RetrogeneDB ID: retro_hsap_3574

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:31255975..31256741(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000231402
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: WASF3
• Ensembl ID: ENSG00000132970
• Aliases: WASF3, Brush-1, SCAR3, WAVE3
• Description: WAS protein family, member 3 [Source:HGNC Symbol;Acc:12734]

Sequence

>retro_hsap_3574
ATGCCTCCCGTGAAGAGGAGCATCTAATCCCAGCATTTGCACCAGGGAACTCTGCCTGAAGGGATTACCAGTGACTTGAA
AGTGTAACCAACAACAATCTTGTCACTATTACGCACCAGCTAAGCAATCTGAACATACATGCTGAAGACATATTTGGTGA
GCTATTTAAGGAGGCTAACTACTTCCACATTAGATCAAATTCTCTTAGAATTTGTTGCCTCATGGTCAAAGTCACTCAGC
TGGATTCAGCAGTGGAAGAGGTGTCACCACAGGACATCAACATGGAAAAAGCCCTCAAAAGTTCCCCAGCCCAAGACCAG
CAAGCAGTTTCAAAGAGCAGCATTCCTACTCCTGCTGCTGACATTTACAATCAGAGTGATTGACCACCTCCCCTGAATAG
CATGAGAGCACATGGAGATGATAAAGACAGGCTGAAGTTCTATACTGATCCTTCCCATTTATTTGACCTCTGGAAAGAAG
AAGTGCTGCAGGACACAGAAGACAAAAGGAAAGACAGAAGGCATCAAAAGTAGCAAAACCACATAGATGGCACCACTTAT
GATGTGAAAAGGATTACAAAAGCCAGAAACAAGCACCATGAGTGGAATATGATGGCATATGACAAAGAGCTTAGACCCAG
CAACAGGTTGTCTCAGTGTGTACCATGGAGCATCCTGCAAGAACCCCTGTCCCTAGACAGCAGGTCCCATACAATGGATG
TTAGGGATGCTCTTATCGAGCTACTCCAAACCATTCTCACGACCCT

Alignment

ORF - retro_hsap_3574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.18 %
• Parental protein coverage: 51.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPLVKRNIEPRHLCRGALPEGITSEL-ECVTNSTLAAIIRQLSSLSKHAEDIFGELFNEANNFYIRANSL
          MP.VKR.I...HL..G.LPEGITS.L.E.VTN..L..I..QLS.L..HAEDIFGELF.EAN.F.IR.NSL
Retrocopy MPPVKRSI*SQHLHQGTLPEGITSDL<ESVTNNNLVTITHQLSNLNIHAEDIFGELFKEANYFHIRSNSL

Parental  QDRIDRLAVKVTQLDSTVEEVSLQDINMKKAFKSSTVQDQQVVSKNSIPNPVADIYNQSDKPPPLNILTP
          ..RI..L.VKVTQLDS.VEEVS.QDINM.KA.KSS..QDQQ.VSK.SIP.P.ADIYNQSD.PPPLN....
Retrocopy --RICCLMVKVTQLDSAVEEVSPQDINMEKALKSSPAQDQQAVSKSSIPTPAADIYNQSD*PPPLNSMRA

Parental  YRDDKKDGLKFYTDPSYFFDLWKEKMLQDTEDKRKEKRRQKEQKRIDGTTREVKKVRKARNRRQEWNMMA
          ..DDK.D.LKFYTDPS..FDLWKE..LQDTEDKRK..R.QK.Q..IDGTT..VK...KARN...EWNMMA
Retrocopy HGDDK-DRLKFYTDPSHLFDLWKEEVLQDTEDKRKDRRHQK*QNHIDGTTYDVKRITKARNKHHEWNMMA

Parental  YDKELRPDNRLSQSVYHGASSEGSLSPDTRSHASDVTD-YSYPATPNHSLHP
          YDKELRP.NRLSQ.V......E..LS.D.RSH..DV.D..SY.ATPNHS..P
Retrocopy YDKELRPSNRLSQCVPWSILQE-PLSLDSRSHTMDVRD<CSYRATPNHSHDP

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	44.35 RPM
bodymap2_adrenal	0.00 RPM	18.95 RPM
bodymap2_brain	0.00 RPM	184.12 RPM
bodymap2_breast	0.00 RPM	80.53 RPM
bodymap2_colon	0.00 RPM	26.80 RPM
bodymap2_heart	0.00 RPM	20.62 RPM
bodymap2_kidney	0.06 RPM	20.56 RPM
bodymap2_liver	0.00 RPM	19.96 RPM
bodymap2_lung	0.00 RPM	19.92 RPM
bodymap2_lymph_node	0.00 RPM	28.16 RPM
bodymap2_ovary	0.00 RPM	50.22 RPM
bodymap2_prostate	0.00 RPM	39.23 RPM
bodymap2_skeletal_muscle	0.00 RPM	12.71 RPM
bodymap2_testis	0.06 RPM	55.82 RPM
bodymap2_thyroid	0.06 RPM	98.11 RPM
bodymap2_white_blood_cells	0.00 RPM	6.16 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3574 was not detected

EST

No EST(s) were mapped for retro_hsap_3574 retrocopy.

TSS

No TSS is located nearby retro_hsap_3574 retrocopy 5' end.

Lab

retro_hsap_3574 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3574 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000132970	1 retrocopy	retro_hsap_3574 ,
Homo sapiens	ENSG00000158195	1 retrocopy	retro_hsap_4682,
Gorilla gorilla	ENSGGOG00000012518	1 retrocopy	retro_ggor_2411,
Tarsius syrichta	ENSTSYG00000005184	3 retrocopies	retro_tsyr_1561, retro_tsyr_366, retro_tsyr_407,