RetrogeneDB ID: retro_pabe_2336

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:115529392..115530273(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THRAP3
• Ensembl ID: ENSPPYG00000001544
• Aliases: None
• Description: thyroid hormone receptor associated protein 3 [Source:HGNC Symbol;Acc:22964]

Sequence

>retro_pabe_2336
TCTTTTGCTCCTGAAACTGATTCTGAGAAGCCTTTTCTGGGCAGTCAGTCTCCCAAAAGGTATAAGCTCCAAAATGACTT
TGAGAAGAAGATGGCTGACTTCCACAAGGAAGAGATGGATGATCAAGATAAGGACAAAGCTAAGGGAAGGAAGGAATCTG
AGTTTGGTGATGAACCCAAAATATGTCTAAAGTCATAGATGCAAACGAAAACCAGGAGGAGAAGTCAGGCAAATGGGAGG
GCCTGGTATATGCACCTCCAGGGAAGGAAAAGCAGAGGAAAACAGAGGAGCTGGAGGGGGAGTCTTTCCCAGAGAGATCC
AAAAAGGAGGATCGGGGCAAGAGAACCAAAGGTGGGCACAGAGGCTTTGTGCCTGAGAAGAATTTCTGAGTGACTGCTTA
CAAAGCAGTCCAGGAGGAAAGCTCATCGCCTCCCCCAAGAAAGACTTCTGAGAGCCGAGACAAGCTGGAAGCAAAAGGAG
ACTTTTCCACAGGGAAGTCTTCCTTTTCCATTACTCGAGAGACACAGGGCAATGTCCGGATGGACTCTTTTGATGAGGAC
TTTGCACGACCCAGTGGCTTATAGGCTCAGGAACGCAAGCTTTGCCGCGATCTAGTACATAGCAACAAAAAGGAACAGGA
GTTTTGTTCCAATTTCCAGCCTATACAGTCAGCTCAGTCTCAGCGTAGCCCCTCAGAACTGTTTGCCCAACATATAGTGA
CCATTATTCACCATGTTAAAGAGCATCACTTTGGGTCCTCAGGAATGACATTACATGAACACTTTACTAAATGCCTAAAG
AGACGAACTGAGCAGGAGGCAGCCAAAAACAAGAAAATCCCAGAGATACAGAGAAGAATAGACGTTTCCCCCAGTACCTG
G

Alignment

ORF - retro_pabe_2336 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.33 %
• Parental protein coverage: 51.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SFAPKTDSEKPFGQAGQSPKRYKLPRMTFEKMTDFHKEEMDDQDKDKAKGRKESEFDDE-PK-MSKVIGA
          SFAP.TDSEKPF....QSPKRYKL......KM.DFHKEEMDDQDKDKAKGRKESEF.DE.PK.MSKVI.A
Retrocopy SFAPETDSEKPF-LGSQSPKRYKLQNDFEKKMADFHKEEMDDQDKDKAKGRKESEFGDE>PK>MSKVIDA

Parental  NKNQEEEKSGKWEGNLVYAPPGKEKQRKTER-EEESFPERSK-EDRGKRSEG-HRGF-PEKNF-RSPYKA
          N.NQEE.KSGKWEG.LVYAPPGKEKQRKTE..E.ESFPERSK.EDRGKR..G.HRGF.PEKNF....YKA
Retrocopy NENQEE-KSGKWEG-LVYAPPGKEKQRKTEELEGESFPERSKKEDRGKRTKGGHRGFVPEKNF*VTAYKA

Parental  VQEKSSSPPPRKTSESRDKLGAKGDFP-GKSSFSITREAQVNVRMDSFDEDLARPSGLLAQERK-CRDLV
          VQE.SSSPPPRKTSESRDKL.AKGDF..GKSSFSITRE.Q.NVRMDSFDED.ARPSGL.AQERK.CRDLV
Retrocopy VQEESSSPPPRKTSESRDKLEAKGDFSTGKSSFSITRETQGNVRMDSFDEDFARPSGL*AQERKLCRDLV

Parental  HSNKKEQEFRSIFQHIQSAQ-QRSPSELFAQHIVTIVHHVKAITLGSSGMTLHERFTKYLKRGTEQEAAK
          HSNKKEQEF.S.FQ.IQSAQ.QRSPSELFAQHIVTI.HHVK....GSSGMTLHE.FTK.LKR.TEQEAAK
Retrocopy HSNKKEQEFCSNFQPIQSAQSQRSPSELFAQHIVTIIHHVKEHHFGSSGMTLHEHFTKCLKRRTEQEAAK

Parental  KPRKAQEIHQTGIDISPSTF
          ...K..EI.Q..ID.SPST.
Retrocopy N-KKIPEI-QRRIDVSPSTW

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	4.87 RPM	81.11 RPM
SRP007412_cerebellum	6.57 RPM	86.94 RPM
SRP007412_heart	3.88 RPM	42.11 RPM
SRP007412_kidney	5.80 RPM	101.96 RPM
SRP007412_liver	4.13 RPM	66.10 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2336 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2336 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2336 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003389	1 retrocopy	retro_cfam_549,
Pongo abelii	ENSPPYG00000001544	1 retrocopy	retro_pabe_2336 ,
Pongo abelii	ENSPPYG00000017032	1 retrocopy	retro_pabe_2767,
Rattus norvegicus	ENSRNOG00000009977	1 retrocopy	retro_rnor_674,