RetrogeneDB ID: retro_ptro_1473

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 21:22272669..22273850(-)
• Located in intron of: ENSPTRG00000013889

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_1473
ATGTCTCACAGAAAGTTCTCCACTCCCAGACATGGGTCCCTCTGCTTCCTGCCATAGGAGCGAAGAAATAGGCAACGTGG
GAAGGTGAAGAGCTTCCCTAAGGATGACCCTTCCAAGCTGGTCAACGTCACAGCCTTCCTGGGATACAAGGCTGGCATGA
CCCACATCACACGGGAAGTCGACAGGCCAAGATCCAAGGTGAAAGCGAAGGAGGTGGTAGAGGCCGTGACTACTGTGGAG
ACACCACCTACGGTGGTTGTGGGCATTGCGGGCTACGTGGAAACCCCTTGAGGCCTCCGGACCTTCAAGGCCATCTTTGC
TGAGCACATCAACGATGAGTGCAAAAGGTGTTTCTCTAACAACCGGCATAAATCTAGGAAGAAGGCCTTTACCAAGTACT
GCAAGAAATGGCAGGATGAGGATGGCAAGAAGCAGCTGGAGAAGACTTCAGCAGCATGAGGAAGCACTGCCAAGTCACCC
GCCTCGCTGCCCACACCCAGACGCGCCTACTTCCTCTGCGCCAGAAGAAGGCCCAGCTGATGGAGATCCAAGTGAACGGA
GGCACCATGGCTGAGAAGCTGGACTGGGCCCAGGAGGGGCTACAGTAGCAGGTACCTGTGAACCAAGCGTTTGGGCTGGA
CGAGATGATCGACATCATCGGGGTGACCAAGGGCAAAGGCTACAAAGGGGTCGCCAGTTGTTGGCACACCAAGAAGCTGC
CCCACAAGACCCACCGAGGCCTGTGCAAGGTGGCCTGGATTGGGGCATGGCATCCTGACCATGTGGCCTTCTCCATGGCA
TGTGCTGGGCAGAAAGGCGACCATCACCATACTGAGATCAACAAGAAGATCTGTAAGATTGACCAGGGCTACCTTACTGA
GGACAGCAAACCGATCAAGAACAATGCCTCCACGGACTATGACCTGTCTGACAAGAGCATCAACCTTCTGGGTGGCTTTG
TCCACTATGGTGAAGTGACCAATGACTCTGTCATGCTGAAAGGCTGTGTGGTGGGAACCAAGAAGCGAGTGCTCACTCTC
TGCACATCTTTGCTGGTGCAGACCAGACGGTGGGCTCTGGAGAAGACTGACCTTAAGTTCACTGACACCACCTCCAAGTT
TGGCTATGGCCGCTTCCAGACCATGGAGGAGAAGAAAGCATTCATGGGACCACTCGAGAAA

Alignment

ORF - retro_ptro_1473 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.82 %
• Parental protein coverage: 96.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSHRKFSAPRHGHLGFLPHKRSHRHRGKVKTWPRDDPSQPVHLTAFLGYKAGMTHTLREVHRPGLKISKR
          MSHRKFS.PRHG.L.FLP..R..R.RGKVK..P.DDPS..V..TAFLGYKAGMTH..REV.RP..K....
Retrocopy MSHRKFSTPRHGSLCFLP*ERRNRQRGKVKSFPKDDPSKLVNVTAFLGYKAGMTHITREVDRPRSKVKAK

Parental  EEVEAVTIVETPPLMVVGVVGYVATPRGLRSFKTIFAEHLSDECRRRFYKDWHKSKKKAFTKACKRWRDT
          E.VEAVT.VETPP..VVG..GYV.TP.GLR.FK.IFAEH..DEC.R.F....HKS.KKAFTK.CK.W.D.
Retrocopy EVVEAVTTVETPPTVVVGIAGYVETP*GLRTFKAIFAEHINDECKRCFSNNRHKSRKKAFTKYCKKWQDE

Parental  DGKKQLQK-DFAAMKKYCKVIRVIVHTQMKLLPFRQKKAHIMEIQLNGGTVAEKVAWAQARLEKQVPVHS
          DGKKQL.K.DF..M.K.C.V.R...HTQ..LLP.RQKKA..MEIQ.NGGT.AEK..WAQ..L..QVPV..
Retrocopy DGKKQLEK<DFSSMRKHCQVTRLAAHTQTRLLPLRQKKAQLMEIQVNGGTMAEKLDWAQEGLQ*QVPVNQ

Parental  VFSQSEVIDVIAVTKGRGVKGVTSRWHTKKLPRKTHKGLRKVACIGAWHPARVGCSIARAGQKGYHHRTE
          .F...E.ID.I.VTKG.G.KGV.S.WHTKKLP.KTH.GL.KVA.IGAWHP..V..S.A.AGQKG.HH.TE
Retrocopy AFGLDEMIDIIGVTKGKGYKGVASCWHTKKLPHKTHRGLCKVAWIGAWHPDHVAFSMACAGQKGDHHHTE

Parental  LNKKIFRIGRGPHMEDGKPVKNNASTSYDVTAKSITPLGGFPHYGEVNNDFVMLKGCIAGTKKRVITLRK
          .NKKI..I..G...ED.KP.KNNAST.YD...KSI..LGGF.HYGEV.ND.VMLKGC..GTKKRV.TL..
Retrocopy INKKICKIDQGYLTEDSKPIKNNASTDYDLSDKSINLLGGFVHYGEVTNDSVMLKGCVVGTKKRVLTLCT

Parental  SLLVHHSRQAVENIELKFIDTTSKFGHGRFQTAQEKRAFMGPQKK
          SLLV...R.A.E...LKF.DTTSKFG.GRFQT..EK.AFMGP..K
Retrocopy SLLVQTRRWALEKTDLKFTDTTSKFGYGRFQTMEEKKAFMGPLEK

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	0.05 RPM	0.02 RPM
SRP007412_cerebellum	0.29 RPM	0.00 RPM
SRP007412_heart	0.06 RPM	38.27 RPM
SRP007412_kidney	0.10 RPM	0.00 RPM
SRP007412_liver	0.10 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_1473 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1473 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1473 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2529
Gorilla gorilla	retro_ggor_1582
Pongo abelii	retro_pabe_1861

---

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,