RetrogeneDB ID: retro_pabe_1571

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:72714268..72715702(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFE2L3
• Ensembl ID: ENSPPYG00000017716
• Aliases: None
• Description: nuclear factor (erythroid-derived 2)-like 3 [Source:HGNC Symbol;Acc:7783]

Sequence

>retro_pabe_1571
TCCGTGCTCCGGGAAGAGCTGCTGTTCCTGGGCGGCCCGGCCAACTCCGCCTGCGCGCTGAGCCCCTTCTCGGCCTCGGG
AGGGTGGGGGCGCACGGGCCAGTTGCACCCCAAGGGCCGGGAGCTGGACCCTGCCGCGCCGCCCCAGGGCCAGCTGCTCC
GGGAGGTGCGCGCGCTAGGGGTCCCCTTCATCCCTTGCACCCAGGTGGATGCGTGGCTGGTGCACAGCGTGGCTGCCGGG
AGCGCGTACGAGGCCCACGGGCTGCTCGGCGCCGCCGCCGCCTCGTCCACCGGAGGAGCCGGCGCCAGCGTGGACGGCGG
CAGCCAGGCTGTGTAGGGGGGCGACGGGGACCCCCGAGCGGCTCGGAGTGGTCCCTTGGACGCCAGGGAAGAGGAGAAGG
CACCCGCGGAACCGACGGCTCGAGTGCCCGACGCTGGCGGGTGTGCGAGCGAGGAGAACAAGGTACTAACAGAAAAGCAC
GAAGCTGTGGATCATAGTTCCCAGGGTGAGGAAAATGAAGAAAGGGTGTCAGCCTAGAAGGAGAACTCACTTCAGCAGAA
TAATGATGATGAAAACAAAATAGCAGAGAAACCTGATTGGGAGGCAGAAGAGATCACTGAATCTAGAAATGAGAGACATC
TGAATGGGACAGATACTTCTTTCTCTCTGGAAGACTTATTCCAGTTGCTTTCATCACAGCCTGAGAATTCACTGGAGGGC
ATCTCATTGGGAGATATTCCTCTTCCAGGCAGTATCAGTGATGGCATGAATTCTTCAGCACATTCTCATGTAAACTTCAG
CCAGGCTATAAGTCAGGATGTGAATCTTCATGAGGCCATCTTGCTTTGTCCCAACAATACATTTAGAAGAGATCCAATAG
CAAGGACTTCACAGTCACAAGAACCATTTCTGCAGTTAAATTCTCATACCACCAATCCTGAGCAAACCCTTCCTGGAACT
AATTTGACAGGATTTCTTTCACTGGTTGACAATCATATGAGGAATCTAACAAGTCAAGACCTACTGTATGACCTTGACGT
AAATATATTTGATGAGATAAGCTTAATGTCATTGGCCGCAGAAGACGACTTTGATCCAATCGATGTTTCTCAGCTTTTTG
ATGAACCAGATTCTGATTCTGGCCTTTCTTTAGATTCAAGTCACAATAGTACCTCTGTCATCAAGTCTAATTCCTCTCAC
TCTGTGTGTGATGAAGGTGCTATAGGTTATTGTACTGACCATGAATCTAGTTCCCATCATGACTTAGAAGGTGCTGTAGG
CGGCTACTACCCAGAACCCAGTAAGCTTTGTCACTTGAATCAGAGTGATTCTGGTTTCCATGGGGATCTTACATTTCAAC
ACATATTTCATAACCACACTTACCACTTACAGCCAAGTGCACCAGAATCTACTTCTGAACCTTTTTCGTGGCCT

Alignment

ORF - retro_pabe_1571 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.21 %
• Parental protein coverage: 68.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TLLQDELLFLGGPASSAYALSPFSASGGWGRTGHLHPKGRELDPAAPPEGQLLREVRALGVPFVPRTRVD
          ..L..ELLFLGGPA.SA.ALSPFSASGGWGRTG.LHPKGRELDPAAPP.GQLLREVRALGVPF.P.T.VD
Retrocopy SVLREELLFLGGPANSACALSPFSASGGWGRTGQLHPKGRELDPAAPPQGQLLREVRALGVPFIPCTQVD

Parental  AWLVHSVAAGSADEAHGPLGAATASSTGGAGASVDGGSQAVQGGGGDPRAARSGPLDAGEEEKAPAEPTA
          AWLVHSVAAGSA.EAHG.LGAA.ASSTGGAGASVDGGSQAV.GG.GDPRAARSGPLDA.EEEKAPAEPTA
Retrocopy AWLVHSVAAGSAYEAHGLLGAAAASSTGGAGASVDGGSQAV*GGDGDPRAARSGPLDAREEEKAPAEPTA

Parental  QVPDPGGCASEENEVLREKHEGVDHSSQHEENEERVSAQKENSFPQNNDDGNKIAEKPDWEAEKTTESRN
          .VPD.GGCASEEN.VL.EKHE.VDHSSQ.EENEERVSA.KENS..QNNDD.NKIAEKPDWEAE..TESRN
Retrocopy RVPDAGGCASEENKVLTEKHEAVDHSSQGEENEERVSA*KENSLQQNNDDENKIAEKPDWEAEEITESRN

Parental  ERHLNGTDTSFSLEDLFQLLSSQPENSLEGISLGDIPLPGSISDGMNSSAHYHVNFSQAISQDVNLHEAI
          ERHLNGTDTSFSLEDLFQLLSSQPENSLEGISLGDIPLPGSISDGMNSSAH.HVNFSQAISQDVNLHEAI
Retrocopy ERHLNGTDTSFSLEDLFQLLSSQPENSLEGISLGDIPLPGSISDGMNSSAHSHVNFSQAISQDVNLHEAI

Parental  LLCPNNTFRRDPIARTSQSQEPFLQLNSHTTNPEQTLPGTNLTGFLSPVDNHTRNLTSQDLLYDLDINIF
          LLCPNNTFRRDPIARTSQSQEPFLQLNSHTTNPEQTLPGTNLTGFLS.VDNH.RNLTSQDLLYDLD.NIF
Retrocopy LLCPNNTFRRDPIARTSQSQEPFLQLNSHTTNPEQTLPGTNLTGFLSLVDNHMRNLTSQDLLYDLDVNIF

Parental  DEINLMSLATEDNFDPIDVSQLFDEPDTDSGLSLDSSHNSTSVIKSNSSHSVCDEGAIGYCTDHESSSHH
          DEI.LMSLA.ED.FDPIDVSQLFDEPD.DSGLSLDSSHNSTSVIKSNSSHSVCDEGAIGYCTDHESSSHH
Retrocopy DEISLMSLAAEDDFDPIDVSQLFDEPDSDSGLSLDSSHNSTSVIKSNSSHSVCDEGAIGYCTDHESSSHH

Parental  DLEGAVGGYYPEPSKLCHLDQSDSGYHGDLTFQHIFHNHTYHLQPSVPESTSEPYLWP
          DLEGAVGGYYPEPSKLCHL.QSDSG.HGDLTFQHIFHNHTYHLQPS.PESTSEP..WP
Retrocopy DLEGAVGGYYPEPSKLCHLNQSDSGFHGDLTFQHIFHNHTYHLQPSAPESTSEPFSWP

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	1.05 RPM
SRP007412_cerebellum	0.00 RPM	7.42 RPM
SRP007412_heart	0.00 RPM	1.26 RPM
SRP007412_kidney	0.00 RPM	4.87 RPM
SRP007412_liver	0.00 RPM	1.10 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1571 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1571 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1571 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000050344	1 retrocopy	retro_hsap_1761,
Pongo abelii	ENSPPYG00000017716	1 retrocopy	retro_pabe_1571 ,