RetrogeneDB ID: retro_pabe_1365

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16:62024224..62025022(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMPO
• Ensembl ID: ENSPPYG00000004857
• Aliases: None
• Description: thymopoietin [Source:HGNC Symbol;Acc:11875]

Sequence

>retro_pabe_1365
ACAACCAGGAAGCTGTATGAGAAAAAGCTTTTGAAACTGAGGGAGCAAGGAACAGAATCAAGATCTTCTCCTTCAGCAAC
AATTTCTTCTTCAGCAGAAAATACAAGGCAGAATGGAAGTAATGATTCTGACAGATACAGTGACAATGAAGAAGACTCTA
AAATAGAGCTCAAGTTTGAGAAGAGAGAACCGCTAAAGAGCGGAGTAAAGACTCCAGTAACCCTCGAGCAAAGAAGAGTT
GAGCACGAGAGCTATTCTCAAGCTGGAATAACTGGGACTGAATGGACAAGTGGATCTTCAAAAGGTGGACCTCTGCAGGC
ATTATTAACTAGGGAATCTACAAGAGGGTCAAGAAGAACTCCAAGGAAAAGGGTGCACACTTCAGAATATTTTCCTATAG
ATGGAGCAGTAATTTCAGCGAGGACTCCCATAGCTGAAACTATAATGGCTTCAAACAACGAATCCTTAGTTGTCAATAGG
GTGACTGGAAACTTCAAGCATGCATTTCCTATTCTGCCGGTCACTGAATTCTCAGACATACCCAGAAGAACACCAAAGAA
ACCATTGACAAGAGCTGAAGTGGGAGAAAAAACACAGGAAAGAAGAGTAGAAAGGGATATTCTTAAGGAAATGTTCCCCT
ATGAAGCAGCTACACCAACAAGAATTAGTGCTAGTTGCCACAGAAAAATCAAAGGAGCTGCAGGCGGGCCATTAGAACTC
AGTGATTTGAGGATGGAGGAGTCGTTTTCATCTGCATATGTTCCTAAGTATGTTCCCTTGGCAGATGTCAAGTGAGAA

Alignment

ORF - retro_pabe_1365 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.43 %
• Parental protein coverage: 58.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TTRKLYEKKLLKLREQGTESRSSTPLPTISSSAENTRQNGSNDSDRYSDNEEDSKIELKLEKREPLKGRA
          TTRKLYEKKLLKLREQGTESRSS.P..TISSSAENTRQNGSNDSDRYSDNEEDSKIELK.EKREPLK...
Retrocopy TTRKLYEKKLLKLREQGTESRSS-PSATISSSAENTRQNGSNDSDRYSDNEEDSKIELKFEKREPLKSGV

Parental  KTPVTLKQRRVEHNQSYSQAGITETEWTSGSSKGGPLQA-LTRESTRGSRRTPRKRVETSEHFRIDGPVI
          KTPVTL.QRRVEH..SYSQAGIT.TEWTSGSSKGGPLQA.LTRESTRGSRRTPRKRV.TSE.F.IDG.VI
Retrocopy KTPVTLEQRRVEH-ESYSQAGITGTEWTSGSSKGGPLQALLTRESTRGSRRTPRKRVHTSEYFPIDGAVI

Parental  SESTPIAETIMASSNESLVVNRVTGNFKHASPILPITEFSDIPRRAPKKPLTRAEVGEKTEERRVERDIL
          S..TPIAETIMAS.NESLVVNRVTGNFKHA.PILP.TEFSDIPRR.PKKPLTRAEVGEKT.ERRVERDIL
Retrocopy SARTPIAETIMASNNESLVVNRVTGNFKHAFPILPVTEFSDIPRRTPKKPLTRAEVGEKTQERRVERDIL

Parental  KEMFPYEASTPTGISASCRRPIKGAAGRPLELSDFRMEESFSSKYVPKYVPLADVKSE
          KEMFPYEA.TPT.ISASC.R.IKGAAG.PLELSD.RMEESFSS.YVPKYVPLADVK.E
Retrocopy KEMFPYEAATPTRISASCHRKIKGAAGGPLELSDLRMEESFSSAYVPKYVPLADVK*E

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	13.44 RPM
SRP007412_cerebellum	0.00 RPM	23.47 RPM
SRP007412_heart	0.00 RPM	7.77 RPM
SRP007412_kidney	0.00 RPM	12.93 RPM
SRP007412_liver	0.00 RPM	8.45 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1365 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1365 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1365 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1652
Pan troglodytes	retro_ptro_1123
Gorilla gorilla	retro_ggor_1247

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000004857	1 retrocopy	retro_pabe_1365 ,
Pan troglodytes	ENSPTRG00000005331	1 retrocopy	retro_ptro_1123,