RetrogeneDB ID: retro_ptro_2741

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:35713672..35714338(-)
• Located in intron of: ENSPTRG00000031006

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_2741
CACATCGTGTGGGAAGCTGGCCGGCTAGGACCCAAGGTGAACAAGAAGGAAGGGGTAGAGGCTATGACCATTGTGGAGAC
ACTGCCCATGGTGGTTGTAGGCATCCTGGGCTACATGGAAACCCCTCAAGGCCTCTGAATTTCCAAGACCATCTTTGTTG
AGCACATTAGCAATGAGTGCAAAAGGCACTTCTATAGGAACTGGCATAAAGCTAAGTAGAAGGCTTTTACCAAGTACTGC
AAGAAACTGCAGGGTGAGGATGACAAGAAGCAGCTGAAGAAGGACTTCAACAGCATGAAAAAGTACTGCCAAGTCATCCA
CATCAATATCTACACCCAGATGCACCTGCTTCCTCTATGTATGAAGAAGACCCACCTGATGGAGATCCAGGTGAACAGAG
GCACTGTGACTGAGAAACTGGACTGGTCTCTGGAGAGGCTAGAGGACCAGGTACCTGTGAAACAAGTGTTTGGGCAGGAC
AAGATGATTGACATCAAACGGGTGACCAAGGGCAAAGGCTACAAAGAGGTCACCAGTCATTGGCATACCAAGAAGCTGCC
CTACAAGACCCACTGAGGGCTGTGCAAGGTTGCCTATATTGGGGCATGGCATCCTGCCCATATGACCTTCTCTGTGGCAC
GTACTAGACACAAACCATCACTGCAC

Alignment

ORF - retro_ptro_2741 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.01 %
• Parental protein coverage: 54.55 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HTLREVHRPGLKISKREEVEAVTIVETPPLMVVGVVGYVATPRGLRSFKTIFAEHLSDECRRRFYKDWHK
          H...E..R.G.K..K.E.VEA.TIVET.P..VVG..GY..TP.GL...KTIF.EH.S.EC.R.FY..WHK
Retrocopy HIVWEAGRLGPKVNKKEGVEAMTIVETLPMVVVGILGYMETPQGL*ISKTIFVEHISNECKRHFYRNWHK

Parental  SKKKAFTKACKRWRDTDGKKQLQKDFAAMKKYCKVIRVIVHTQMKLLPFRQKKAHIMEIQLNGGTVAEKV
          .K.KAFTK.CK.....D.KKQL.KDF..MKKYC.VI.....TQM.LLP...KK.H.MEIQ.N.GTV.EK.
Retrocopy AK*KAFTKYCKKLQGEDDKKQLKKDFNSMKKYCQVIHINIYTQMHLLPLCMKKTHLMEIQVNRGTVTEKL

Parental  AWAQARLEKQVPVHSVFSQSEVIDVIAVTKGRGVKGVTSRWHTKKLPRKTHKGLRKVACIGAWHPARVGC
          .W...RLE.QVPV..VF.Q...ID...VTKG.G.K.VTS.WHTKKLP.KTH.GL.KVA.IGAWHPA....
Retrocopy DWSLERLEDQVPVKQVFGQDKMIDIKRVTKGKGYKEVTSHWHTKKLPYKTH*GLCKVAYIGAWHPAHMTF

Parental  SIARAGQKGYHH
          S.AR...K...H
Retrocopy SVARTRHKPSLH

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	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	38.27 RPM
SRP007412_kidney	0.00 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_2741 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2741 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2741 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3318
Macaca mulatta	retro_mmul_2334

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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,