RetrogeneDB ID: retro_hsap_3546

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:1514285..1515524(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000218027
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ELF2
• Ensembl ID: ENSG00000109381
• Aliases: ELF2, EU32, NERF, NERF-1A, NERF-1B, NERF-1a,b, NERF-2
• Description: E74-like factor 2 (ets domain transcription factor) [Source:HGNC Symbol;Acc:3317]

Sequence

>retro_hsap_3546
GTGGCAACGTCTCTGCATGAGGGACCCATGAACCAGCTGGATCTGCTCATCTCGGGGGTGGAAGCATCTGCTCACAGCAG
TAATGTACACTGTACAGATAAGACAGTCGAAGCTGCTGAAGCCCTGCTTCATGTGGAATCTCCTACCTGCTTGAGGGATT
CGAGAAGTCCTGTGGAAGTATTTGTCCCTCCTGTGTATCAACTCCAGAATTTATCCATGCTGCTATGAGGCCAGATGTCA
TTACAGAAACTACAGTGGAGGCGTCAACTGAAGAGTCTGAACCAATGGATACCTCTCCTATTCCTACATCACCAGATAGC
TGTGAACCAAGGAAAAAGAAAACAGTTGGCCATAAACCAAAGACCCAGCAATCACCAATTTCCAGTGGATCTCCTGAGTT
AGGTATAAAGAAACTGAGAGAAGGAAAAGGAAACACAACCTATTTGTGGGAGTTTCTTTTAGATCTACTTCAAGATAAAA
ATACTTGTCCCCGGTATATTAAATGGCCTCAGAGAGAAAAAGGCATATTCAAGCTGGTGGATTCAAAAGCTGTCTCTAAG
CTTTGGGGAAAGCATAAGAACAAACCAGACGTGAACTATGAAACCATGGGACGAGCTTTGAGATACTATTACCAAAGGGG
AATTCTTGCAAAGATTGAAGGACAGAGGCTTGTATATCAGTTCAAGGATATGCCGAAAAACATAGTGGTCATAGACGATA
AAAAAGTGAAACCTGTAATGAAGACTTAGCAGGAGCTATGGATGAAAAATTATTAGAACAATGTCACTGTCTGCAGAAAG
TCTCCTGAAAGCAGCATCCTCTGTTCATGGTGGAAGAAATTCATCCCCTATAAACTGCTCCAGAGCAGAGAAGGGTGTGG
CTAGATTTGTGAGTATCACTTCCCCTGGTCATGATGCTTCATCCAGGTCTCCTGCTATCACTGCATCTGTATCAGCAACA
GCAGCTCCAAGGACAGTTCGTGTGGCAATGCAAGTACCTGTTGTAATGACGTCATTGGGCCAGAAAATTTCAGCTGTGGC
AGTTCAGTCAAATAGTGCAGGTGCACCATTAATAATCAGCACTAGTCCAACAACAGCCACCTCTCCAAAGGCAGTCATTC
AGGCAATCCCTACTGTGATGCCAGCTTCTACCGAAAATGGAAACAAAATCACCATGCAGTGTCCCCAAATTATTTCCATC
CCAGCTACACAGCTCGCTCAGTGTCAACTGCAAAGTCAA

Alignment

ORF - retro_hsap_3546 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.28 %
• Parental protein coverage: 77.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MATSLHEGPTNQLDLLIRAVEASVHSSNAHCTDKTIEAAEALLHMESPTCLRDSRSPVEVFVPP-CVSTP
          .ATSLHEGP.NQLDLLI..VEAS.HSSN.HCTDKT.EAAEALLH.ESPTCLRDSRSPVEVFVPP.CVSTP
Retrocopy VATSLHEGPMNQLDLLISGVEASAHSSNVHCTDKTVEAAEALLHVESPTCLRDSRSPVEVFVPP<CVSTP

Parental  EFIHAAMRPDVITETVVEVSTEESEPMDTSPIPTSPDSHEPMKKKKVGRKPKTQQSPISNGSPELGIKKK
          EFIHAAMRPDVITET.VE.STEESEPMDTSPIPTSPDS.EP.KKK.VG.KPKTQQSPIS.GSPELGIKK.
Retrocopy EFIHAAMRPDVITETTVEASTEESEPMDTSPIPTSPDSCEPRKKKTVGHKPKTQQSPISSGSPELGIKKL

Parental  PREGKGNTTYLWEFLLDLLQDKNTCPRYIKWTQREKGIFKLVDSKAVSKLWGKHKNKPDMNYETMGRALR
          .REGKGNTTYLWEFLLDLLQDKNTCPRYIKW.QREKGIFKLVDSKAVSKLWGKHKNKPD.NYETMGRALR
Retrocopy -REGKGNTTYLWEFLLDLLQDKNTCPRYIKWPQREKGIFKLVDSKAVSKLWGKHKNKPDVNYETMGRALR

Parental  YYYQRGILAKVEGQRLVYQFKDMPKNIVVIDDDK-SETCNEDLAGTTDEKSLER-VSLSAESLLKAASSV
          YYYQRGILAK.EGQRLVYQFKDMPKNIVVIDD.K.SETCNEDLAG..DEK.LE...SLSAESLLKAASSV
Retrocopy YYYQRGILAKIEGQRLVYQFKDMPKNIVVIDDKK<SETCNEDLAGAMDEKLLEQ<MSLSAESLLKAASSV

Parental  RSGKNSSPINCSRAEKGVARVVNITSPGHDASSRSPTTTASVSATAAPRTVRVAMQVPVVMTSLGQKIST
          ..G.NSSPINCSRAEKGVAR.V.ITSPGHDASSRSP..TASVSATAAPRTVRVAMQVPVVMTSLGQKIS.
Retrocopy HGGRNSSPINCSRAEKGVARFVSITSPGHDASSRSPAITASVSATAAPRTVRVAMQVPVVMTSLGQKISA

Parental  VAVQSVNAGAPLITSTSPTTATSPKVVIQTIPTVMPASTENGDKITMQPAKIITIPATQLAQCQLQTK
          VAVQS..AGAPLI.STSPTTATSPK.VIQ.IPTVMPASTENG.KITMQ...II.IPATQLAQCQLQ..
Retrocopy VAVQSNSAGAPLIISTSPTTATSPKAVIQAIPTVMPASTENGNKITMQCPQIISIPATQLAQCQLQSQ

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	50.63 RPM
bodymap2_adrenal	0.04 RPM	57.66 RPM
bodymap2_brain	0.05 RPM	23.30 RPM
bodymap2_breast	0.00 RPM	37.32 RPM
bodymap2_colon	0.00 RPM	46.54 RPM
bodymap2_heart	0.00 RPM	25.48 RPM
bodymap2_kidney	0.00 RPM	33.38 RPM
bodymap2_liver	0.00 RPM	11.53 RPM
bodymap2_lung	0.00 RPM	54.87 RPM
bodymap2_lymph_node	0.00 RPM	49.67 RPM
bodymap2_ovary	0.10 RPM	49.16 RPM
bodymap2_prostate	0.00 RPM	50.35 RPM
bodymap2_skeletal_muscle	0.00 RPM	25.24 RPM
bodymap2_testis	0.49 RPM	76.66 RPM
bodymap2_thyroid	0.00 RPM	43.39 RPM
bodymap2_white_blood_cells	0.00 RPM	47.88 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3546 was not detected

EST

No EST(s) were mapped for retro_hsap_3546 retrocopy.

TSS

No TSS is located nearby retro_hsap_3546 retrocopy 5' end.

Lab

retro_hsap_3546 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3546 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2410

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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,