RetrogeneDB ID: retro_hsap_1465

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 14:106012942..106013709(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000234402
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ELK1
• Ensembl ID: ENSG00000126767
• Aliases: None
• Description: ELK1, member of ETS oncogene family [Source:HGNC Symbol;Acc:3321]

Sequence

>retro_hsap_1465
CCACCTTCACATCCAGTCTCTGCAGCCGCAGCCACCCCCTCAGCCTCGGCCTGCTGCGGTGCTCCCCAACGCAGCTCCTG
CAGTCCAAGCCCCTGGGAGGCCTGCCTGGAGGCTGAGGAAGCCGGCTTCCCTCTGCAGGTCATCCTGACCCCGCCCGAGG
CCCCAAACCTGAAATTGGAAGAGCCGAATGTGGAGCCGGGCTTGCGCCGCCCTTTGCCCCCGGAAGTGGAAGTGGAAGGG
CCCGAGGAAGAGCTGGAATTCGCGGGGGAGAGAGGGTTCGTGCCAGAAACCGCCAAGGCCGAGCCTGAAGTCCCTCCACA
GGAGGGCGTGCCAGCGTGGCTGCCGAGGTCCTTATGGACACCGCAGGGCAGGCGGGCGGCCACGCGGCTTCCAGCCCTCA
GATCTCCCAGCCGCAGAAGGGCCGGAAGCCCCGGGACCTAGAGCTTCCACTCAGCCCGAGCCTGCTAGGTGCGCCGGGAG
CCGAACGGACCCCAGGATCGGGAACTGGCTCCGGCCTCCAGGCGCCGAGGCCGGCGCTGACCCTGTCCCTGCTTCCTACG
CACACGTTGACCCCGGCGCTGCTGACACCCAGCTCGCTGCCTCCCAGCGTTCACTTCCGGAGCAGCCTGAGTCCCGCTGC
GCCCCGCAGCCCGGCCAAGCTCTCCTGCCAGCTTCCGTCCAGTGGCGGCGCCCAGGTGCACATCCCTTCCATCGGCGTGG
CTGGCCTCTCGACCCCCGCGGTGCTCTCGCCAGGGCCCCAGAGGCCA

Alignment

ORF - retro_hsap_1465 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.31 %
• Parental protein coverage: 68.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPPHPRPAVVLPSAAPAGAAAPPSGSRSTSPSPLEACLEAEEAGLPLQVILTPPEAPNLKSEELNVEPGL
          PP.HP..A......A.A...AP...S...SPSP.EACLEAEEAG.PLQVILTPPEAPNLK.EE.NVEPGL
Retrocopy PPSHPVSAAAATPSASACCGAPQRSS--CSPSPWEACLEAEEAGFPLQVILTPPEAPNLKLEEPNVEPGL

Parental  GRALPPEVKVEGPKEELEVAGERGFVPETTKAEPEVPPQEGVPARLPA-VVMDTAGQAGGHAASSPEISQ
          .R.LPPEV.VEGP.EELE.AGERGFVPET.KAEPEVPPQEGVPA.LP..V.MDTAGQAGGHAASSP.ISQ
Retrocopy RRPLPPEVEVEGPEEELEFAGERGFVPETAKAEPEVPPQEGVPAWLPR<VLMDTAGQAGGHAASSPQISQ

Parental  PQKGRKPRDLELPLSPSLLGGPGPERTPGSGSGSGLQAPGPALTPSLLPTHTLTPVLLTPSSLPPSIHFW
          PQKGRKPRDLELPLSPSLLG.PG.ERTPGSG.GSGLQAP.PALT.SLLPTHTLTP.LLTPSSLPPS.HF.
Retrocopy PQKGRKPRDLELPLSPSLLGAPGAERTPGSGTGSGLQAPRPALTLSLLPTHTLTPALLTPSSLPPSVHFR

Parental  STLSPIAPRSPAKLSFQFPSSGSAQVHIPSISVDGLSTPVVLSPGPQKP
          S.LSP.APRSPAKLS.Q.PSSG.AQVHIPSI.V.GLSTP.VLSPGPQ.P
Retrocopy SSLSPAAPRSPAKLSCQLPSSGGAQVHIPSIGVAGLSTPAVLSPGPQRP

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	19.40 RPM
bodymap2_adrenal	0.00 RPM	21.19 RPM
bodymap2_brain	0.00 RPM	22.74 RPM
bodymap2_breast	0.00 RPM	11.38 RPM
bodymap2_colon	0.00 RPM	12.22 RPM
bodymap2_heart	0.00 RPM	13.62 RPM
bodymap2_kidney	0.00 RPM	13.26 RPM
bodymap2_liver	0.00 RPM	18.70 RPM
bodymap2_lung	0.00 RPM	17.42 RPM
bodymap2_lymph_node	0.00 RPM	20.69 RPM
bodymap2_ovary	0.00 RPM	63.98 RPM
bodymap2_prostate	0.00 RPM	12.82 RPM
bodymap2_skeletal_muscle	0.00 RPM	24.77 RPM
bodymap2_testis	0.57 RPM	34.67 RPM
bodymap2_thyroid	0.00 RPM	28.25 RPM
bodymap2_white_blood_cells	0.00 RPM	24.94 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1465 was not detected

EST

No EST(s) were mapped for retro_hsap_1465 retrocopy.

TSS

No TSS is located nearby retro_hsap_1465 retrocopy 5' end.

Lab

retro_hsap_1465 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1465 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000126767	2 retrocopies	retro_hsap_1465 , retro_hsap_1466,
Homo sapiens	ENSG00000154727	1 retrocopy	retro_hsap_3737,
Gorilla gorilla	ENSGGOG00000008714	1 retrocopy	retro_ggor_1126,
Macaca mulatta	ENSMMUG00000019420	2 retrocopies	retro_mmul_1559, retro_mmul_2276,