RetrogeneDB ID: retro_pabe_3168

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:105233874..105234789(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: BUB3
• Ensembl ID: ENSPPYG00000002731
• Aliases: None
• Description: mitotic checkpoint protein BUB3 [Source:RefSeq peptide;Acc:NP_001125579]

Sequence

>retro_pabe_3168
TCCAGTTCCTGCTTGTCTCCTCCTGGGACACGTCACTGCTCTTCTACAATGTGCGGAACACGTGCTCAGGTAATAGCACT
TGCTCTCAGGTCCATGCGCTCAGGTACCAGCACGCCGGCACCATCCTGGACTGAGCCTTCTACGATCCAGCACAGGCCTG
GAGAGGAGGACTAGATCATCAATTGAAAATGCATGATTTGAACACTGATCAAGAAAATCTTGCTGGGACCCATGATGCCC
CCATCAGATGTATTGAATACTGTCCATAAGTGAACATGATGTTTACTGGAAGTTGGGATCAGACAGTTAAATTGTGGGAT
CCCAGAAATCCTTGTAATGCCAGGACCTTCTCTCGGCCTGAAAAGGTAGATACCTTCTCAGTGTCTGGAGACGAGCTGAT
TGTGAGAACAGCGGGCTGCAGAGTGTTGGTGTGGGGCTTATGGAACATGGGTTATGTGCAGCAGAGCAGGGAGTCCAGCC
TGAAATACCAGACTCGCTGCATATAAGCGTTTCCAAACAAGCAGGGTTATGTATTAAGCTCTATAGAAGGTGGAGTGGCA
GTTGAATCCTTGGCCCAAGCCCTGAGGTACAGAAGAAATATGCCTTCAAATGTCACAGACTGAAAGAAAATAATATTGAG
CAGGTTTACCCAGTCAATGCCATTTCTTTCCAGAATATCCATAATACATTTGCCATAGGTGGTTCTGATGGCTTTGTAAA
TATTTGGAATCCATTTAACAAAAAGCAACTGTGCCAGTTCCATTGGTACCCCATAAACATCGCATCACTTGCCTTCAGTA
ATGATGGGACTACACTTGCAATAGCATCATCATATATTATGAAATGGATGACATGGAACATCCTGAAGATCGTATCTTCA
TTCACCAAGTGACAGACGCAGAAACAAAACCCAAG

Alignment

ORF - retro_pabe_3168 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.74 %
• Parental protein coverage: 93.6 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SSVKFSPNTSQFLLVSSWDTSVRLYDVPANSMR-LKYQHTGAVLDCAFYDPTHAWSGGLDHQLKMHDLNT
          SS...SP............T..........SMR.L.YQH.G..LD.AFYDP..AW.GGLDHQLKMHDLNT
Retrocopy SSSCLSPPGTRHCSSTMCGTRAQVIALALRSMR<LRYQHAGTILD*AFYDPAQAWRGGLDHQLKMHDLNT

Parental  DQENLVGTHDAPIRCVEYCPEVNVMVTGSWDQTVKLWDPRTPCNAGTFSQPEKVYTLSVSGDRLIVGTAG
          DQENL.GTHDAPIRC.EYCP.VN.M.TGSWDQTVKLWDPR.PCNA.TFS.PEKV.T.SVSGD.LIV.TAG
Retrocopy DQENLAGTHDAPIRCIEYCP*VNMMFTGSWDQTVKLWDPRNPCNARTFSRPEKVDTFSVSGDELIVRTAG

Parental  RRVLVWDLRNMGYVQQRRESSLKYQTRCIRAFPNKQGYVLSSIEGRVAVE-YLDPSPEVQKKKYAFKCHR
          .RVLVW.L.NMGYVQQ.RESSLKYQTRCI.AFPNKQGYVLSSIEG.VAVE..L.PSPEVQ.KKYAFKCHR
Retrocopy CRVLVWGLWNMGYVQQSRESSLKYQTRCI*AFPNKQGYVLSSIEGGVAVE<ILGPSPEVQ-KKYAFKCHR

Parental  LKENNIEQIYPVNAISFHNIHNTFATGGSDGFVNIWDPFNKKRLCQFHRYPTSIASLAFSNDGTTLAIAS
          LKENNIEQ.YPVNAISF.NIHNTFA.GGSDGFVNIW.PFNKK.LCQFH.YP..IASLAFSNDGTTLAIAS
Retrocopy LKENNIEQVYPVNAISFQNIHNTFAIGGSDGFVNIWNPFNKKQLCQFHWYPINIASLAFSNDGTTLAIAS

Parental  SYM-YEMDDTEHPEDGIFIRQVTDAETKPK
          SY..YEMDD.EHPED.IFI.QVTDAETKPK
Retrocopy SYI<YEMDDMEHPEDRIFIHQVTDAETKPK

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	19.02 RPM
SRP007412_cerebellum	0.00 RPM	37.09 RPM
SRP007412_heart	0.00 RPM	10.96 RPM
SRP007412_kidney	0.00 RPM	30.69 RPM
SRP007412_liver	0.00 RPM	23.93 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3168 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3168 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3168 has 0 orthologous retrocopies within eutheria group .

---

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,