RetrogeneDB ID: retro_pabe_2929

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:1470255..1471453(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ELF2
• Ensembl ID: ENSPPYG00000015068
• Aliases: None
• Description: E74-like factor 2 (ets domain transcription factor) [Source:HGNC Symbol;Acc:3317]

Sequence

>retro_pabe_2929
ATCTCGGGGGTGGAAGCATCTGCTCACAGCAGTAGTGTACACTGTACAGATAAGACAATCGAAGCTGCTGAAGCCCTGCT
TCATATGGAATCTCCTACCTGCTTGAGGGATTCGAGAAGTCCTGTGGAAGTATTTGTCCCTCCTGTGTATCAACTCCAGA
ATTTATCCATGCTGCTATGAGGCCAGATGTCATTACAGAAACTGTAGTGGAGGCGTCAACTGAAGAGTCTGAACCAATGG
ATACCTCTCCTATTCCTACATCACCAGATAGCTGTGAACCAATGAAAAAGAAAACAGTTGGCCATAAACCAAAGACCCAG
CAATCACCAATTTCCAGTGGGTCTCCTGAGTTAGGTATAAAGAAGAAACTGAGAGAAGGAAAAGGAAACGCAACCTATTT
GTGGGAGTTTCTTTTAGATCTACTTCAAGATAAAAATACTTGTCCCCGGTATATTAAATGGCCTCAGAGAGAAAAAGGCA
TATTCAAGCTGGTGGATTCAAAAGCTGTCTCTAAGCTTTGGGTAAAGCATAAAAACAAACCCGACATGAACTATGAAACC
ATGGGATGAGCTTTGAGATACTATTACCAAAGGGGAATTCCTGCAAAGACTGAAGGACAGAGGCTTGTATATCAGTTCAA
GGATATGCCTAAAAACATAGTGGTCATAGACGATAACAAAAGTGAAACCTGTAATGAAGATTTAGCAGGAGCTATGGATG
AAAAATTATTAGAACGAGTGTCACACTGTCTGCAGAAAGTCTCCTGAAAGCAGCATCCTCTGTTTGTGGTGGAAGAAATT
CATCCCCTATAAACTGCTCCAGAGCAGAGCAGGGTGTGGCTAGATTTGTGAGTATCACTTCCCCTGGTCATGATGCTTCA
CCCAGGTCTCCTACTATCACTGCATCTGTATCAGCAACAGCAGCTCCAAGGCCAGTTCGTGTGGCAATGTAAGTACCTGT
TATAATGATGTCATTGGGCCAGAAAATTCCAGCTGTGGCAGTTTAGTCACTTAATGCAGGCACACCATTAATAATCAGCA
CTAGTCCAACAACAGCCTCCTCTCCAAAGGCAGTCATTCAGGTAATCCCTACTGTGATGCCAGCTTCTACTGAAAACGGA
GACAAAATCACCATGCAATGTCCCCAAATTATTTCCATCCCAGCTACACAGCTTGCACAGTGTCAACTGCAAAGTGAA

Alignment

ORF - retro_pabe_2929 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.33 %
• Parental protein coverage: 67.28 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VETVEASVHSSNAHCTDKTIEAAEALLHMESPTCLRDSRSPVEVFVPP-CVSTPEFIHAAMRPDVITETV
          ...VEAS.HSS..HCTDKTIEAAEALLHMESPTCLRDSRSPVEVFVPP.CVSTPEFIHAAMRPDVITETV
Retrocopy ISGVEASAHSSSVHCTDKTIEAAEALLHMESPTCLRDSRSPVEVFVPP<CVSTPEFIHAAMRPDVITETV

Parental  VEVSTEESEPMDTSPIPTSPDSHEPMKKKKVGRKPKTQQSPISNGSPELGIKKKPREGKGNTTYLWEFLL
          VE.STEESEPMDTSPIPTSPDS.EPMKKK.VG.KPKTQQSPIS.GSPELGIKKK.REGKGN.TYLWEFLL
Retrocopy VEASTEESEPMDTSPIPTSPDSCEPMKKKTVGHKPKTQQSPISSGSPELGIKKKLREGKGNATYLWEFLL

Parental  DLLQDKNTCPRYIKWTQREKGIFKLVDSKAVSKLWGKHKNKPDMNYETMGRALRYYYQRGILAKVEGQRL
          DLLQDKNTCPRYIKW.QREKGIFKLVDSKAVSKLW.KHKNKPDMNYETMG.ALRYYYQRGI.AK.EGQRL
Retrocopy DLLQDKNTCPRYIKWPQREKGIFKLVDSKAVSKLWVKHKNKPDMNYETMG*ALRYYYQRGIPAKTEGQRL

Parental  VYQFKDMPKNIVVIDDDKSETCNEDLGGTTDEKSLERVSLSAESL-LKAASS-VRSGKNSSPVNCSRAEK
          VYQFKDMPKNIVVIDD.KSETCNEDL.G..DEK.LERVS.......L..A.S.V..G.NSSP.NCSRAE.
Retrocopy VYQFKDMPKNIVVIDDNKSETCNEDLAGAMDEKLLERVSHCLQKV<LLKAASSVCGGRNSSPINCSRAEQ

Parental  GVARVVNITSPGHDASSRSPTTTASVSATAAPRTVRVAMQVPVVMTSLGQKISTVAVQSVNAGAPLITST
          GVAR.V.ITSPGHDAS.RSPT.TASVSATAAPR.VRVAM.VPV.M.SLGQKI..VAV.S.NAG.PLI.ST
Retrocopy GVARFVSITSPGHDASPRSPTITASVSATAAPRPVRVAM*VPVIMMSLGQKIPAVAV*SLNAGTPLIIST

Parental  SPTTATSPKVVIQTIPTVMPASTENGDKITMQPAKIITIPATQLAQCQLQTK
          SPTTA.SPK.VIQ.IPTVMPASTENGDKITMQ...II.IPATQLAQCQLQ..
Retrocopy SPTTASSPKAVIQVIPTVMPASTENGDKITMQCPQIISIPATQLAQCQLQSE

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	10.56 RPM
SRP007412_cerebellum	0.12 RPM	25.66 RPM
SRP007412_heart	0.00 RPM	13.34 RPM
SRP007412_kidney	0.00 RPM	12.43 RPM
SRP007412_liver	0.00 RPM	12.55 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2929 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2929 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2929 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003174	1 retrocopy	retro_cjac_540,
Homo sapiens	ENSG00000109381	1 retrocopy	retro_hsap_3546,
Macaca mulatta	ENSMMUG00000004984	1 retrocopy	retro_mmul_1813,
Pongo abelii	ENSPPYG00000015068	1 retrocopy	retro_pabe_2929 ,
Pan troglodytes	ENSPTRG00000016449	1 retrocopy	retro_ptro_2410,