTGAACAAGAAGGAGGTGGTAGAGGCTGTGACCATTGTGGAGATAACCATGGTGGTCGTGGGCATT
GTGGGCTATGTGGGAACCCCTCGAGACCTCTGGACCTTCAAGACCGTCTTCACTGAGCACATCAGTGATGAGTGCAAGAG
GCATTTCTATAAGAACTGGCATAAATCTAAGAAGAAGGCCTTCACCAAGTACTGCAACAAATGGCTGGATGAGGATGGCA
AGAAGCAGCTGGAGAAGGACTTCAGCAGCATGAAGAAGTAATGCCAAGTCATCCATATCATTACCCACAACCAGATGTTG
TGCTTCCTCTGCACCATAAGAAGGCCCATGTGATGGAGATCCAGGTGAACAGAGGCACTGTGGCTGAGAAGCTGGACTGG
GCCCGCGAGAGGCTTGAGCAGCAGGTACCTGTGAACCAGGTGTTTGGGCAGGACGAGATGATTGATGTCATTGGGGTGAC
AAAGAGCAAAGGCTACAAAGGGGTCACCAGTCATTGGCACACCAAGAAGCTGTCCCGCAAGATCTGCTGAGGCCTCTGCA
AGGTGGCCTGTATTGAGGCATGGCATCCTGACCGTGTGGCCTTCTCTGGGGCACGCACTGGGCAGAAAGAGTACCATCAC
TGCACTAAGATCAACAAGAAGATCTATAAGATCGGCCAGAGCTACCTTATCAAGGGTGGCAAACTGATCAAGAACAATGC
CTCCACTGACTATGACCTGTCTGTCAAGAGCATCAACCCTCTGGGTGGCTTTGTCCACTATGGTGAAGTGACCAATGACT
TTGTCATGCTGAAAGCTGTGTGGTTGTAACCAAGAAACGAGTGCTCATCCTCCGCAAGTCCTTGCTGGTGCAGACCAAAT
GACAGGCTCTGGAGAAGACTGACCTTAAGTTCATTGACACCACCTCCAAGTTTGGCCATGGCTGCTTCCAGACCATGGAG
GAGAAGAAAGCATTTGTGGGAGCACTCAAGAAA

Alignment

ORF - retro_ptro_2767 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.49 %
• Parental protein coverage: 94.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PRHGHLGFLPHKRSHRHRGKVKTWPRDDPSQPVHLTAFLGYKAGMTHTLREVHRPGLKISKREEVEAVTI
          PRHG.L.FLP.K.S.RH..KVK..P..DPS.PVHL.AFLGYKAGMTH..REV.RPG.K..K.E.VEAVTI
Retrocopy PRHGSLSFLPQKCSRRHHRKVKSFPKEDPSKPVHLIAFLGYKAGMTHIVREVDRPGSKVNKKEVVEAVTI

Parental  VETPPLMVVGVVGYVATPRGLRSFKTIFAEHLSDECRRRFYKDWHKSKKKAFTKACKRWRDTDGKKQLQK
          VE.....VVG.VGYV.TPR.L..FKT.F.EH.SDEC.R.FYK.WHKSKKKAFTK.C..W.D.DGKKQL.K
Retrocopy VEIT-MVVVGIVGYVGTPRDLWTFKTVFTEHISDECKRHFYKNWHKSKKKAFTKYCNKWLDEDGKKQLEK

Parental  DFAAMKKYCKVIRVIVHTQMK-LLPFRQKKAHIMEIQLNGGTVAEKVAWAQARLEKQVPVHSVFSQSEVI
          DF..MKK.C.VI..I.H.QM...LP...KKAH.MEIQ.N.GTVAEK..WA..RLE.QVPV..VF.Q.E.I
Retrocopy DFSSMKK*CQVIHIITHNQML<VLPLHHKKAHVMEIQVNRGTVAEKLDWARERLEQQVPVNQVFGQDEMI

Parental  DVIAVTKGRGVKGVTSRWHTKKLPRKTHKGLRKVACIGAWHPARVGCSIARAGQKGYHHRTELNKKIFRI
          DVI.VTK..G.KGVTS.WHTKKL.RK...GL.KVACI.AWHP.RV..S.AR.GQK.YHH.T..NKKI..I
Retrocopy DVIGVTKSKGYKGVTSHWHTKKLSRKIC*GLCKVACIEAWHPDRVAFSGARTGQKEYHHCTKINKKIYKI

Parental  GRGPHMEDGKPVKNNASTSYDVTAKSITPLGGFPHYGEVNNDFVMLK-GCIAGTKKRVITLRKSLLVHHS
          G.......GK..KNNAST.YD...KSI.PLGGF.HYGEV.NDFVMLK..C...TKKRV..LRKSLLV...
Retrocopy GQSYLIKGGKLIKNNASTDYDLSVKSINPLGGFVHYGEVTNDFVMLK<SCVVVTKKRVLILRKSLLVQTK

Parental  RQAVENIELKFIDTTSKFGHGRFQTAQEKRAFMGPQKK
          .QA.E...LKFIDTTSKFGHG.FQT..EK.AF.G..KK
Retrocopy *QALEKTDLKFIDTTSKFGHGCFQTMEEKKAFVGALKK

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	0.00 RPM	0.02 RPM
SRP007412_cerebellum	0.07 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	38.27 RPM
SRP007412_kidney	0.10 RPM	0.00 RPM
SRP007412_liver	0.13 RPM	0.03 RPM
SRP007412_testis	0.11 RPM	0.84 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2767 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2767 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2767 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4081
Gorilla gorilla	retro_ggor_2736
Pongo abelii	retro_pabe_3349

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008489	1 retrocopy	retro_amel_1881,
Nomascus leucogenys	ENSNLEG00000008850	9 retrocopies	retro_nleu_1107, retro_nleu_1130, retro_nleu_1249, retro_nleu_1305, retro_nleu_1673, retro_nleu_1824, retro_nleu_2046, retro_nleu_2060, retro_nleu_3126,
Pongo abelii	ENSPPYG00000006973	1 retrocopy	retro_pabe_2854,
Pan troglodytes	ENSPTRG00000007617	12 retrocopies	retro_ptro_1439, retro_ptro_1473, retro_ptro_1753, retro_ptro_2150, retro_ptro_2339, retro_ptro_2462, retro_ptro_2501, retro_ptro_2646, retro_ptro_2741, retro_ptro_2767 , retro_ptro_3163, retro_ptro_916,
Ictidomys tridecemlineatus	ENSSTOG00000012921	2 retrocopies	retro_itri_1344, retro_itri_867,