RetrogeneDB ID: retro_hsap_840

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 11:4231579..4232686(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000255387
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RDX
• Ensembl ID: ENSG00000137710
• Aliases: RDX, DFNB24
• Description: radixin [Source:HGNC Symbol;Acc:9944]

Sequence

>retro_hsap_840
ACTGAATTGTGCCTAGGTGTTGATGCTTTGGGTCTGAATATTTATGAGCATGATGACAAGTTAACACCTAAAACTGGTTT
TCCGTGGAGTGAAATCAGAAATGTTTCATTTAATGACAAAAAATTTGTTATAAAGCCAATCAATAAAAAGCCACCTGATT
TTGGTTTTTATGCCCCTCACCTGAGAGTCAATAAGCAGATTTTGGCCTTATGTATGGGAAACCACGAACTATACATGCGA
AGAAGGAAGCCTGATACTATTGAAGTATGACAGATGAGGGCTCAGGCTAGGGAGGAGAAACATCAGAAGCAGTTGGAGAG
GGCACAATTAGAGAATAAAAAGAAGAAAAGAGAAATAGCAGAAAAGGAAAGAATAGAATGTGAAAAGGAAGAGCTAATGG
AACGTCTAAAACAAATAGAAGAACAGACGATTAAAGCCCAGAAATAACTAGAAGAACAGACGCAAAAAGCTCTAGAACTG
GATCAAGAATGAAAACAAGCAAAAGAAGCAGCAGAGTGGCTTGAAAAGGAGCGTCGAGCTGCTGAAGAGGCGAAGTCTGC
CATAGCAAAACAAGCTGCCGACCAGAAGAATCAGGAGCAGCTAGCAGCAAAACTTGCTCAATTCACTGCCAAGATTGTAC
TTCTAGAAGAAGCCAAGAAGAAAAAGGAAGAGGAAGCTACTGAGTGGCAACACAAAGCTTTTGCAGCCCAGAAGACTTGG
AAAAGACCAAAGAAGAGTTAAAAACTGTGATGTCTGCCCCCCCCTCCACCTCCACCACCACCAACACCAGTCATTCCTTC
GACAGAAAACGAACATGATGAACATGATGAGATTAATGCTAAGGCTGGTGCTGAATTATCAAATGAAGGGGTAATGAACC
ATAGAAGCAAAGAAGAACATGTAACAGAAACACAGAAAAATGAGCGTGTTAAGAAGCTACTTCAGGCCTTAAGTTCAGAA
TTAGCCCAAGCCAGAGATGAAAGCAAGGAAACACAAAAGGATGTTCTTCAGGCTAAGAATGTTAAAACAGGCCATGGTAA
GTACAAGACTCTGTGACCGATTCGACAAGGCAACACAAAGCAGCGTATCAATGAGTTTGAAGCAATG

Alignment

ORF - retro_hsap_840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.21 %
• Parental protein coverage: 61.26 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TELWLGVDALGLNIYEHDDKLTPKIGFPWSEIRNISFNDKKFVIKPIDKKAPDFVFYAPRLRINKRILAL
          TEL.LGVDALGLNIYEHDDKLTPK.GFPWSEIRN.SFNDKKFVIKPI.KK.PDF.FYAP.LR.NK.ILAL
Retrocopy TELCLGVDALGLNIYEHDDKLTPKTGFPWSEIRNVSFNDKKFVIKPINKKPPDFGFYAPHLRVNKQILAL

Parental  CMGNHELYMRRRKPDTIEVQQMKAQAREEKHQKQLERAQLENEKKKREIAEKEKERIEREKEELMERLKQ
          CMGNHELYMRRRKPDTIEV.QM.AQAREEKHQKQLERAQ..................E.E..ELMERLKQ
Retrocopy CMGNHELYMRRRKPDTIEV*QMRAQAREEKHQKQLERAQXXXXXXXXXXXXXXXXECEKE--ELMERLKQ

Parental  IEEQTIKAQKELEEQTRKALELDQERKRAKEEAERLEKERRAAEEAKSAIAKQAADQMKNQEQLAAELAE
          IEEQTIKAQK.LEEQT.KALELDQE.K.AKE.AE.LEKERRAAEEAKSAIAKQAADQ.KNQEQLAA.LA.
Retrocopy IEEQTIKAQK*LEEQTQKALELDQE*KQAKEAAEWLEKERRAAEEAKSAIAKQAADQ-KNQEQLAAKLAQ

Parental  FTAKIALLEEAKKKKEEEATEWQHKAFAAQ-EDLEKTKEELKTVMS-APPPPPPP--PVIPPTENEHDEH
          FTAKI.LLEEAKKKKEEEATEWQHKAFAAQ.EDLEKTKEELKTVMS....PPPPP..PVIP.TEN.....
Retrocopy FTAKIVLLEEAKKKKEEEATEWQHKAFAAQ<EDLEKTKEELKTVMS>XXXPPPPPPTPVIPSTENXXXXX

Parental  DENNAEASAELSNEGVMNHRSEEERVTETQKNERVKKQLQALSSELAQARDETKKTQNDVLHAENVKAGR
          ...NA.A.AELSNEGVMNHRS.EE.VTETQKNERVKK.LQALSSELAQARDE.K.TQ.DVL.A.NVK.G.
Retrocopy XXINAKAGAELSNEGVMNHRSKEEHVTETQKNERVKKLLQALSSELAQARDESKETQKDVLQAKNVKTGH

Parental  DKYKTLRQIRQGNTKQRIDEFEAM
          .KYKTL..IRQGNTKQRI.EFEAM
Retrocopy GKYKTL*PIRQGNTKQRINEFEAM

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	155.94 RPM
bodymap2_adrenal	0.00 RPM	90.64 RPM
bodymap2_brain	0.00 RPM	159.63 RPM
bodymap2_breast	0.00 RPM	132.80 RPM
bodymap2_colon	0.00 RPM	145.00 RPM
bodymap2_heart	0.00 RPM	118.41 RPM
bodymap2_kidney	0.00 RPM	129.71 RPM
bodymap2_liver	0.00 RPM	81.37 RPM
bodymap2_lung	0.00 RPM	133.88 RPM
bodymap2_lymph_node	0.00 RPM	105.69 RPM
bodymap2_ovary	0.00 RPM	218.79 RPM
bodymap2_prostate	0.00 RPM	101.08 RPM
bodymap2_skeletal_muscle	0.00 RPM	208.87 RPM
bodymap2_testis	0.23 RPM	207.35 RPM
bodymap2_thyroid	0.00 RPM	150.61 RPM
bodymap2_white_blood_cells	0.00 RPM	45.09 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_840 was not detected

EST

No EST(s) were mapped for retro_hsap_840 retrocopy.

TSS

No TSS is located nearby retro_hsap_840 retrocopy 5' end.

Lab

retro_hsap_840 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_840 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000019413	1 retrocopy	retro_dnov_1663,
Homo sapiens	ENSG00000137710	1 retrocopy	retro_hsap_840 ,
Homo sapiens	ENSG00000147065	1 retrocopy	retro_hsap_3153,
Gorilla gorilla	ENSGGOG00000027218	1 retrocopy	retro_ggor_689,
Pan troglodytes	ENSPTRG00000004259	1 retrocopy	retro_ptro_2281,