RetrogeneDB ID: retro_hsap_2890

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:180546300..180547634(-)
• Located in intron of: ENSG00000145075

Retrocopy information

• Ensembl ID: ENSG00000239516
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FLYWCH1
• Ensembl ID: ENSG00000059122
• Aliases: None
• Description: FLYWCH-type zinc finger 1 [Source:HGNC Symbol;Acc:25404]

Sequence

>retro_hsap_2890
ATGCCCCTGCCCAAGCCCAGTGAGCCGGAGGGCGAGAGTGGGAAGGCTGGGCAGGAGCCGTCCCCCGAGCCAAGCACGGA
CGTCATCCTGGCAGCCTCAGGAAGCCCGGGAAGTTCTCCAAACTGGTCCTGCTCACGGCCTCCAACCAAGATGAGGTTGG
GGTGGGCTTCAAGCCCCAGGAAGTGCACTGTGTCTTGTCCCTGGAGATGGCCGGCCCCGCCACCCTCGCCAGCACCTTGC
ATATCCTGCCAGCTGAGGAGCAGGGAGGGGTGGTCCAGCCAGCCCCCCAGATGCCTGAACAGAAGAGCAGCAAGCTGGAC
ACAGCCCCGCCATTCCCTGGAGTTCCTGAGGACACCATTTGGGGGCCGCCTCCTGATGCTTGAGTCCTTCCTGTACAAGC
AGGAGAAGGCTGTCGGGGACAAGGTGTACTGGAAGTGCCGCCAGCATGCTGAGCTGGGCTGCCGGGGCCAGGCCATCACC
CGAGGTCTGCGGGCCACAGTGATGCGGGGCTGCTGCCAAGCGCCCGATGAGCAAGGCCTGGAGCCCTGGCGCCAGAGGGA
GAAGCTGCCCAGCCTGGCCCTGCCAGAGGTCTTGGGACATCCCCGGGGTCCTGAGGGCTCTGGAAGCCGAGTGGAGGAGC
CGCTGGAGAGGGGGGGCCTGTGGCAGTGCCCCAAGGAGCCGGAGCCAGAGCCCACCCCTGGGCTAGTGCTGAGCAAGCCG
GCCCGGAGGACGACGACGGACCCCGAATCCTGTAGCTGCTGAGCCTGACGCCCAAGAAGTGCTCGATCCTGGGCCTGGGA
CAGGCCCGGCCCCTTGAGTTCCTGAGGACGTGCTACGGGGATAGCTTCCTGGTGCACGAGTCGTTCCTCTACAAGCGGGA
GAAGGCCGTGGGGGAGAAGGCGTATTGGACCTGCCGGGACCACGCGCTGCACAGCTGCCGGAGCCGGGCCATCACCCAGG
GACAGCAGGTGACCGTGATGCGTGGCCACTGCTACCCGCCCGACGTGGAGGGCCTGGAGGCCCGGCGGCAGCAGGAGAAG
GCCATGGAGACGCTGCAGGCTGTGCAGGCCGGCCCTGGGAGCCAAGTGGACACTCTCCTCCAAGGCGTGAACAGTTTTCT
CTGCCTCAGGGGCCCCGGCCCCCTGACTCTCACCAGGCCCCGGCCCAGAAAGCGAGCGAAGGTCGAAGACCAGGAGCTGC
CAACCCATCCCCAAGCCCTGGAAGGATTCCTGGACGAGGACCAGGACATGGATGCCGACCCCGGAAGCCCTGAGTTCCTG
CGGACCCCGCTGGAGGGCAGCTTCCTGGTATACGAGTCCTTCCTCTATAAGCAG

Alignment

ORF - retro_hsap_2890 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.37 %
• Parental protein coverage: 61.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPLPEPSEQEGESVKAGQEPSPKPGTDVI-PAAPRKPREFSKLVLLTASDQDEDGVGSKPQEVHCVLSLE
          MPLP.PSE.EGES.KAGQEPSP.P.TDVI.P...RKP..FSKLVLLTAS.QDE.GVG.KPQEVHCVLSLE
Retrocopy MPLPKPSEPEGESGKAGQEPSPEPSTDVI<PGSLRKPGKFSKLVLLTASNQDEVGVGFKPQEVHCVLSLE

Parental  MAGPATLASTLQILPVEEQGGVVQPALEMPEQKCSKLDAAP-QSLEFLRTPFGGRLLVLESFLYKQEKAV
          MAGPATLASTL.ILP.EEQGGVVQPA..MPEQK.SKLD.AP..SLEFLRTPFGGRLL.LESFLYKQEKAV
Retrocopy MAGPATLASTLHILPAEEQGGVVQPAPQMPEQKSSKLDTAP>HSLEFLRTPFGGRLLMLESFLYKQEKAV

Parental  GDKVYWKCRQHAELGCRGRAITRGLRATVMRGHCHAPDEQGLEARRQREKLPSLALPEGLGEPQGPEGPG
          GDKVYWKCRQHAELGCRG.AITRGLRATVMRG.C.APDEQGLE..RQREKLPSLALPE.LG.P.GPEG.G
Retrocopy GDKVYWKCRQHAELGCRGQAITRGLRATVMRGCCQAPDEQGLEPWRQREKLPSLALPEVLGHPRGPEGSG

Parental  GRVEEPLEGVGPWQCPEEPEP--TPGLVLSKPAL-EEEEAPRALSLLSLPPKKRSILGLGQARPLEFLRT
          .RVEEPLE..G.WQCP.EPEP..TPGLVLSKPA..E....PR.L.LLSL.PKK.SILGLGQARPLEFLRT
Retrocopy SRVEEPLERGGLWQCPKEPEPEPTPGLVLSKPAR<EDDDGPRIL*LLSLTPKKCSILGLGQARPLEFLRT

Parental  CYGGSFLVHESFLYKREKAVGDKVYWTCRDHALHGCRSRAITQGQRVTVMRGHCHQPDMEGLEARRQQEK
          CYG.SFLVHESFLYKREKAVG.K.YWTCRDHALH.CRSRAITQGQ.VTVMRGHC..PD.EGLEARRQQEK
Retrocopy CYGDSFLVHESFLYKREKAVGEKAYWTCRDHALHSCRSRAITQGQQVTVMRGHCYPPDVEGLEARRQQEK

Parental  AVETLQAGQDGPGSQVDTLLRGVDSLLYRRGPGPLTLTRPRPRKRAKVEDQELPTQPEAPD----EHQDM
          A.ETLQA.Q.GPGSQVDTLL.GV.S.L..RGPGPLTLTRPRPRKRAKVEDQELPT.P.A......E.QDM
Retrocopy AMETLQAVQAGPGSQVDTLLQGVNSFLCLRGPGPLTLTRPRPRKRAKVEDQELPTHPQALEGFLDEDQDM

Parental  DADPGGPEFLKTPLGGSFLVYESFLYRR
          DADPG.PEFL.TPL.GSFLVYESFLY..
Retrocopy DADPGSPEFLRTPLEGSFLVYESFLYKQ

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	0.02 RPM	17.17 RPM
bodymap2_adrenal	0.00 RPM	28.90 RPM
bodymap2_brain	0.00 RPM	21.66 RPM
bodymap2_breast	0.00 RPM	13.97 RPM
bodymap2_colon	0.00 RPM	18.89 RPM
bodymap2_heart	0.00 RPM	12.15 RPM
bodymap2_kidney	0.00 RPM	15.18 RPM
bodymap2_liver	0.00 RPM	4.04 RPM
bodymap2_lung	0.00 RPM	18.57 RPM
bodymap2_lymph_node	0.00 RPM	15.24 RPM
bodymap2_ovary	0.00 RPM	23.06 RPM
bodymap2_prostate	0.00 RPM	28.51 RPM
bodymap2_skeletal_muscle	0.00 RPM	19.93 RPM
bodymap2_testis	0.00 RPM	14.74 RPM
bodymap2_thyroid	0.00 RPM	22.52 RPM
bodymap2_white_blood_cells	0.00 RPM	8.13 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2890 was not detected

EST

No EST(s) were mapped for retro_hsap_2890 retrocopy.

TSS

No TSS is located nearby retro_hsap_2890 retrocopy 5' end.

Lab

retro_hsap_2890 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2890 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000059122	1 retrocopy	retro_hsap_2890 ,
Nomascus leucogenys	ENSNLEG00000009480	2 retrocopies	retro_nleu_3085, retro_nleu_628,