RetrogeneDB ID: retro_ptro_1771

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:31967881..31969916(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THRAP3
• Ensembl ID: ENSPTRG00000000535
• Aliases: None
• Description: None

Sequence

>retro_ptro_1771
AACAAATCCAAGTCTGGATCTCGCTCTCCTCGCTCAGGATCTGCATCAAGATCTCGTTCTCGTTCACGTTGGAAGTCTCG
GTCCCTAAGGCCATCTGTCTCTGGTTCAAGGAAGTGCAGGCTGAGTTCTAGGTCTCGTTCCAGATTATATTCTCCAGCTC
ATAACAGAGAAAGAAACCACCCAAGAGTATAACAGAATCGGGATTTCCGAGGTCACAACAAAGGCTATATAGAAGGCCCT
ATTATTTCCGTGGGCGCAACAGAGGCTTTTATCCATGGGGCCAGTATAACCGAGGAGGCTATGGAAACTACCGCTCAAAT
TGGCAGAATTGCCGGCAAGCATACGGGCCGTTCAAGATCCCGGTCCCCAGCGAGAAGGTCCCCTTCACCAAGGTCCAGGA
GCCATTCTAGAAACTCTGATAAGTCGTCTTCTGACCAGTCAAGGCGCTCCTCATCCTCTCGTTCTTCCTCCAACCATAGC
CGAGTTGAATCTTCTAAGCGCAAGTCTGCAAAGGAGAAAAGTCCTCTTCCAAGGATAGCCGGCCATCTCAGGCTACCGGG
GATAACCAGGGAGATGAGGCCAGGGAGCAGACATTCTCTGGAGGCACCTCTCAAGATACAAAAGAATCTGAGAGCTCGAA
GCCATGGCCAGATGCCACCTACGGCACTGGTTCTGCATCAGGGGCCTCAGCAGTTTCTGAGCTGAGTCCTCGGGAGCAAA
TTGCAGCTCTCAAAAGCCCCCTCCAGTCTGTGGTGGTGAGGCAGCGGTCACTCCTTCCTAGCCCCGTGCCAAAACCTAGT
CCTCCACTTTCCAGCACATCCCAGATGAGCTCAACTCTGCCAAGCGGTGCTGAGTATCAGCCTGGGACACACCAAGTTCA
GTTCGACCATGGTTCTTGGGTCCCTGAGTCCATCCAAAAACAGCCCTGTGGGTAAGAATTTACCATCCATTGGCTCCACG
TATGTCTCATCTCAGAAGGAGGAGAGTGCTGCTCCAGGAGGACCAGCCTGTACAAAGAGGTACCTAGAAGAGCAGAAGAC
AGAGAATAGAAAAAATAAGGAACGGAAACAAACAAATACAGATAAAGAAAAAATAAAAGAGAAAGGGAGCTTCTCTGACA
CAGACTTGGGTGATGGAAAAATGAAATCTGATTCTTTTGCTCCCAAAACTGATTCTGAGAAGCCTTTTCGGGGCAGTCAG
TCTCCCAAAAGGTATAAGCTCCGAAATGACTTTGAGAAGAAGATGGCTGACTTCCACAAGGAAGAGATGGATGATCAAGA
TAAGGACAAAGCTAAGGGAAGGAAGGAATCTGAGTTTGATGATGAACCCAAAATATGTCTAAAGTCATAGATGCAAACGA
AAACCAGGAGGAGGAGAAGTCAGGCAAATGGGAGGGCCTGGTATATGCACCTCCAGAGAAGGAAAAGCAGAGGAAAACAG
AGGAGCTGGAGGAGGAGTCTTTCCCAGAGAGATCCAAAAAGGAGGATCGGGGCAAGAGAACCAAAGGTGGGCACAAGGGC
TTTGTGCCTGAGAAGAATTTCTGAGTGACTGCTTACAAAGCAGTCCAGGAGAAAAGCTCATCGCCTCCCCCAAGAAAGAC
TTCTGAGAGCCGAGACAAGCTGGAAGTGAAAGGAGACTTTTCCACAGGGAAGTCTTCCTTTTCCATTACTCGAGAGACAC
AGGGCAATGTCCGGATGGACTCTTTTGATGAGGACTTTGCACGACCCAATGGCTTATTGGCTCAGGAACGCAAGCTTTGC
CGAGATCTAGTCCATAGCAACAAAAAGGAACAGGAGTTTTGTTCCATTTTCCAGCACATACAGTCAGCTCAGTCTCAGCG
TAGCCCCTCAGAACTGTTTGCCCAACATATAGTGACCATTATTCACCATGTTAAAGAGCATCACTTTCGGTCCTCAGGAA
TGACATTACATGAACGCTTTACTAAATACTAAAGAGACGAACTGAGCAGGAGGCAGCCAAAAACAAGAAAAGCCCAGAGA
TACACAGAAGAATAGACGTTTCCCCCAGTACCTGG

Alignment

ORF - retro_ptro_1771 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.95 %
• Parental protein coverage: 71.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  NKSKSGSRSSRSRSASRSRSRSFSKSRSRSRSLSRSRKRRLSSRSRSRSYSPAHNRERNHPRVYQNRDFR
          NKSKSGSRS.RS.SASRSRSRS..KSRS...S.S.SRK.RLSSRSRSR.YSPAHNRERNHPRV.QNRDFR
Retrocopy NKSKSGSRSPRSGSASRSRSRSRWKSRSLRPSVSGSRKCRLSSRSRSRLYSPAHNRERNHPRV*QNRDFR

Parental  GHNRGY-RRPYYF-RGRNRGFYPWGQYNRGGYGNYRSNWQNYRQAYSP-RRGRSRSRSPKRRSPSPRSRS
          GHN.GY..R..Y..RGRNRGFYPWGQYNRGGYGNYRSNWQN.RQAY.P..R.RS..R....RSPSPRSRS
Retrocopy GHNKGY<YRRPYYFRGRNRGFYPWGQYNRGGYGNYRSNWQNCRQAYGP>SRSRSPAR----RSPSPRSRS

Parental  HSRNSDKSSSDRSRRSSSSRSSSNHSRVESSKRKSAKEK-KSSSKDSRPSQAAGDNQGDEAKEQTFSGGT
          HSRNSDKSSSD.SRRSSSSRSSSNHSRVESSKRKSAKEK.KSSSKDSRPSQA.GDNQGDEA.EQTFSGGT
Retrocopy HSRNSDKSSSDQSRRSSSSRSSSNHSRVESSKRKSAKEK<KSSSKDSRPSQATGDNQGDEAREQTFSGGT

Parental  SQDTKASESSKPWPDATYGTGSASRASAVSELSPRERSPALKSPLQSVVVRRRSPRPSPVPKPSPPLSST
          SQDTK.SESSKPWPDATYGTGSAS.ASAVSELSPRE...ALKSPLQSVVVR.RS..PSPVPKPSPPLSST
Retrocopy SQDTKESESSKPWPDATYGTGSASGASAVSELSPREQIAALKSPLQSVVVRQRSLLPSPVPKPSPPLSST

Parental  SQMGSTLPSGAGYQSGTHQGQFDHGS-GSLSPSKKSPVGKSPPSTGSTYGSSQKEESAASGGAAYTKRYL
          SQM.STLPSGA.YQ.GTHQ.QFDHGS.GSLSPSK.SPVGK..PS.GSTY.SSQKEESAA.GG.A.TKRYL
Retrocopy SQMSSTLPSGAEYQPGTHQVQFDHGS>GSLSPSKNSPVGKNLPSIGSTYVSSQKEESAAPGGPACTKRYL

Parental  EEQKTENGKDKEQKQTNTDKEKIKEKGSFSDTGLGDGKMKSDSFAPKTDSEKPFRGSQSPKRYKLRDDFE
          EEQKTEN.K.KE.KQTNTDKEKIKEKGSFSDT.LGDGKMKSDSFAPKTDSEKPFRGSQSPKRYKLR.DFE
Retrocopy EEQKTENRKNKERKQTNTDKEKIKEKGSFSDTDLGDGKMKSDSFAPKTDSEKPFRGSQSPKRYKLRNDFE

Parental  KKMADFHKEEMDDQDKDKAKGRKESEFDDEPKF-MSKVIGANKNQEEEKSGKWEGLVYAPPGKEKQRKTE
          KKMADFHKEEMDDQDKDKAKGRKESEFDDEPK..MSKVI.AN.NQEEEKSGKWEGLVYAPP.KEKQRKTE
Retrocopy KKMADFHKEEMDDQDKDKAKGRKESEFDDEPKI<MSKVIDANENQEEEKSGKWEGLVYAPPEKEKQRKTE

Parental  ELEEESFPERSKKEDRGKRSEGGHRGFVPEKNFRVTAYKAVQEKSSSPPPRKTSESRDKLGAKGDFPTGK
          ELEEESFPERSKKEDRGKR..GGH.GFVPEKNF.VTAYKAVQEKSSSPPPRKTSESRDKL..KGDF.TGK
Retrocopy ELEEESFPERSKKEDRGKRTKGGHKGFVPEKNF*VTAYKAVQEKSSSPPPRKTSESRDKLEVKGDFSTGK

Parental  SSFSITREAQVNVRMDSFDEDLARPSGLLAQERKLCRDLVHSNKKEQEFRSIFQHIQSAQSQRSPSELFA
          SSFSITRE.Q.NVRMDSFDED.ARP.GLLAQERKLCRDLVHSNKKEQEF.SIFQHIQSAQSQRSPSELFA
Retrocopy SSFSITRETQGNVRMDSFDEDFARPNGLLAQERKLCRDLVHSNKKEQEFCSIFQHIQSAQSQRSPSELFA

Parental  QHIVTIVHHVKEHHFGSSGMTLHERFTKY-LKRGTEQEAAKNKKSPEIHRRIDISPSTF
          QHIVTI.HHVKEHHF.SSGMTLHERFTKY.LKR.TEQEAAKNKKSPEIHRRID.SPST.
Retrocopy QHIVTIIHHVKEHHFRSSGMTLHERFTKY<LKRRTEQEAAKNKKSPEIHRRIDVSPSTW

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	75.70 RPM
SRP007412_cerebellum	0.00 RPM	140.02 RPM
SRP007412_heart	0.00 RPM	107.20 RPM
SRP007412_kidney	0.03 RPM	120.12 RPM
SRP007412_liver	0.00 RPM	114.90 RPM
SRP007412_testis	0.42 RPM	124.25 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1771 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1771 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1771 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003389	1 retrocopy	retro_cfam_549,
Microcebus murinus	ENSMICG00000007920	1 retrocopy	retro_mmur_671,
Mus musculus	ENSMUSG00000043962	1 retrocopy	retro_mmus_2939,
Pan troglodytes	ENSPTRG00000000535	1 retrocopy	retro_ptro_1771 ,
Pan troglodytes	ENSPTRG00000018635	1 retrocopy	retro_ptro_2287,
Rattus norvegicus	ENSRNOG00000009977	1 retrocopy	retro_rnor_674,