RetrogeneDB ID: retro_ptro_2646

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:111487622..111488799(-)
• 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_2646
CTGTCTAACTGGAAGTTCACTGTTCCCTGGCTTGGGTCCCTAGGCTTCCTGCTTTGGAAGCGCAGCAGCAGGCTTCATGG
GAAGGTGAAGAGCTTCCCTAAGGATGAACCTTCCAAGCCATTCCACCTCACAGCCTTCCTGGGATACAAGGCTGGTATGG
CCTACATCATGTGAGAAGCTGACAGCCCAGGATCCAAGGTGAACAAGAAGGAAGTGGTAGAGGCTGTGACAGTTGTGGAG
ACACTGCCCATGGCAGTTGTGGGCATTGTGGCTATATGGAAATCGCTCAAGGCCTCCAGACCTTCAAGACTGTCTTTGCT
GAGCACATCAGCAATGAATGCAAAGGTGCTTCCATAAGAACCGGCATAATCTATAAAGATGGCCTTTACCAAGTACCACA
AGAAATGGCAGAATGAGGATGCAACAAGCAGCTGGAGAAGGAATTCAACAGCATGAAAATGTACTGCCAAGTCATCTCTA
TCATTGCCCATACTTAGATGTGCCTGCTTCCTCTGTGCCAGAAGAAGGCACGCCGATGGAGATCCAGGTGAACTGAGGCA
CTGTGGCTGAGAAACTGGACTGGACCTGGGAAATGCTAGAGCACCAGGTCCCTGTGAACCAAGTATTTGGGTAGGACAGG
GTAATTGATGCCATTGAGGTGACCAAGTGCAAAGGCTACAAAAGGGGTCACCAGTCATTGGCACACCAAGAAGCTGACCC
ACAAGACCCACCAAAGGCTGTGTAAGGCTCCTTATATCAGGACGTGGCATCCTGCCTGTGTGGCCTTCTCTGTGGCATGT
GCTGGGCAGAAAGGCTACCATCACTGCACTGAGAATAACAAGAAGATCTGTAACATTGGCCATGGCTACCTTACGAAGGA
TGAAAAATGGATCAAGAACAATGCCTCCACTGATGGTGACCTGTCCGACAAGAGCATCAACCCTCTGGGTGGCTTTGTCC
ACTATAATGAAATGAACATTGACTTTGTCATGCTGAAAGGCTGTGTGGTGGGAATCAAGAAGTGAGTGCTCACCTCCGCA
AGCCTTTGATGGTGCAGACCAAGCGTCTTGCTCTGGAGAAGACTGACCTTAAGTTCATCAACACTGTTTCCAGGTTTGGC
CGTGGCCACTTCCAGACCATGGAGGAGAAGAAAGCGTTCATGGAACCACTAAAAAGA

Alignment

ORF - retro_ptro_2646 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.86 %
• Parental protein coverage: 96.81 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MSHRKFSAPRHGHLGFLPHKRSHRHRGKVKTWPRDDPSQPVHLTAFLGYKAGMTHTLREVHRPGLKISKR
          .S..KF..P..G.LGFL..KRS.R..GKVK..P.D.PS.P.HLTAFLGYKAGM.....E...PG.K..K.
Retrocopy LSNWKFTVPWLGSLGFLLWKRSSRLHGKVKSFPKDEPSKPFHLTAFLGYKAGMAYIM*EADSPGSKVNKK

Parental  EEVEAVTIVETPPLMVVGVV-GYVATPRGLRSFKTIFAEHLSDECR-RRFYKDWHK-SKKKAFTKACKRW
          E.VEAVT.VET.P..VVG.V.GY.....GL..FKT.FAEH.S.EC..R.F.K..H..S.K.AFTK..K.W
Retrocopy EVVEAVTVVETLPMAVVGIV<GYMEIAQGLQTFKTVFAEHISNECK<RCFHKNRHN<SIKMAFTKYHKKW

Parental  RDTDG-KKQLQKDFAAMKKYCKVIRVIVHTQMKLLPFRQKKAHI-MEIQLNGGTVAEKVAWAQARLEKQV
          ...D...KQL.K.F..MK.YC.VI..I.HT.M.LLP..QKKA...MEIQ.N.GTVAEK..W....LE.QV
Retrocopy QNEDA<NKQLEKEFNSMKMYCQVISIIAHT*MCLLPLCQKKARR<MEIQVN*GTVAEKLDWTWEMLEHQV

Parental  PVHSVFSQSEVIDVIAVTKGRG-VKGVTSRWHTKKLPRKTHKGLRKVACIGAWHPARVGCSIARAGQKGY
          PV..VF....VID.I.VTK..G..KGVTS.WHTKKL..KTH..L.K...I..WHPA.V..S.A.AGQKGY
Retrocopy PVNQVFG*DRVIDAIEVTKCKG>TKGVTSHWHTKKLTHKTHQRLCKAPYIRTWHPACVAFSVACAGQKGY

Parental  HHRTELNKKIFRIGRGPHMEDGKPVKNNASTSYDVTAKSITPLGGFPHYGEVNNDFVMLKGCIAGTKKRV
          HH.TE.NKKI..IG.G....D.K..KNNAST..D...KSI.PLGGF.HY.E.N.DFVMLKGC..G.KK.V
Retrocopy HHCTENNKKICNIGHGYLTKDEKWIKNNASTDGDLSDKSINPLGGFVHYNEMNIDFVMLKGCVVGIKK*V

Parental  IT-LRKSLLVHHSRQAVENIELKFIDTTSKFGHGRFQTAQEKRAFMGPQKK
          .T.LRK.L.V...R.A.E...LKFI.T.S.FG.G.FQT..EK.AFM.P.K.
Retrocopy LT<LRKPLMVQTKRLALEKTDLKFINTVSRFGRGHFQTMEEKKAFMEPLKR

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	0.00 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_2646 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2646 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2646 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3889
Gorilla gorilla	retro_ggor_2616
Pongo abelii	retro_pabe_3170

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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,