RetrogeneDB ID: retro_hsap_637

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:125751263..125752188(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000213438
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YBX2
• Ensembl ID: ENSG00000006047
• Aliases: YBX2, CONTRIN, CSDA3, DBPC, MSY2
• Description: Y box binding protein 2 [Source:HGNC Symbol;Acc:17948]

Sequence

>retro_hsap_637
ATGAGCGAGGTGGAGGCGGCAGCGGTGGCGACAGCGGTCCCCGCGGCGACGGTGCCCGCGACGGTGGCAGGGGTGGTAGC
GGTGGTGGTACCGGTGCCCGCAGGGGAGCCGCAGAAAGCAGGCGGCGGGGCGGGCGGCTGCGGCGGGGACGCAGCCGCCT
TGGACCCCGCTGCTGGGACCCCCTCGGCGCCGGGCCCCCGCACCCCTGGCAACCCGGCGACGGCGGCCTCGGGAACCCCC
GCCCGGAGTCAGGCGGACAAGCCGGTGCTGGCAACCCGAGTCCTGCCTGGGCACTGCCAAACGGTTCAACGTCCGGAGTG
GTTACGGATTCACCAACAGGAATGACGCCAAGGAAGATGTCTTCGTTCACTGGACAGCTGTTAAAAGAAACAACCCCAGG
AAGTTTCTGCGCAGCGTTAGAGATGGGGAGACTGTGGAATTTGATGTCGTGGAAGGAGAGAAGGGCGCAGAAGCCACTAA
TGTAACTGGGCCCAGGGCGGCGGGGGTGCCCATGAAGGGCACCGTTATGCCCCCAACCGACGTAGGTTCCGCTGATTCAT
CCCCGGCCTCCCTCAGTTGCCCCACCACCCATGGTGGCAGAGATCCCCTCTCGGGGGACAGAACCTGGCGGCGAAGGGGA
GCGGGCCGAAGACTCTGGGCAGCGGCCCAGACGATGGCGCCCCCCACCCTTCTACCTACGGCGGTTTGTGCGAGGCCCCC
GGCCCCCCAACCAGCAGCAGCCTATAGAGGGCACTGATGGGGTAGAACCAAACAGACAGCCCCATTGGAGGGGCACCAAC
AGCAGGGAGATGAGTGGGTCCCCCCGCCCAGATTCCGGCCCAGGTACCTAAGGCCTTTACGCCCCAGGCCACCCCAGCAG
CCTACCATGGAAGGTGGGGACAGTGATACCAAGCCCAGCCAAGGA

Alignment

ORF - retro_hsap_637 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.75 %
• Parental protein coverage: 84.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSEVEAAAGATAVPAATVPATAAGVVAVVVPV-PAGEPQKGGGAGGGGGAASGPAAGTPSAPGSRTPGNP
          MSEVEAAA.ATAVPAATVPAT.AGVVAVVVPV.P.G...K...AG....A...P.......P..R....P
Retrocopy MSEVEAAAVATAVPAATVPATVAGVVAVVVPV>PQGSRRKQA-AGRAAAAGTQPPWTPLLGPPRRRAPAP

Parental  ATAVSGTPA--PPARSQADKPVLAIQVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNPRKFLRS
          .......P...PP..............LGT.K.FNVR.GYGF.NRND.KEDVFVH.TA.KRNNPRKFLRS
Retrocopy LATRRRRPREPPPGVRRTSRCWQPESCLGTAKRFNVRSGYGFTNRNDAKEDVFVHWTAVKRNNPRKFLRS

Parental  VGDGETVEFDVVEGEKGAEATNVTGP--GGVPVKGS-RYAPNRRKSRRFI-PRPPSVAPPPMVAEIPSAG
          V.DGETVEFDVVEGEKGAEATNVTGP...GVP.KG..RYAPNRR..R.FI.PRPPSVAPPPMVAEIPS.G
Retrocopy VRDGETVEFDVVEGEKGAEATNVTGPRAAGVPMKGT<RYAPNRRRFR*FI<PRPPSVAPPPMVAEIPSRG

Parental  TGPGSKGERAEDSGQRPRRWCPPPFFYRRRFVRGPRPPNQQQPIEGTDRVEP-KETAPLEGHQQQGDERV
          T.PG..GERAEDSGQRPRRW.PPP.FY.RRFVRGPRPPNQQQPIEGTD.VEP.K.TAPLEGHQQQGDE.V
Retrocopy TEPGGEGERAEDSGQRPRRWRPPP-FYLRRFVRGPRPPNQQQPIEGTDGVEP<KQTAPLEGHQQQGDEWV

Parental  PPPRFRPRYRRPFRPRPRQQPTTEGGDGETKPSQG
          PPPRFRPRY.RP.RPRP.QQPT.EGGD..TKPSQG
Retrocopy PPPRFRPRYLRPLRPRPPQQPTMEGGDSDTKPSQG

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	1.93 RPM
bodymap2_adrenal	0.00 RPM	2.33 RPM
bodymap2_brain	0.02 RPM	0.52 RPM
bodymap2_breast	0.00 RPM	6.07 RPM
bodymap2_colon	0.00 RPM	2.94 RPM
bodymap2_heart	0.00 RPM	0.72 RPM
bodymap2_kidney	0.00 RPM	1.57 RPM
bodymap2_liver	0.00 RPM	0.42 RPM
bodymap2_lung	0.02 RPM	0.32 RPM
bodymap2_lymph_node	0.00 RPM	1.11 RPM
bodymap2_ovary	0.02 RPM	0.25 RPM
bodymap2_prostate	0.00 RPM	1.89 RPM
bodymap2_skeletal_muscle	0.00 RPM	3.07 RPM
bodymap2_testis	0.21 RPM	244.41 RPM
bodymap2_thyroid	0.00 RPM	1.92 RPM
bodymap2_white_blood_cells	0.04 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_637 was not detected

EST

1 EST(s) were mapped to retro_hsap_637 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
HY029655	125751208	125751670	99.8	460	1	459

TSS

No TSS is located nearby retro_hsap_637 retrocopy 5' end.

Lab

retro_hsap_637 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_637 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_464

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016581	1 retrocopy	retro_cjac_1473,
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,
Macaca mulatta	ENSMMUG00000022712	1 retrocopy	retro_mmul_2237,
Nomascus leucogenys	ENSNLEG00000008063	1 retrocopy	retro_nleu_1954,
Oryctolagus cuniculus	ENSOCUG00000015064	1 retrocopy	retro_ocun_1762,
Pan troglodytes	ENSPTRG00000008673	3 retrocopies	retro_ptro_1264, retro_ptro_464, retro_ptro_50,