RetrogeneDB ID: retro_ptro_2462

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:109056444..109057626(-)
• 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_2462
ATGTCTCACAGAAAGTTTTCTGCTCCCAGACATGGGTCCCTCGGCTTCCTGCCTCAGAAGCGCAGCAGCAGGCATCGTGG
GAAGGTGAAGAGCTTCCCTAAGGATGATCCGTCCAAGCCGGTCCACCTCACAGCCTTCCTGGGATACAAAGCTGGCATGA
CCCACATCATGAGGGAAGTCGACAGCCCAGCATCCAAGGTGAACAAGAAGGAGGTGGTGGAGGCTGTGACCATTGTGGAG
ACGCCACCCATGGTGGTTGTGGGCATTGTGGGCTATGTGGAAACCCCTCGAGGCCTCCGGACCTTCAAGACTGTCTTTGC
TGAGCACATCAGTAATGAATGCAAGAGGCGTTTCTATAAGAACTGGCATACATCTAAAAAGAAGGCCTTTACGAAGTACC
GCAAGAAATGGCAGGATGAGGATGTCAAGAAGCAGCTGGAGAAGGACTTCAGCAGCATGAAGAAATACTGCCACGTCATC
CGCATCATTGCCCACACCCAGATGCGCCTGCTTCTTCTGCGCCAGAAGAAGGCCCACCTGATGGAGATCCAGGTGAACGG
AGGCACCGTGGCTGAGAAGCTGGACTGGGTCTGCGAGAGGCTCGAGCAGCAGGTAAATGTGAACCAAGTGTTTGGGAAGG
ATGAGATGATCGACGTCATTGGGGTGACCAAGGGCAAAGGCTACAAAGGGGTCACCAGTCGTTGGCACACCAAGAAGCTG
CCCCGCGAGACCCACCGAGGCCTGCGCAAGGTGGCCTGTATTGGGGCATGGCATCCTGCTCGTGTGGCCTTCTCTGTGGC
ACGTGCTGGGCAGAAAGGCTACCGTCACCGCACTGAGATCAACAAGAAGATCTATAAGATTGGCCAGGGCTACCTTATCA
AGGATGGCAAGCTGATCAAGAACAATGCCTCCACTGACTCTGACCTGTCTGACAAGAGCACCAATCCTCTGGGTGGCTTT
GTCCACTATGGTGAAGTGACCAATGACCTTGTCATGCTGAAAGGCTGTGTGGTGGGAACCAAGAAGCGGGTGCTCACCCT
CCACGAGTCCTTGCTGGTGCAGATGAAGCGGCAGGCTCTGGAGAAGATTGACCTTAAGTTCATTGACACCACCTCCAAGT
TTGGCCATGGCTGCTTCCAGACCATGGAGTAGAAGAAAGCATTCATGGGACCACTCAAGAAA

Alignment

ORF - retro_ptro_2462 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.6 %
• Parental protein coverage: 96.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSHRKFSAPRHGHLGFLPHKRSHRHRGKVKTWPRDDPSQPVHLTAFLGYKAGMTHTLREVHRPGLKISKR
          MSHRKFSAPRHG.LGFLP.KRS.RHRGKVK..P.DDPS.PVHLTAFLGYKAGMTH..REV..P..K..K.
Retrocopy MSHRKFSAPRHGSLGFLPQKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIMREVDSPASKVNKK

Parental  EEVEAVTIVETPPLMVVGVVGYVATPRGLRSFKTIFAEHLSDECRRRFYKDWHKSKKKAFTKACKRWRDT
          E.VEAVTIVETPP..VVG.VGYV.TPRGLR.FKT.FAEH.S.EC.RRFYK.WH.SKKKAFTK..K.W.D.
Retrocopy EVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISNECKRRFYKNWHTSKKKAFTKYRKKWQDE

Parental  DGKKQLQKDFAAMKKYCKVIRVIVHTQMKLLPFRQKKAHIMEIQLNGGTVAEKVAWAQARLEKQVPVHSV
          D.KKQL.KDF..MKKYC.VIR.I.HTQM.LL..RQKKAH.MEIQ.NGGTVAEK..W...RLE.QV.V..V
Retrocopy DVKKQLEKDFSSMKKYCHVIRIIAHTQMRLLLLRQKKAHLMEIQVNGGTVAEKLDWVCERLEQQVNVNQV

Parental  FSQSEVIDVIAVTKGRGVKGVTSRWHTKKLPRKTHKGLRKVACIGAWHPARVGCSIARAGQKGYHHRTEL
          F...E.IDVI.VTKG.G.KGVTSRWHTKKLPR.TH.GLRKVACIGAWHPARV..S.ARAGQKGY.HRTE.
Retrocopy FGKDEMIDVIGVTKGKGYKGVTSRWHTKKLPRETHRGLRKVACIGAWHPARVAFSVARAGQKGYRHRTEI

Parental  NKKIFRIGRGPHMEDGKPVKNNASTSYDVTAKSITPLGGFPHYGEVNNDFVMLKGCIAGTKKRVITLRKS
          NKKI..IG.G....DGK..KNNAST..D...KS..PLGGF.HYGEV.ND.VMLKGC..GTKKRV.TL..S
Retrocopy NKKIYKIGQGYLIKDGKLIKNNASTDSDLSDKSTNPLGGFVHYGEVTNDLVMLKGCVVGTKKRVLTLHES

Parental  LLVHHSRQAVENIELKFIDTTSKFGHGRFQTAQEKRAFMGPQKK
          LLV...RQA.E.I.LKFIDTTSKFGHG.FQT...K.AFMGP.KK
Retrocopy LLVQMKRQALEKIDLKFIDTTSKFGHGCFQTME*KKAFMGPLKK

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	0.20 RPM	0.02 RPM
SRP007412_cerebellum	0.36 RPM	0.00 RPM
SRP007412_heart	0.09 RPM	38.27 RPM
SRP007412_kidney	0.63 RPM	0.00 RPM
SRP007412_liver	0.59 RPM	0.03 RPM
SRP007412_testis	0.42 RPM	0.84 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2462 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2462 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2462 has 0 orthologous retrocopies within eutheria group .

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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,