RetrogeneDB ID: retro_pabe_3447

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:119538610..119539616(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TLK1
• Ensembl ID: ENSPPYG00000012926
• Aliases: None
• Description: tousled-like kinase 1 [Source:HGNC Symbol;Acc:11841]

Sequence

>retro_pabe_3447
AGAGAGAAGAGTATGCAAGATTGATTGTGTCTCAGGCACTTTACAACAGTTAGACATGGCACTTCATTTACTGAATAACG
GATAGATGGTTTTGCATTTCAGAATCTTGTGAAGCAACAAGAATGGGTGAATCAGCAAAGGGAAGATATTGAAAGGCAAA
GGAAAATTCTAGCCAAATGCAAACCTCCCACAGCTAATAATTCTCAGGCACCCTCTACCAATTCTGAACCAAAACAAAGG
AAAAACAAAGCAGTCAATGGAGCAGAAAATGATCCCTTTGTTAGACCAAATTTACCACAACTGTTGACTTTGGCAGAATA
TTATGAACAGGAAGAAATTTTCAAACTTAGACTAGGACATCTCAGAAAAGAAGAGGCAGAAATCCAAGCAGAACTTGAAC
GTTTGGAAAGAGTCAGAAATCTTCACATACATGAGCTGAGAAGAATAAACAATGAAGATAATTCACAATTCAAAGATCAC
CCAACGTTAAATGAAAGATATTTATTACTTCATCTGCTTGGTAGAGGTGGCTTTAGTGAAGTGTATAAGGCTTTTGACCT
TTATGAACAAAGCTACGCTTCTGTGAAGCTACATCAGCTTAATAAAAGCTGGAGAGATAAGAAAAAAGAAAACTACTACA
AACATGCCTGCAGTATAGAATACACAAAGAACTGGATCACCCCCAAATAGTTAAACTCTATGATTATTTCTCCTTGGATA
CAGATACATTTTGTACAGTGTTAGAATACTGTGAAGGCAATGACTTGGATTTCTATCTGAAGCAACACAAGCTAGTGTCA
GAGAAAGAAGCTGAGTCTATTGTAATGCAGATTGTAAATGCACTAAGATATACCAATGAGATCAACCCCCCATTATACAT
TATGATCTTAAGCCAGGAAACATCCTTTTGGTAGATAGAATAGCATGTGGTGAAATCAAAATCACTGATTTTGGTCTGTC
CAAGATTATGGATGATGACAGCTGTGGTGCAGATGGAATTAATCTA

Alignment

ORF - retro_pabe_3447 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.5 %
• Parental protein coverage: 51.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  REKSMQDRLRLGHFTTVRHGASFTEQWTDGFAFQNLVKQQEWVNQQREDIERQRKLLAKRKPPTANNSQA
          REKSMQD.L.L.HFTTVRHG.SFTE...DGFAFQNLVKQQEWVNQQREDIERQRK.LAK.KPPTANNSQA
Retrocopy REKSMQD*LCLRHFTTVRHGTSFTE*RIDGFAFQNLVKQQEWVNQQREDIERQRKILAKCKPPTANNSQA

Parental  PSTNSEPKQRKNKAVNGAENDPFVRPNLPQLLTLAEYHEQEEIFKLRLGHLKKEEAEIQAELERLERVRN
          PSTNSEPKQRKNKAVNGAENDPFVRPNLPQLLTLAEY.EQEEIFKLRLGHL.KEEAEIQAELERLERVRN
Retrocopy PSTNSEPKQRKNKAVNGAENDPFVRPNLPQLLTLAEYYEQEEIFKLRLGHLRKEEAEIQAELERLERVRN

Parental  LHIRELKRINNEDNSQFKDHPTLNERYLLLHLLGRGGFSEVYKAFDLYEQRYAAVKIHQLNKSWRDEKKE
          LHI.EL.RINNEDNSQFKDHPTLNERYLLLHLLGRGGFSEVYKAFDLYEQ.YA.VK.HQLNKSWRD.KK.
Retrocopy LHIHELRRINNEDNSQFKDHPTLNERYLLLHLLGRGGFSEVYKAFDLYEQSYASVKLHQLNKSWRD-KKK

Parental  NYHK-HACREYRIHKELDHPRIVKLYDYFSLDTDTFCTVLEYCEGNDLDFYLKQHKLMSEKEARSIVMQI
          .......C..YRIHKELDHP.IVKLYDYFSLDTDTFCTVLEYCEGNDLDFYLKQHKL.SEKEA.SIVMQI
Retrocopy ENYY<QTCLQYRIHKELDHPQIVKLYDYFSLDTDTFCTVLEYCEGNDLDFYLKQHKLVSEKEAESIVMQI

Parental  VNALRYLNEI-KPPIIHYDLKPGNILLVDGTACGEIKITDFGLSKIMDDDSYGVDGMDL
          VNALRY.NEI..PPIIHYDLKPGNILLVD..ACGEIKITDFGLSKIMDDDS.G.DG..L
Retrocopy VNALRYTNEI<QPPIIHYDLKPGNILLVDRIACGEIKITDFGLSKIMDDDSCGADGINL

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	30.47 RPM
SRP007412_cerebellum	0.00 RPM	32.22 RPM
SRP007412_heart	0.00 RPM	9.78 RPM
SRP007412_kidney	0.00 RPM	28.54 RPM
SRP007412_liver	0.00 RPM	18.76 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3447 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3447 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3447 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000011189	1 retrocopy	retro_mmul_2277,
Pongo abelii	ENSPPYG00000012926	1 retrocopy	retro_pabe_3447 ,