RetrogeneDB ID: retro_hsap_2704

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:130546504..130547197(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000232829
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GSTO1
• Ensembl ID: ENSG00000148834
• Aliases: GSTO1, GSTO 1-1, GSTTLp28, HEL-S-21, P28, SPG-R
• Description: glutathione S-transferase omega 1 [Source:HGNC Symbol;Acc:13312]

Sequence

>retro_hsap_2704
ATGTTAGAGGAGTCAGCCAGGAGCCCGGGGAAGGGAAGCACGCCCCTGGGGCTGGTCCCAGAGGGCCTGATCTGCATTTG
CAGCATGAGGTTCTGCCCGTTTGCTGAGAGGACGCATCTGGTTCTGAAGGCCGAGGGAATCAGGCATGAAGTAATCTATA
TCAACCTGAAAGATAAGCCTGAGTGGTTCTTTAAGAAAAATCCCTTTAGTTTGGTGCCAGTTCTGGAAAACAGTCAGGGT
CAGCTGATCTACGAGTCTGCCATCACCTGTGAGTACCTGGATGAAGCATACTCAGGGAAGAAGCTGTTGCCGGATGACCC
CTATGACAAAGCTTGCCAGAAGATGGTCTTTGAGTTGTTTTCTAAGGTGCCATCTTTGGTAGGAAGCTTCCTTAGAACCC
AAAATAAGGAAGATGGTGCTGGCCTGAAAGAAGCATTGTGTAAAGAATTTAGCAAGCTAGAGGAGGTTCTGATTAATAAG
AAGACAACCTTCTTTGGTGGCAGTTCCATCTCTATGATTGACTACGTCATCTGGCCCTCGTTTGAACGGCTGGAAGCAAT
GAAGTTAAATGAGTGTGTAGAACACACTCCAGAACTTAAACTGTGGATGGCAGCCATGAGGGAAGATCCCACAGTCTCAG
CCCTGCTCACTGGTGTGAAGGACTGGCAAGGTTTCACAGAGCTCTACTTACAG

Alignment

ORF - retro_hsap_2704 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.85 %
• Parental protein coverage: 95.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGESARSLGKGSAPPGPVPEGSIRIYSMRFCPFAERTRLVLKAKGIRHEVININLKNKPEWFFKKNPFG
          M..ESARS.GKGS.P.G.VPEG.I.I.SMRFCPFAERT.LVLKA.GIRHEVI.INLK.KPEWFFKKNPF.
Retrocopy MLEESARSPGKGSTPLGLVPEGLICICSMRFCPFAERTHLVLKAEGIRHEVIYINLKDKPEWFFKKNPFS

Parental  LVPVLENSQGQLIYESAITCEYLDEAYPGKKLLPDDPYEKACQKMILELFSKVPSLVGSFIRSQNKEDYA
          LVPVLENSQGQLIYESAITCEYLDEAY.GKKLLPDDPY.KACQKM..ELFSKVPSLVGSF.R.QNKED.A
Retrocopy LVPVLENSQGQLIYESAITCEYLDEAYSGKKLLPDDPYDKACQKMVFELFSKVPSLVGSFLRTQNKEDGA

Parental  GLKEEFRKEFTKLEEVLTNKKTTFFGGNSISMIDYLIWPWFERLEAMKLNECVDHTPKLKLWMAAMKEDP
          GLKE...KEF.KLEEVL.NKKTTFFGG.SISMIDY.IWP.FERLEAMKLNECV.HTP.LKLWMAAM.EDP
Retrocopy GLKEALCKEFSKLEEVLINKKTTFFGGSSISMIDYVIWPSFERLEAMKLNECVEHTPELKLWMAAMREDP

Parental  TVSALLTSEKDWQGFLELYLQ
          TVSALLT..KDWQGF.ELYLQ
Retrocopy TVSALLTGVKDWQGFTELYLQ

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
bodymap2_adipose	0.00 RPM	57.25 RPM
bodymap2_adrenal	0.00 RPM	84.54 RPM
bodymap2_brain	0.00 RPM	58.01 RPM
bodymap2_breast	0.00 RPM	33.00 RPM
bodymap2_colon	0.00 RPM	59.28 RPM
bodymap2_heart	0.00 RPM	69.12 RPM
bodymap2_kidney	0.00 RPM	67.29 RPM
bodymap2_liver	0.00 RPM	149.83 RPM
bodymap2_lung	0.00 RPM	141.23 RPM
bodymap2_lymph_node	0.00 RPM	54.22 RPM
bodymap2_ovary	0.00 RPM	57.95 RPM
bodymap2_prostate	0.02 RPM	61.14 RPM
bodymap2_skeletal_muscle	0.00 RPM	26.32 RPM
bodymap2_testis	0.00 RPM	30.71 RPM
bodymap2_thyroid	0.00 RPM	70.11 RPM
bodymap2_white_blood_cells	0.00 RPM	76.84 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2704 was not detected

EST

No EST(s) were mapped for retro_hsap_2704 retrocopy.

TSS

No TSS is located nearby retro_hsap_2704 retrocopy 5' end.

Lab

retro_hsap_2704 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2704 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1825
Pongo abelii	retro_pabe_2256

---

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,