RetrogeneDB ID: retro_hsap_3887

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:108634090..108634910(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000227968
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BUB3
• Ensembl ID: ENSG00000154473
• Aliases: BUB3, BUB3L, hBUB3
• Description: BUB3 mitotic checkpoint protein [Source:HGNC Symbol;Acc:1151]

Sequence

>retro_hsap_3887
CTCAGGTACCAGCACACTGGCACCATCCTGGACTGAGCCTTCTACGATCCAGCACAGGCCTGGAGAGGACTAGATCATCA
ATTGAAAATGCATGATTTGAACACTGATCAAGAAAATCTTGTTGGGACCCATGATGCCCCCATCAGATGTATTGAATACT
GTCCGGAAGTGAACGTGATGGTTACTGGAAGTTGGGATCAGACAGTTAAATTGTGGGATCCCAGAAATCCTTGTAATGCC
AGGACCTTCTCTCAGCCTGAAAAGGTAGATACCTTCTCAGTGCCTGGAGACCAGCTGATTGTGAGAACAGCGGGCTGCAG
AGTGTTGGTGTGGGGCTTATGGAACATGGATTACGTGCAGCAGAGCAGGGAGTCCAGCCTGAAATACCAGACTCACTGCA
TATAAGCGTTTCCAAACAAGCAGAGTTGTGTATTAAGCTCTATAGAAGGCGGAGTGGCAGTTGAATACTTGGCCCAAGCC
CTGAGGTACAGAAGAAATATGCCTTCAAATGTCACAGACTAAAAGAAAATAATATTGAGCAGGTTTACCCAGTCAATGCC
ATTTCTTTCCAGAATATCCATAATACATTTGCCATAGGTGGTTCTGATGGCTTTGTAAATATTTGGAATCCATTTAACAA
AAAGCAACTGTGCCAGTTCCATTGGTACCCCATAAGCATTGCATCACTTGCCTTCAGTAATGATGGGACTACGCTTGCAA
TAGCATCATCATATATTATGAAATGGATGACACGGAACATCCTGAAGATGGTATCTTCATTCACCAAGTGACAGAGGCAG
AAACAAAACCCAAGTGCACC

Alignment

ORF - retro_hsap_3887 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.25 %
• Parental protein coverage: 84.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKYQHTGAVLDCAFYDPTHAWSGGLDHQLKMHDLNTDQENLVGTHDAPIRCVEYCPEVNVMVTGSWDQTV
          L.YQHTG..LD.AFYDP..AW..GLDHQLKMHDLNTDQENLVGTHDAPIRC.EYCPEVNVMVTGSWDQTV
Retrocopy LRYQHTGTILD*AFYDPAQAWR-GLDHQLKMHDLNTDQENLVGTHDAPIRCIEYCPEVNVMVTGSWDQTV

Parental  KLWDPRTPCNAGTFSQPEKVYTLSVSGDRLIVGTAGRRVLVWDLRNMGYVQQRRESSLKYQTRCIRAFPN
          KLWDPR.PCNA.TFSQPEKV.T.SV.GD.LIV.TAG.RVLVW.L.NM.YVQQ.RESSLKYQT.CI.AFPN
Retrocopy KLWDPRNPCNARTFSQPEKVDTFSVPGDQLIVRTAGCRVLVWGLWNMDYVQQSRESSLKYQTHCI*AFPN

Parental  KQGYVLSSIEGRVAVEY-LDPSPEVQKKKYAFKCHRLKENNIEQIYPVNAISFHNIHNTFATGGSDGFVN
          KQ..VLSSIEG.VAVEY.L.PSPEVQ.KKYAFKCHRLKENNIEQ.YPVNAISF.NIHNTFA.GGSDGFVN
Retrocopy KQSCVLSSIEGGVAVEY<LGPSPEVQ-KKYAFKCHRLKENNIEQVYPVNAISFQNIHNTFAIGGSDGFVN

Parental  IWDPFNKKRLCQFHRYPTSIASLAFSNDGTTLAIASSYM-YEMDDTEHPEDGIFIRQVTDAETKPKST
          IW.PFNKK.LCQFH.YP.SIASLAFSNDGTTLAIASSY..YEMDDTEHPEDGIFI.QVT.AETKPK.T
Retrocopy IWNPFNKKQLCQFHWYPISIASLAFSNDGTTLAIASSYI<YEMDDTEHPEDGIFIHQVTEAETKPKCT

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	43.67 RPM
bodymap2_adrenal	0.00 RPM	65.05 RPM
bodymap2_brain	0.00 RPM	62.73 RPM
bodymap2_breast	0.00 RPM	47.86 RPM
bodymap2_colon	0.00 RPM	50.80 RPM
bodymap2_heart	0.00 RPM	23.21 RPM
bodymap2_kidney	0.00 RPM	66.03 RPM
bodymap2_liver	0.00 RPM	24.10 RPM
bodymap2_lung	0.00 RPM	38.71 RPM
bodymap2_lymph_node	0.00 RPM	94.20 RPM
bodymap2_ovary	0.00 RPM	71.57 RPM
bodymap2_prostate	0.00 RPM	69.66 RPM
bodymap2_skeletal_muscle	0.00 RPM	31.54 RPM
bodymap2_testis	0.00 RPM	83.97 RPM
bodymap2_thyroid	0.00 RPM	56.44 RPM
bodymap2_white_blood_cells	0.00 RPM	88.36 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3887 was not detected

EST

No EST(s) were mapped for retro_hsap_3887 retrocopy.

TSS

No TSS is located nearby retro_hsap_3887 retrocopy 5' end.

Lab

retro_hsap_3887 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3887 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012700	1 retrocopy	retro_cfam_399,
Callithrix jacchus	ENSCJAG00000001066	1 retrocopy	retro_cjac_3085,
Cavia porcellus	ENSCPOG00000011957	1 retrocopy	retro_cpor_997,
Homo sapiens	ENSG00000154473	1 retrocopy	retro_hsap_3887 ,
Gorilla gorilla	ENSGGOG00000023971	1 retrocopy	retro_ggor_2614,
Myotis lucifugus	ENSMLUG00000017732	1 retrocopy	retro_mluc_627,
Macaca mulatta	ENSMMUG00000003092	1 retrocopy	retro_mmul_1729,
Nomascus leucogenys	ENSNLEG00000027075	1 retrocopy	retro_nleu_1887,
Procavia capensis	ENSPCAG00000007736	1 retrocopy	retro_pcap_412,
Pongo abelii	ENSPPYG00000002731	1 retrocopy	retro_pabe_3168,
Ictidomys tridecemlineatus	ENSSTOG00000021785	1 retrocopy	retro_itri_1095,
Tarsius syrichta	ENSTSYG00000013444	2 retrocopies	retro_tsyr_1652, retro_tsyr_732,
Tursiops truncatus	ENSTTRG00000016194	1 retrocopy	retro_ttru_1136,