RetrogeneDB ID: retro_hsap_1433

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 14:66479550..66480507(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000224861
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YBX1
• Ensembl ID: ENSG00000065978
• Aliases: YBX1, BP-8, CSDA2, CSDB, DBPB, MDR-NF1, NSEP-1, NSEP1, YB-1, YB1
• Description: Y box binding protein 1 [Source:HGNC Symbol;Acc:8014]

Sequence

>retro_hsap_1433
ATGAGCAGCGAGGCCGAGACCCAGCAGCCGCCCGCCGCCCCCGCCCTCAGCGCCGCCGACACCAAGCCCGGCACTACCGG
CAGCGGCGCAGGGAGCGGTGGCCCGGGCGGCCTCACATCGGCGGCGCCTGCCGGCGGGCACAAAAAGGTCATCGCAACGA
AGGTTTTGGGAACGGTAAAATGGTTCAATGTAAGGAACGGATATGGTTTCATCCACAGGAACGACACCAAGGAAGATGTA
TTTGTACACCACACTGCCATGAAGAAGAATAACCCCAGGAAGTACCTTCGCAGTGTAGGAGATGGAGAGACTGTGGAGTT
TGATGTTGTTGAAGGAGAAAAGGGTGCGAAGGCAGCAAATGTTACAGGTCCTGGTGGTGTTCCAGTTCAAGGCAGTAAAT
ATGCAGCAGACCGTAACCATTATAGACGCTATCCACGTCCTAGGGGTCCTCCACGCAATTACCAGCAAAATTACCAGAAT
AGTGAGAGTGGGGAAAAGAACGAGGGATCGGAGAGTGCTCCCGAAGGCCAGGCCCAACAACGCCGGCCCTACCGCAGGCG
AAGGTTCCCACCTTACTACATGCGGAGACCCTATGGGCGTCGACCACAGTATTCCAACCCTCCTGTGCAGGGAGAAGTGA
TGGAGGGTGCTGACAACCAGGGTGCAGGAGAACAAGGTAGACCAGTGAGGCAGAATATGTATCGGGGATATAGACCACGA
TTCCGCAGAGGCCCTCCTCTCCAAAGACAGCCTAGAGAGGACGGCAATGAAGAAGATAAAGAAAATCAAGGAGATGAGAC
CCAAGGTCAGCAGCCACCTCAACGTCGGTACCGCCGCAACTTCAATTACCGACGCCGACGCCCAGAAAACCCTAAACCAC
AAGATGGCAAAGAGACAAAAGCAGCCAATCCACCAGCTGAGAATTCGTCCGCTCCCGAGGCTGAGCAGGGCGGGGCT

Alignment

ORF - retro_hsap_1433 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.28 %
• Parental protein coverage: 99.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSEAETQQPPAAPPAAPALSAADTKPGTTGSGAGSGGPGGLTSAAPAGGDKKVIATKVLGTVKWFNVRN
          MSSEAETQQ....PPAAPALSAADTKPGTTGSGAGSGGPGGLTSAAPAGG.KKVIATKVLGTVKWFNVRN
Retrocopy MSSEAETQQ----PPAAPALSAADTKPGTTGSGAGSGGPGGLTSAAPAGGHKKVIATKVLGTVKWFNVRN

Parental  GYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPGGVPVQGSKYAA
          GYGFI.RNDTKEDVFVH.TA.KKNNPRKYLRSVGDGETVEFDVVEGEKGA.AANVTGPGGVPVQGSKYAA
Retrocopy GYGFIHRNDTKEDVFVHHTAMKKNNPRKYLRSVGDGETVEFDVVEGEKGAKAANVTGPGGVPVQGSKYAA

Parental  DRNHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSESAPEGQAQQRRPYRRRRFPPYYMRRPYGRRPQYSN
          DRNHYRRYPR.RGPPRNYQQNYQNSESGEKNEGSESAPEGQAQQRRPYRRRRFPPYYMRRPYGRRPQYSN
Retrocopy DRNHYRRYPRPRGPPRNYQQNYQNSESGEKNEGSESAPEGQAQQRRPYRRRRFPPYYMRRPYGRRPQYSN

Parental  PPVQGEVMEGADNQGAGEQGRPVRQNMYRGYRPRFRRGPPRQRQPREDGNEEDKENQGDETQGQQPPQRR
          PPVQGEVMEGADNQGAGEQGRPVRQNMYRGYRPRFRRGPP.QRQPREDGNEEDKENQGDETQGQQPPQRR
Retrocopy PPVQGEVMEGADNQGAGEQGRPVRQNMYRGYRPRFRRGPPLQRQPREDGNEEDKENQGDETQGQQPPQRR

Parental  YRRNFNYRRRRPENPKPQDGKETKAADPPAENSSAPEAEQGGA
          YRRNFNYRRRRPENPKPQDGKETKAA.PPAENSSAPEAEQGGA
Retrocopy YRRNFNYRRRRPENPKPQDGKETKAANPPAENSSAPEAEQGGA

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	1.17 RPM	808.89 RPM
bodymap2_adrenal	0.57 RPM	729.35 RPM
bodymap2_brain	0.16 RPM	92.05 RPM
bodymap2_breast	0.39 RPM	645.42 RPM
bodymap2_colon	0.39 RPM	666.41 RPM
bodymap2_heart	0.41 RPM	399.44 RPM
bodymap2_kidney	0.33 RPM	285.62 RPM
bodymap2_liver	0.06 RPM	200.65 RPM
bodymap2_lung	0.25 RPM	440.84 RPM
bodymap2_lymph_node	0.51 RPM	413.70 RPM
bodymap2_ovary	0.35 RPM	409.27 RPM
bodymap2_prostate	0.55 RPM	513.49 RPM
bodymap2_skeletal_muscle	2.38 RPM	1157.31 RPM
bodymap2_testis	1.21 RPM	1126.79 RPM
bodymap2_thyroid	0.43 RPM	666.53 RPM
bodymap2_white_blood_cells	0.12 RPM	398.62 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1433 was not detected

EST

No EST(s) were mapped for retro_hsap_1433 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_39714	411 libraries	697 libraries	692 libraries	25 libraries	4 libraries

The graphical summary, for retro_hsap_1433 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_1433 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1433 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 118 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000494	9 retrocopies	retro_amel_1280, retro_amel_1358, retro_amel_141, retro_amel_1486, retro_amel_215, retro_amel_418, retro_amel_625, retro_amel_837, retro_amel_909,
Canis familiaris	ENSCAFG00000002541	4 retrocopies	retro_cfam_1312, retro_cfam_2118, retro_cfam_758, retro_cfam_91,
Callithrix jacchus	ENSCJAG00000003155	6 retrocopies	retro_cjac_1261, retro_cjac_1701, retro_cjac_2718, retro_cjac_3156, retro_cjac_4172, retro_cjac_817,
Cavia porcellus	ENSCPOG00000010888	3 retrocopies	retro_cpor_654, retro_cpor_833, retro_cpor_905,
Felis catus	ENSFCAG00000022604	6 retrocopies	retro_fcat_145, retro_fcat_1554, retro_fcat_1956, retro_fcat_241, retro_fcat_503, retro_fcat_631,
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,
Loxodonta africana	ENSLAFG00000007597	1 retrocopy	retro_lafr_804,
Microcebus murinus	ENSMICG00000014984	19 retrocopies	retro_mmur_1098, retro_mmur_1285, retro_mmur_1326, retro_mmur_1435, retro_mmur_1437, retro_mmur_1445, retro_mmur_1621, retro_mmur_199, retro_mmur_315, retro_mmur_413, retro_mmur_581, retro_mmur_640, retro_mmur_676, retro_mmur_679, retro_mmur_726, retro_mmur_837, retro_mmur_900, retro_mmur_919, retro_mmur_942,
Macaca mulatta	ENSMMUG00000013136	5 retrocopies	retro_mmul_1139, retro_mmul_1423, retro_mmul_2017, retro_mmul_423, retro_mmul_861,
Nomascus leucogenys	ENSNLEG00000012324	7 retrocopies	retro_nleu_1053, retro_nleu_1188, retro_nleu_1312, retro_nleu_1601, retro_nleu_1749, retro_nleu_1888, retro_nleu_270,
Oryctolagus cuniculus	ENSOCUG00000028047	2 retrocopies	retro_ocun_1519, retro_ocun_1953,
Otolemur garnettii	ENSOGAG00000006784	25 retrocopies	retro_ogar_1127, retro_ogar_1246, retro_ogar_1350, retro_ogar_1371, retro_ogar_1497, retro_ogar_2011, retro_ogar_2018, retro_ogar_2302, retro_ogar_2359, retro_ogar_2607, retro_ogar_2654, retro_ogar_3170, retro_ogar_3225, retro_ogar_324, retro_ogar_3303, retro_ogar_3316, retro_ogar_3317, retro_ogar_3366, retro_ogar_3416, retro_ogar_3474, retro_ogar_448, retro_ogar_572, retro_ogar_678, retro_ogar_690, retro_ogar_753,
Pongo abelii	ENSPPYG00000001466	7 retrocopies	retro_pabe_1216, retro_pabe_1320, retro_pabe_2054, retro_pabe_2292, retro_pabe_3167, retro_pabe_3388, retro_pabe_3502,
Pteropus vampyrus	ENSPVAG00000005504	7 retrocopies	retro_pvam_1255, retro_pvam_1348, retro_pvam_1391, retro_pvam_145, retro_pvam_405, retro_pvam_76, retro_pvam_971,
Sorex araneus	ENSSARG00000007896	1 retrocopy	retro_sara_559,
Tarsius syrichta	ENSTSYG00000006915	6 retrocopies	retro_tsyr_1030, retro_tsyr_173, retro_tsyr_2037, retro_tsyr_610, retro_tsyr_840, retro_tsyr_996,
Tursiops truncatus	ENSTTRG00000001353	2 retrocopies	retro_ttru_461, retro_ttru_746,
Vicugna pacos	ENSVPAG00000000068	2 retrocopies	retro_vpac_235, retro_vpac_647,