RetrogeneDB ID: retro_ptro_3163

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:123033042..123034217(+)
• 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_3163
CACAGAAAGTTCTCCACTCCCAGACATGGGTCCCTCGGCTTCCTGCCTTGAAAGCACAATTGCAGGCATTGTGGGAAGGT
GAAGAGTTTCCCTAAGGATGACCCTTCAAAGCTGGTCCACCTCACAGCCTTCTTGAGATACAAGGTTGGCATGACCCACA
TCGTGAGGGGAAGTCAATAGGCCAGGATCCAAGGTGAGTACGAAGGAGGTGGTAGAGGCTGTGGCCATTGTGGAGACAAC
CACCCACAATGGTGGTTGTGGGCATTGTGGGATATGGGGAAACCCTTCGAGGCATCTGGACTTTCAAGACCATCTTTGCT
GAGCACATCAGCAGTGAGTGCAAAAGGCGTTTCTATAAGAACTGACATAAATCTAAGAAGAAGCCCTTTACCAAGTACTG
CAAGAAACGGCAGAAAGAGGATGGCAAAAAGCAGGTGTAGAAGGACTTCAGCAGCATGAAGAAGTACTGCCAAGTCATCC
GCGTCATTGCCCACACCCAGATACGCCTGCTTCCTCTGCACCAGAAAGCCCACCTGATGGAGATCTAGGTGAACAGAGGC
ACTGTGGCCGAGAAGCTGGACTGGGCCCAGAAGAGGCTCGAGCAGCAGGTACCTGTGAACCAAGTGTTTGGGCAAGATGA
GATGATCAAAGTCATCGGGGTGACCAAGGGCAAAGGCTACAAAGGGGTCACCAGTTGTTGGCACACCAAGAAGCTGCCCC
ACAAGACCCACCAAGGCTTATGCAAGGTGGCCTGTATTGGGGCATGGCATCTTGCCCATGTGGCCTTCTCTGTGGCACAC
GCTGGTCAGAAAGGCTACCATCATGGCACTGAGATCAACAAGAAGATCTATAAGATCGGCCAGGGCTACCCTATCATGGA
CGGCAAACTGATCAAGAACAATGCCTCCATTGACTATGACCTGTCTGACAAGAGCATCAACTCTCTGGGTGGCTTTGTCC
ACTGTGGCAAAGTGACCAATGACTTTGTCATGCTGAAAGGCTATGTGGTGGGAACCAAGAAGCAAGTGCTCACCCTCTGC
AAGTCCTTGCTGGTCCAGACCAAATGGCAGGCTCTGGAGAAGACTGACCTTAAGTTCATTGACACCACCTCCAACTTTGG
CCATTGCCACTTCCAGACCATGAAGAAGAAAGCATTCATGAGACCACTCAAGAAA

Alignment

ORF - retro_ptro_3163 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.34 %
• Parental protein coverage: 96.31 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HRKFSAPRHGHLGFLPHKRSHRHRGKVKTWPRDDPSQPVHLTAFLGYKAGMTHTLR-EVHRPGLKISKRE
          HRKFS.PRHG.LGFLP.K...RH.GKVK..P.DDPS..VHLTAFL.YK.GMTH..R.EV.RPG.K.S..E
Retrocopy HRKFSTPRHGSLGFLP*KHNCRHCGKVKSFPKDDPSKLVHLTAFLRYKVGMTHIVR>EVNRPGSKVSTKE

Parental  EVEAVTIVET-PPLMVV-GVVGYVATPRGLRSFKTIFAEHLSDECRRRFYKDWHKSKKKAFTKACKRWRD
          .VEAV.IVET.PP.MVV.G.VGY..T.RG...FKTIFAEH.S.EC.RRFYK..HKSKKK.FTK.CK....
Retrocopy VVEAVAIVET>PPTMVVVGIVGYGETLRGIWTFKTIFAEHISSECKRRFYKN*HKSKKKPFTKYCKKRQK

Parental  TDGKKQLQKDFAAMKKYCKVIRVIVHTQMKLLPFRQKKAHIMEIQLNGGTVAEKVAWAQARLEKQVPVHS
          .DGKKQ..KDF..MKKYC.VIRVI.HTQ..LLP..QK.AH.MEI..N.GTVAEK..WAQ.RLE.QVPV..
Retrocopy EDGKKQV*KDFSSMKKYCQVIRVIAHTQIRLLPLHQK-AHLMEI*VNRGTVAEKLDWAQKRLEQQVPVNQ

Parental  VFSQSEVIDVIAVTKGRGVKGVTSRWHTKKLPRKTHKGLRKVACIGAWHPARVGCSIARAGQKGYHHRTE
          VF.Q.E.I.VI.VTKG.G.KGVTS.WHTKKLP.KTH.GL.KVACIGAWH.A.V..S.A.AGQKGYHH.TE
Retrocopy VFGQDEMIKVIGVTKGKGYKGVTSCWHTKKLPHKTHQGLCKVACIGAWHLAHVAFSVAHAGQKGYHHGTE

Parental  LNKKIFRIGRGPHMEDGKPVKNNASTSYDVTAKSITPLGGFPHYGEVNNDFVMLKGCIAGTKKRVITLRK
          .NKKI..IG.G....DGK..KNNAS..YD...KSI..LGGF.H.G.V.NDFVMLKG...GTKK.V.TL.K
Retrocopy INKKIYKIGQGYPIMDGKLIKNNASIDYDLSDKSINSLGGFVHCGKVTNDFVMLKGYVVGTKKQVLTLCK

Parental  SLLVHHSRQAVENIELKFIDTTSKFGHGRFQTAQEKRAFMGPQKK
          SLLV....QA.E...LKFIDTTS.FGH..FQT...K.AFM.P.KK
Retrocopy SLLVQTKWQALEKTDLKFIDTTSNFGHCHFQT-MKKKAFMRPLKK

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

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3163 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3163 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3163 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4749
Gorilla gorilla	retro_ggor_2955
Pongo abelii	retro_pabe_3696

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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,