RetrogeneDB ID: retro_hsap_1674

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 16:31579707..31580818(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000261614
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YBX3
• Ensembl ID: ENSG00000060138
• Aliases: YBX3, CSDA, CSDA1, DBPA, ZONAB
• Description: Y box binding protein 3 [Source:HGNC Symbol;Acc:2428]

Sequence

>retro_hsap_1674
ATGAGCGAGGCGGGCGAGGCCACCATCATCACCACCACCCTCCAGCAGGCTCCTGCGGTGGCGGCCGCCGCGGCTCCCCA
GGACCCCGCGACCAAGAGCCGGGTGGGCAGCGGTGCACCCCAAGCCGCGGCCCCGGCGCCCGCCGCCCTCGTCGCAGGAA
ACCCGGGTGGGGACGGGGCCCCCGCAGCCACGGGCACCGCGGCCGCCGCCTCTTTAGCCACCGCCGCCGACAGCGAAGAC
GCGGAGAAAAAAGTTCTCGCCACCAAAGTCCTTGGCACTGTCAAATGGTTCAACGTCAGAAATGGATATGGATTTATAAA
TCGAAATGACACCAAAGAAGATCTATTTATACATCAGACTGCCATCAAGAAGAATAACCCACAGAAATATCTGCGCAGTG
TAGGAGATGGAGAAACTGTAGAGTTTGATGTGGTTTAAGGAGAGAAGGGTGCAGAAGCAGCCAGTGTGACTGGCCGGGGT
GGAGTTCCTGTGGAGGGCAGTCGTTACGCGCTGATTGGCGCCGTTACAGACGTGGCTACTATGGAAGGCGCCATGGCCCT
CCCCGGGATTACGCTGGGAGGAGGAGGAAGAAGGGAGCGGCAGCAGTGAAGGATTTGACCCCCCTACCACTGATAGGCAG
TTCTCTGGGGCCCGGAATCGGCTGCGCCGCCCCCAGTATCGCCCCCAGTACAGGCAGCAGCGGTTCCCGCCTTACCACGT
GGGACAGACGTTTGACCGTCGCTCACCGGTCTTACCCCATCCCAACAGAATACAGGCTGTTGAGATTGGAGAGCTGAAGG
ATGGAGTCCCAGAAGGAGCACAACTTCAGGGACCATTTCATCGAAATCCAACTTACCGCCCAAGGTACCATAGCAGGGGA
CCTCCTCGCCCACGACCTGCCCCAGCAGTTGGAGAGGCTGAAGATAAAGAAAATCAGCAAGCCTCCAGTGGTCCAAACCA
GCCGCCTGTTCGCCGTGGATACCGGCGTCCCTACAATTACCGGCGTCGCCCACGTTCTCCTAACGCTCCTTCACAAGATG
GCAAAGAGGCCACGGCAGGTGAAGCACCAACTGAGAACCCTGCTCCATCCACCGAGCAGAGCAGTGCTGAG

Alignment

ORF - retro_hsap_1674 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.11 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSEAGEATTTTTTTLPQAPTEAAAAAPQDPAPKSPVGSGAPQAAAPAPAAHVAGNPGGDAAPAATGTAAA
          MSEAGEAT..TTT.L.QAP..AAAAAPQDPA.KS.VGSGAPQAAAPAPAA.VAGNPGGD.APAATGTAAA
Retrocopy MSEAGEATIITTT-LQQAPAVAAAAAPQDPATKSRVGSGAPQAAAPAPAALVAGNPGGDGAPAATGTAAA

Parental  ASLATAAGSEDAEKKVLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGET
          ASLATAA.SEDAEKKVLATKVLGTVKWFNVRNGYGFINRNDTKED.F.HQTAIKKNNP.KYLRSVGDGET
Retrocopy ASLATAADSEDAEKKVLATKVLGTVKWFNVRNGYGFINRNDTKEDLFIHQTAIKKNNPQKYLRSVGDGET

Parental  VEFDVVEGEKGAEAANVTGPDGVPVEGSRYA-ADRRRYRRGYYGRRRGPPRNYAG-EEEEEGSGSSEGFD
          VEFDVV.GEKGAEAA.VTG..GVPVEGSRYA.AD.RRYRRGYYGRR.GPPR.YAG.EEEEEGSGSSEGFD
Retrocopy VEFDVV*GEKGAEAASVTGRGGVPVEGSRYA<ADWRRYRRGYYGRRHGPPRDYAG<EEEEEGSGSSEGFD

Parental  PPATDRQFSGARNQLRRPQYRPQYRQRRFPPYHVGQTFDRRSRVLPHPNRIQAGEIGEMKDGVPEGAQLQ
          PP.TDRQFSGARN.LRRPQYRPQYRQ.RFPPYHVGQTFDRRS.VLPHPNRIQA.EIGE.KDGVPEGAQLQ
Retrocopy PPTTDRQFSGARNRLRRPQYRPQYRQQRFPPYHVGQTFDRRSPVLPHPNRIQAVEIGELKDGVPEGAQLQ

Parental  GPVHRNPTYRPRYRSRGPPRPRPAPAVGEAEDKENQQATSGPNQPSVRRGYRRPYNYRRRPRPPNAPSQD
          GP.HRNPTYRPRY.SRGPPRPRPAPAVGEAEDKENQQA.SGPNQP.VRRGYRRPYNYRRRPR.PNAPSQD
Retrocopy GPFHRNPTYRPRYHSRGPPRPRPAPAVGEAEDKENQQASSGPNQPPVRRGYRRPYNYRRRPRSPNAPSQD

Parental  GKEAKAGEAPTENPAPPTQQSSAE
          GKEA.AGEAPTENPAP.T.QSSAE
Retrocopy GKEATAGEAPTENPAPSTEQSSAE

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	442.46 RPM
bodymap2_adrenal	0.00 RPM	238.31 RPM
bodymap2_brain	0.02 RPM	42.03 RPM
bodymap2_breast	0.00 RPM	253.56 RPM
bodymap2_colon	0.00 RPM	476.92 RPM
bodymap2_heart	0.07 RPM	406.36 RPM
bodymap2_kidney	0.19 RPM	152.11 RPM
bodymap2_liver	0.00 RPM	18.14 RPM
bodymap2_lung	0.00 RPM	679.40 RPM
bodymap2_lymph_node	0.00 RPM	252.78 RPM
bodymap2_ovary	0.00 RPM	207.34 RPM
bodymap2_prostate	0.05 RPM	380.76 RPM
bodymap2_skeletal_muscle	1.71 RPM	8342.22 RPM
bodymap2_testis	3.54 RPM	472.40 RPM
bodymap2_thyroid	0.04 RPM	720.65 RPM
bodymap2_white_blood_cells	0.00 RPM	79.07 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1674 was not detected

EST

No EST(s) were mapped for retro_hsap_1674 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_51293	1028 libraries	686 libraries	105 libraries	9 libraries	1 library
TSS #2	TSS_51294	319 libraries	442 libraries	844 libraries	175 libraries	49 libraries

The graphical summary, for retro_hsap_1674 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_1674 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1674 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000006047	1 retrocopy	retro_hsap_637,
Homo sapiens	ENSG00000060138	1 retrocopy	retro_hsap_1674 ,
Homo sapiens	ENSG00000065978	4 retrocopies	retro_hsap_1433, retro_hsap_3886, retro_hsap_4250, retro_hsap_4301,
Pongo abelii	ENSPPYG00000004279	1 retrocopy	retro_pabe_1420,
Tupaia belangeri	ENSTBEG00000012570	1 retrocopy	retro_tbel_996,