RetrogeneDB ID: retro_pabe_2256

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:133181057..133181749(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTO1
• Ensembl ID: ENSPPYG00000002633
• Aliases: None
• Description: glutathione S-transferase omega 1 [Source:HGNC Symbol;Acc:13312]

Sequence

>retro_pabe_2256
ATGTTACAGGAGTCAGCCAGGAGCCTGGGAAAGGGAAGCACATCCCTGGGGCTGGTCCCAGAGGGCTTGATCTGCATCTG
CAGCATGAGGTTCTGCCCGTTTACTGAGAGGACGTGTCTGGTTCTGAAGGTCGAGGGAATCAGGCATGAAGTCATCTATA
TCAACCTGAAAGATAAGCCTGAGTGGTTCTTTAAGAAAAATCCCTTTAGTTTGGTGCCAGTTCTGGAAAACAGTCAGGGT
CAGCTGATCTACGAGTCTGCCATCACCTGTGAGTACCTGGATGAAGCATACTCAGGGAAGAAGCTGTTGCCAGATGACCC
CTATGAGAAAGCTTGCCAGAAGATGGTCTTTGAGTTGTTTTCTAAGGTGCTATCTTTGGTAGGAAGCTTCCTTAGAAGCC
AAAATAAGGAGGACAGTGCTGGCCTGAAAGAAGCATTGTGTAAAGAATTTAGCAAGCTAGGGGAGGTTCTGATTAATAAG
AAGAAAACCTTCTTTGGCGGCAATTCCATCTCTGTGATTGACTACGTCATCTGGCCCTGGTTTGAACGGCTGGAAGCAAT
GAAGTTAAATGAGTGTGTAGACCACACTCCAGAACTTAAACTGTGATGGCAGCCATGAGGGAAGATCCCACAGTCTCAGC
CCTGCTCACTGGTGTGAAGGACTGGCAAGCTTTCATAGAGCTCTACTTACAG

Alignment

ORF - retro_pabe_2256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.9 %
• Parental protein coverage: 95.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGESARSLGKGSAPPGPVPEGSIRVYSMRFCPFAERTLLVLKAKGIRHEVININLKNKPEWFFKKNPFG
          M..ESARSLGKGS...G.VPEG.I...SMRFCPF.ERT.LVLK..GIRHEVI.INLK.KPEWFFKKNPF.
Retrocopy MLQESARSLGKGSTSLGLVPEGLICICSMRFCPFTERTCLVLKVEGIRHEVIYINLKDKPEWFFKKNPFS

Parental  LVPVLENSQGQLIYESAITCEYLDEAYPGKKLLPDDPYEKACQKMILELFSKVPSLVGSFIRSQNKEDYA
          LVPVLENSQGQLIYESAITCEYLDEAY.GKKLLPDDPYEKACQKM..ELFSKV.SLVGSF.RSQNKED.A
Retrocopy LVPVLENSQGQLIYESAITCEYLDEAYSGKKLLPDDPYEKACQKMVFELFSKVLSLVGSFLRSQNKEDSA

Parental  GLKEEFRKEFTKLEEVLTNKKTTFFGGSSISMIDYLIWPWFERLEAMKLNECVGHTPKLKL-WMAAMKED
          GLKE...KEF.KL.EVL.NKK.TFFGG.SIS.IDY.IWPWFERLEAMKLNECV.HTP.LKL..MAAM.ED
Retrocopy GLKEALCKEFSKLGEVLINKKKTFFGGNSISVIDYVIWPWFERLEAMKLNECVDHTPELKL<VMAAMRED

Parental  PTVSALLTSEKDWQGFLELYLQ
          PTVSALLT..KDWQ.F.ELYLQ
Retrocopy PTVSALLTGVKDWQAFIELYLQ

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	28.81 RPM
SRP007412_cerebellum	0.00 RPM	45.72 RPM
SRP007412_heart	0.00 RPM	13.19 RPM
SRP007412_kidney	0.00 RPM	53.90 RPM
SRP007412_liver	0.00 RPM	107.44 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2256 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2256 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2256 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2704
Pan troglodytes	retro_ptro_1825

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018474	1 retrocopy	retro_cjac_295,
Echinops telfairi	ENSETEG00000017967	1 retrocopy	retro_etel_1413,
Homo sapiens	ENSG00000148834	1 retrocopy	retro_hsap_2704,
Gorilla gorilla	ENSGGOG00000005064	1 retrocopy	retro_ggor_24,
Macaca mulatta	ENSMMUG00000015334	1 retrocopy	retro_mmul_142,
Nomascus leucogenys	ENSNLEG00000015358	1 retrocopy	retro_nleu_1577,
Pongo abelii	ENSPPYG00000002633	1 retrocopy	retro_pabe_2256 ,
Pan troglodytes	ENSPTRG00000002925	1 retrocopy	retro_ptro_1825,