RetrogeneDB ID: retro_ptro_2339

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:31648977..31650150(+)
• 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_2339
ATGTCTCACAGAAAGTTCTCCACTCCCAGACATGGGTCCCTCGGCTTCCTGCCTTGGAAGCGCAGCAGCAGGCATCGTGG
GAAGGTGAAGAACTTCCCTAAGGATGACCCGTCCAAGCCGGTCCACCTCACAGCCTTCCTGGGATACAAGGCTGGCATGA
CCCACATCGTGAGGGAAGTCAACAGGCCAGGATCCAAGGTGAACAAGAAGGAGGTGGTGGAGGCTGTGACCATTGTGGAG
AGGCCACCAGTGGGCATTGTGGGCTACGTGGAAACCCCTCAAGGCCTCCGGACTTGCAAGACTGTCTTCGCTGAGCACAT
CAGTGATGAATGCAAGAGGCGTTTCTACAAGAACTGGCAAAAATCTAAGAAGAAGGCCTTTACCAAGTACTGCAAGAAAT
GGCAGGATGAGGATGGCAAGAAGCAGCTGGAGAAGGACTTCAGCAGCATGAAGAAGTACTGCCAAGTCATCCGCGTCATT
GCCCACACCCAGATGCACCTGCTTCCTCTGTGCCAGAAGAAGGCCCACCTGATGGAGATCCAAGTGAATGGAGGCACTGT
GGCTGAGAAGCTGGACTGGGCTGGCGAGAGGCTCAAGCAGCAGGTACCTGTGAACCAAGTGTTTGGGCAGGATGAGATGA
TCGACGTCATCAGGGTGACCAAGGGCAAAGGCTACAAAAGGGTCACCAGTCATTGGCACACCAAGAAGCTGCCCCGCAAG
ACCCACCAAGGCCTGTGCAAGGTGGCCTGTATTGGGGCATGGCATCCTGCTTGTGTGGGCTTCTCTGTGGTACGTGGTGG
GCAGAAAGGCTACCGTCACCGCACTGAGATCAACAAGAAGATCTATAGGATTGGCTAGGGCTACCTTATCAAGGATGGCA
AGCTGATCAAGAACAATGCCTCCACTGACTATGACCTGTCTGACAAGAGCATCAACCCTTTTGGTGGCTTTGTCCACTAT
GGTGAAGTGTCCAATGACTTTGTCATGCTGAAAGGCTGTGTGGTGGGAACCAAGAAGTGGGTGCTCACCCTCCGCAAGTC
CTTGCTGGTGCAGACAAAGCAGCGGGCTCTGGAGAAGATTGACCTTAAGTTCATTGACACCACCTCCAAGTTTGGCCATG
GCCGCTTCCGGACCATGGAGGAGAAGAAAGCATTCATGGGACCACTCAAGAAA

Alignment

ORF - retro_ptro_2339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.11 %
• Parental protein coverage: 96.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSHRKFSAPRHGHLGFLPHKRSHRHRGKVKTWPRDDPSQPVHLTAFLGYKAGMTHTLREVHRPGLKISKR
          MSHRKFS.PRHG.LGFLP.KRS.RHRGKVK..P.DDPS.PVHLTAFLGYKAGMTH..REV.RPG.K..K.
Retrocopy MSHRKFSTPRHGSLGFLPWKRSSRHRGKVKNFPKDDPSKPVHLTAFLGYKAGMTHIVREVNRPGSKVNKK

Parental  EEVEAVTIVETPPLMVVGVVGYVATPRGLRSFKTIFAEHLSDECRRRFYKDWHKSKKKAFTKACKRWRDT
          E.VEAVTIVE.PP...VG.VGYV.TP.GLR..KT.FAEH.SDEC.RRFYK.W.KSKKKAFTK.CK.W.D.
Retrocopy EVVEAVTIVERPP---VGIVGYVETPQGLRTCKTVFAEHISDECKRRFYKNWQKSKKKAFTKYCKKWQDE

Parental  DGKKQLQKDFAAMKKYCKVIRVIVHTQMKLLPFRQKKAHIMEIQLNGGTVAEKVAWAQARLEKQVPVHSV
          DGKKQL.KDF..MKKYC.VIRVI.HTQM.LLP..QKKAH.MEIQ.NGGTVAEK..WA..RL..QVPV..V
Retrocopy DGKKQLEKDFSSMKKYCQVIRVIAHTQMHLLPLCQKKAHLMEIQVNGGTVAEKLDWAGERLKQQVPVNQV

Parental  FSQSEVIDVIAVTKGRGVKGVTSRWHTKKLPRKTHKGLRKVACIGAWHPARVGCSIARAGQKGYHHRTEL
          F.Q.E.IDVI.VTKG.G.K.VTS.WHTKKLPRKTH.GL.KVACIGAWHPA.VG.S..R.GQKGY.HRTE.
Retrocopy FGQDEMIDVIRVTKGKGYKRVTSHWHTKKLPRKTHQGLCKVACIGAWHPACVGFSVVRGGQKGYRHRTEI

Parental  NKKIFRIGRGPHMEDGKPVKNNASTSYDVTAKSITPLGGFPHYGEVNNDFVMLKGCIAGTKKRVITLRKS
          NKKI.RIG.G....DGK..KNNAST.YD...KSI.P.GGF.HYGEV.NDFVMLKGC..GTKK.V.TLRKS
Retrocopy NKKIYRIG*GYLIKDGKLIKNNASTDYDLSDKSINPFGGFVHYGEVSNDFVMLKGCVVGTKKWVLTLRKS

Parental  LLVHHSRQAVENIELKFIDTTSKFGHGRFQTAQEKRAFMGPQKK
          LLV.....A.E.I.LKFIDTTSKFGHGRF.T..EK.AFMGP.KK
Retrocopy LLVQTKQRALEKIDLKFIDTTSKFGHGRFRTMEEKKAFMGPLKK

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	0.38 RPM	0.02 RPM
SRP007412_cerebellum	0.43 RPM	0.00 RPM
SRP007412_heart	0.12 RPM	38.27 RPM
SRP007412_kidney	0.89 RPM	0.00 RPM
SRP007412_liver	0.75 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_2339 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2339 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2339 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3448

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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,