RetrogeneDB ID: retro_ptro_3108

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:44477558..44478378(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RBM23
• Ensembl ID: ENSPTRG00000006151
• Aliases: None
• Description: RNA binding motif protein 23 [Source:HGNC Symbol;Acc:20155]

Sequence

>retro_ptro_3108
AGCAAAAGTCCACTCAGAAAAGACAAGAGCCCTGTGAGGGAACCTATTGATAATCTAACTCCTGAGGAAAGAGATGCAAG
GATAGTCTTCTGTATGCAGCTGGCGGCAGGAATTCGACCAAAGGATTTGGAAGAGTTTTTCTCTACAGTAGGAAAGGCTC
GAGGCGTGAGGATGATTTCCGATAGAAATTCAAGACGTTCCAAAGGAATTGCTTACGTGGAGTTCGTGGGTGTTAGTTCA
GTGCCTCTAGCAATAGGATTAACTGGCCAACGAGTTTTAGGAGTGCCAATCATAGTACAGGCATCACAGGCAGAAAAAAA
CAGAGCTGCAGCCATGGCAAACAATGTACAAAAGGGAAGTGCTGGACCTAAGAGGCTTTATGTGGACTCATTACACTTTT
AACATAACTGAAGATACGCTTCGTGGGATCTTTGAGCCTTTCGGAAGGATTGAAAGTATCCAGCTGACGATAGACAGTGA
AACTGGTCGATCCAAGGGATATGGATTTATTACATTTTCTGATTCAGAATGTGCCAAAAAGTCTTTGGAACAATTTAATG
GATTTGAACTAGCAGGGAGGCCAATGAAAGTTGGTCATGTTATTGAACGTGCTGATGCTTCGAGTACTAGTTCATTTTTG
GACAGTGATGAACTGGAAAGGACTAGAATTGATTTGGGAACAAGTGGTCGTCTTCAGTTAGTGGCAAGACTTGCAGAGGA
TACAGGTTTGCAGATTCCACCAGCAGCACAGCAAGCTCTACAAATGAGTGGCTCTTTGGCATTTGGTGCTGTGGCAGAAT
TTTCTTTTGTTATGGATTTG

Alignment

ORF - retro_ptro_3108 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68. %
• Parental protein coverage: 61.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SKSPHFREKSPVREPIDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGI
          SKSP....KSPVREPIDNL.PEERDAR.VFCMQLAA.IRP.DLE.FFS.VGK.R.VR.ISDRNSRRSKGI
Retrocopy SKSPLRKDKSPVREPIDNLTPEERDARIVFCMQLAAGIRPKDLEEFFSTVGKARGVRMISDRNSRRSKGI

Parental  AYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRLAAMANNLQKGNGGPMRLYVGSLH-FNITEDM
          AYVEF....SVPLAIGLTGQR.LGVPIIVQASQAEKNR.AAMANN.QKG..GP.RLYV.SLH.FNITED.
Retrocopy AYVEFVGVSSVPLAIGLTGQRVLGVPIIVQASQAEKNRAAAMANNVQKGSAGPKRLYVDSLH>FNITEDT

Parental  LRGIFEPFGKIDNIVLMKDSDTGHSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLDGGTD
          LRGIFEPFG.I..I.L..DS.TG.SKGYGFITFSDSECA...LEQ.NGFELAGRPM.VGHV.ER.D....
Retrocopy LRGIFEPFGRIESIQLTIDSETGRSKGYGFITFSDSECAKKSLEQFNGFELAGRPMKVGHVIERADASST

Parental  ITFPDGDQ----ELDLGSAGGRFQLIAKLAEGAGIQLPSTATAAAAAAAAAAQAAALQLNGAVPL
          ..F.D.D.......DLG...GR.QL.A.LAE..G.Q.P..A..A.......A..A.........L
Retrocopy SSFLDSDELERTRIDLGTS-GRLQLVARLAEDTGLQIPPAAQQALQMSGSLAFGAVAEFSFVMDL

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	0.39 RPM	45.38 RPM
SRP007412_cerebellum	2.08 RPM	60.80 RPM
SRP007412_heart	2.01 RPM	16.03 RPM
SRP007412_kidney	2.30 RPM	68.81 RPM
SRP007412_liver	2.03 RPM	30.15 RPM
SRP007412_testis	2.85 RPM	39.73 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3108 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3108 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3108 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4679
Gorilla gorilla	retro_ggor_2902
Pongo abelii	retro_pabe_3634

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008482	1 retrocopy	retro_cjac_1069,
Myotis lucifugus	ENSMLUG00000012923	1 retrocopy	retro_mluc_2430,
Ochotona princeps	ENSOPRG00000001092	2 retrocopies	retro_opri_126, retro_opri_412,
Pan troglodytes	ENSPTRG00000006151	1 retrocopy	retro_ptro_3108 ,
Ictidomys tridecemlineatus	ENSSTOG00000010354	1 retrocopy	retro_itri_1902,