RetrogeneDB ID: retro_pabe_205

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:169823510..169825391(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000015166
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TKTL1
• Ensembl ID: ENSPPYG00000020870
• Aliases: None
• Description: transketolase-like 1 [Source:HGNC Symbol;Acc:11835]

Sequence

>retro_pabe_205
ATCATGGCCGACTACGCCAAGCCCGACGTGAGGACGGTGCAGGTGCTGCGGGACACAGCCAACCGCCTGCGGATCCATTC
CATCAGGGTCACGTGTGCCTCTGGTTCTGGCCAGCTCACGTCGTGCTGCAGTGCAGCAGAGGTCGTGTCTGTCCTCTTCT
TCCACACGATGAAGTATAAACAGACAGACCCAGAACACCCGGACAACGACCGGTTCATCCTCTCCAGGGGACATGCTGCT
CCTATCCTCTATGCTGCTTGGGTGGAGGTGGGTGACATCTGTGAATCTGACTTGCTGAACCTGAGGAAACTTCACAGCGA
CTTGGAGAGACACCCTACCCGCCGACTGCCGTTTGTTGACGTGGCAACAGGGTCCCTAGGTCAGGGATTAGGTGCTGCAT
GTGGAATGGCTTATACTGGCAAGTACCTTGACAAGGCCAGCTACCGGGTGTTCTGCCTTATGGGAGATGGCGAATCCTCA
GAAGGCTCTGTGTGGGAGGCTTTTGCTTTTGCCTCCCACTACAACTTGGACAATCTCGTGGCGGTCTTCGACGTGAACCG
CTTGGGACAAAGTGGCCCTGCACCCCTTGAGCATGGCGCAGACATCTACCAGAATTGCTGTGAAGCCTTTGGATGGAATA
CTTACGTAGTGGATGGCCATGATGTGGAGGCCTTGTGCCAAGCATTTTGGCAAGCAAGTCAAGTGAAGAACAAGCCTACT
GCTATAGTTGCCAAGACCTTCAAAGGTCGGGGTATTGCAAATATTGAGGATGCAGAAAATTGGCATGGAAAGCCAGTGCC
AAAAGAAAGAGCAGATGCAATTGTCAAACTAATTGAGAGTCAGATACAGACCAATGAGAATCTCATACCAAAATCGCCTG
TGGAAGACTCACCTCAAATCAGCATCACAGATATAAAAATGACCTCCCCACCTGCTTACAAAGTTGGTGACAAGATAGCT
ACTCAGAAAACATATGGTTTGGCTCTGGCTAAACTGGGCCGTGCAAATGAAAGAGTTATTGTTCTGAGTGGTGACACGAT
GAACTCCACCTTTTCTGAGATATTCAGGAAAGAACACCCTGAGCGTTTCATAGAATGTGTTATTGCTGAACAAAACATGG
TAAGTGTGGCACTAGGCTGTGCTACACGTGGTCGAACCATTGCTTTTGCTAGTGCTTTTGCTGCCTTTTTTACTAGAGCA
TTTGATCAGCTCCGAATGGGAGCCATTTCTCAAGCCAATATCAACCTTATTGGTTCCCACTGTGGGGTATCCACTGGAGA
AGATGGAGTCTCCCAGATGGCCCTGGAGGATCTAGCCATGTTCCGAAGCATTCCGAATTGTACTGTTTTCTATCCAAGTG
ATGCCATCTCGACAGAGCATGCTGTTTATCTAGCCGCCAATACCAAGGGAATGTGCTTCATTCGAACCAGCCAACCAGAA
ACTGCAGTTATTTATACCCCACAAGAAAATTTTGAGATTGGCCAGGCCAAGGTGGTCCGTCACAGTGTCAATGATAAAGT
CACAGTAATTGGAGCTGGAGTTACTCTCCATGAAGCCTTAGCAGCTGCTGACCATCTTTCTCAACAAGGTATTTCTGTCC
GTGTCATCGACCCATTTACCATTAAACCCCTGGATGCTGCCACCATCATCTCCAGTGCAAAAGCCACAGGCGGCCGAGTT
ATCACAGTGGAGGATCACTACAGGGAAGGTGGCATTGGAGAAGCTGTTTGTGCAGCTGTCTCCAGGGAGCCTGATATCCT
TGTTCATCAACTGGCAGTGTCAGGAGTGCCTCAACGTGGGAAAACTAGTGAATTGCTGGATATGTTTGGAATCAGTACCA
GACACATTATAGCAGCCGTAACACTTACTTTAATGAAGTAA

Alignment

ORF - retro_pabe_205 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.76 %
• Parental protein coverage: 85.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KRLSFVDVATGWLGQGLGVACGMAYTGKYFDRASYRVFCLMSDGESSEGSVWEAMAFASYHSLDNLVAIF
          .RL.FVDVATG.LGQGLG.ACGMAYTGKY.D.ASYRVFCLM.DGESSEGSVWEA.AFAS...LDNLVA.F
Retrocopy RRLPFVDVATGSLGQGLGAACGMAYTGKYLDKASYRVFCLMGDGESSEGSVWEAFAFASHYNLDNLVAVF

Parental  DVNRLGHSGALPAEHCIEIYQRRCEAFGWNTYVVDGRDVEALCQVFWQASQVKHKPTAVVAKTFKGRGTP
          DVNRLG.SG..P.EH...IYQ..CEAFGWNTYVVDG.DVEALCQ.FWQASQVK.KPTA.VAKTFKGRG..
Retrocopy DVNRLGQSGPAPLEHGADIYQNCCEAFGWNTYVVDGHDVEALCQAFWQASQVKNKPTAIVAKTFKGRGIA

Parental  SIEDAESWHGKPMPRERADAIIKLIESQIQTSRNLDPQLPIEDSPEVNITDVRMTSPPDYRVGDKIATRK
          .IEDAE.WHGKP.P.ERADAI.KLIESQIQT..NL.P..P.EDSP...ITD..MTSPP.Y.VGDKIAT.K
Retrocopy NIEDAENWHGKPVPKERADAIVKLIESQIQTNENLIPKSPVEDSPQISITDIKMTSPPAYKVGDKIATQK

Parental  ACGLALAKLGYVNNRVVVLDGDTKHSTFSEIFNKEYPERFIECFMAEQNMVSVALGCASRGRTIAFASTF
          ..GLALAKLG..N.RV.VL.GDT..STFSEIF.KE.PERFIEC..AEQNMVSVALGCA.RGRTIAFAS.F
Retrocopy TYGLALAKLGRANERVIVLSGDTMNSTFSEIFRKEHPERFIECVIAEQNMVSVALGCATRGRTIAFASAF

Parental  AAFLTRAFDHIRIGGLSESNINIIGSHCGVSVGEDGASQMALEDIAMFRTIPKCTIFYPTDAVSTENAVA
          AAF.TRAFD..R.G..S..NIN.IGSHCGVS.GEDG.SQMALED.AMFR.IP.CT.FYP.DA.STE.AV.
Retrocopy AAFFTRAFDQLRMGAISQANINLIGSHCGVSTGEDGVSQMALEDLAMFRSIPNCTVFYPSDAISTEHAVY

Parental  LAANAKGMCFIRTTRPETMVIYTPQERFEIGQAKVLRHCVSDKVTVIGAGITVYEALAAADELLKQDIFI
          LAAN.KGMCFIRT..PET.VIYTPQE.FEIGQAKV.RH.V.DKVTVIGAG.T..EALAAAD.L..Q.I..
Retrocopy LAANTKGMCFIRTSQPETAVIYTPQENFEIGQAKVVRHSVNDKVTVIGAGVTLHEALAAADHLSQQGISV

Parental  RVIDLFTIKPLDVATIISSAKATEGRIVT-EDHYPQGGIGEAVCAAVSMDPDIQVHSLAVSGVPQSGKSE
          RVID.FTIKPLD.ATIISSAKAT.GR..T.EDHY..GGIGEAVCAAVS..PDI.VH.LAVSGVPQ.GK..
Retrocopy RVIDPFTIKPLDAATIISSAKATGGRVITVEDHYREGGIGEAVCAAVSREPDILVHQLAVSGVPQRGKTS

Parental  ELLDMYGISARHIIVAVKCMLL
          ELLDM.GIS.RHII.AV...L.
Retrocopy ELLDMFGISTRHIIAAVTLTLM

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	0.06 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.03 RPM	0.12 RPM
SRP007412_kidney	0.00 RPM	0.10 RPM
SRP007412_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_205 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_205 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_205 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018441	1 retrocopy	retro_amel_119,
Equus caballus	ENSECAG00000021992	1 retrocopy	retro_ecab_6,
Felis catus	ENSFCAG00000011392	1 retrocopy	retro_fcat_84,
Loxodonta africana	ENSLAFG00000005145	1 retrocopy	retro_lafr_6,
Pongo abelii	ENSPPYG00000020870	1 retrocopy	retro_pabe_205 ,
Ictidomys tridecemlineatus	ENSSTOG00000005014	1 retrocopy	retro_itri_30,