RetrogeneDB ID: retro_ptro_916

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:55961341..55962390(+)
• 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_916
ATGTCTCACAGAAAGTTCTTCGCTCCCAGACATGGGTCCCTCAGCTTCCTGCCCCAGAAGTGCAACAGCGGGCATTGTGG
GAAGGTGAAGAGCCTCCCTAAGGATGACCCTTCCAAGCCGGTCTGCCTCACAGGCTTCCTGGGATACAAGGCTGGCATGA
CTCACATCGTGCAGGAAGTTGACAGGCCAGGATCCAAGGTGAATAAGAAGGAGGTGGTAGAGGCTGTGACCATTGTACAG
ACACTGCCCATGATGGTTGTGGGCATTGTGGGCTATGTGGAAACCCCTCAAGGCCTCCGGACCTTCAAGACTGTCTTCGC
TGAGCACATCAGTGATGAGTGCAAGAGGTGCTTCTATAAGAACTGGCATAAATCTAAGAAGAAGGCCTTTACCAAGTACT
GCAAGAAATGGCAGGATGAGAATGGCAAGAAGCAGCTGGAGAAGGACTTCAGCAGCATGAAGAAGTACTGCCAAGTCATC
CATGTCATTGCCCACACCCAGATGCACCGCTTCCTCTGCACCAGAAGAAGGCCCACCTGATGGAGATCCAGGTGAATGGA
GACACCATGGCCAAGAAGCTGGACTGGGCCCGCGAGAGGTTTGAGCAGCAGTTACCTGTGAACCATGTGTTTGGGCAGGA
TGAGATGATTGACATCATCAGAATGACAAAGGGCAGAGGCTACAAAGGGGTCACCAGTCGTTGGCACGCCAAGAAGCTGC
CCCGCAAGACCCACCAAGGCCCGCGCAAGGTGTCCTGTACTGGGGCATGGCATCTTGTCCATGTGGCCTTCTCTGTGGCA
CGCACTTGGCAGAAAGGCTACTGTCACCACACTGAGATCAATAAGAAGATCCATAAGATTGGCCAGGGCTACCTTATCAA
GGATGACAAACTGATCAAGAACAATGCCTCCACTGACTATGACCTGTCTGACAAGAGCATCAACCCTCTAGGTGTCTTTG
GCCACTATGGTGAAGTGACCAATGACTTTGTCATGCTGAAGGGCTGTGTGGTAGGAACCAAGAAGCGAGTGCTCACCCTC
CCCACAAGT

Alignment

ORF - retro_ptro_916 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.09 %
• Parental protein coverage: 86. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSHRKFSAPRHGHLGFLPHKRSHRHRGKVKTWPRDDPSQPVHLTAFLGYKAGMTHTLREVHRPGLKISKR
          MSHRKF.APRHG.L.FLP.K....H.GKVK..P.DDPS.PV.LT.FLGYKAGMTH...EV.RPG.K..K.
Retrocopy MSHRKFFAPRHGSLSFLPQKCNSGHCGKVKSLPKDDPSKPVCLTGFLGYKAGMTHIVQEVDRPGSKVNKK

Parental  EEVEAVTIVETPPLMVVGVVGYVATPRGLRSFKTIFAEHLSDECRRRFYKDWHKSKKKAFTKACKRWRDT
          E.VEAVTIV.T.P.MVVG.VGYV.TP.GLR.FKT.FAEH.SDEC.R.FYK.WHKSKKKAFTK.CK.W.D.
Retrocopy EVVEAVTIVQTLPMMVVGIVGYVETPQGLRTFKTVFAEHISDECKRCFYKNWHKSKKKAFTKYCKKWQDE

Parental  DGKKQLQKDFAAMKKYCKVIRVIVHTQMKL-LPFRQKKAHIMEIQLNGGTVAEKVAWAQARLEKQVPVHS
          .GKKQL.KDF..MKKYC.VI.VI.HTQM...LP..QKKAH.MEIQ.NG.T.A.K..WA..R.E.Q.PV..
Retrocopy NGKKQLEKDFSSMKKYCQVIHVIAHTQMHR<LPLHQKKAHLMEIQVNGDTMAKKLDWARERFEQQLPVNH

Parental  VFSQSEVIDVIAVTKGRGVKGVTSRWHTKKLPRKTHKGLRKVACIGAWHPARVGCSIARAGQKGYHHRTE
          VF.Q.E.ID.I..TKGRG.KGVTSRWH.KKLPRKTH.G.RKV.C.GAWH...V..S.AR..QKGY.H.TE
Retrocopy VFGQDEMIDIIRMTKGRGYKGVTSRWHAKKLPRKTHQGPRKVSCTGAWHLVHVAFSVARTWQKGYCHHTE

Parental  LNKKIFRIGRGPHMEDGKPVKNNASTSYDVTAKSITPLGGFPHYGEVNNDFVMLKGCIAGTKKRVITLRK
          .NKKI..IG.G....D.K..KNNAST.YD...KSI.PLG.F.HYGEV.NDFVMLKGC..GTKKRV.TL..
Retrocopy INKKIHKIGQGYLIKDDKLIKNNASTDYDLSDKSINPLGVFGHYGEVTNDFVMLKGCVVGTKKRVLTLPT

Parental  S
          S
Retrocopy S

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	0.11 RPM	0.00 RPM
SRP007412_heart	0.03 RPM	38.27 RPM
SRP007412_kidney	0.08 RPM	0.00 RPM
SRP007412_liver	0.03 RPM	0.03 RPM
SRP007412_testis	0.21 RPM	0.84 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_916 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_916 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_916 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1341
Gorilla gorilla	retro_ggor_1043
Pongo abelii	retro_pabe_1113

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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,