RetrogeneDB ID: retro_pabe_2137

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:86925080..86925745(-)
• Located in intron of: ENSPPYG00000013036

Retrocopy information

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

Parental gene information

• Parental gene symbol: E2F3
• Ensembl ID: ENSPPYG00000016269
• Aliases: None
• Description: E2F transcription factor 3 [Source:HGNC Symbol;Acc:3115]

Sequence

>retro_pabe_2137
GTGGGCTACAGTCTGTCTGAGGATGAGGGCATGCTGGCCCAATGTCAAGGCCTGTCAAAAGAAGCAACCAAGCTCAGTCA
GGAAGAGAAAAAATTAGATGAACTGATCCAAAGCTGCACCCTGGACCTCAAACTATTAACCACAGATTCAGAGAATCAAA
GGTTAGCTTATATTGCGTATCAAAATATTTGAAAACTTAGTGGCCTTAAAGACCAAACGGTTATAAGTTGTGAAAGCCCC
TCCAGAAATAAGACTTGAAGCACTTTACTCAATAGAGAGCCTACAGACATATTTGGCAAGTACCCAAGGACCAATTGAGG
TTTACTCCTGTCCAGAAGAGATGGAAACACACAATCCAGTGAAAACAAACAACCAAGACCCACAATGGGAATATCTCTAA
ACCCAATTCCAAAGACTTGGATTCAACCAACTCAGGACATAGTGATTGGTCAATTTCTATGGCAAACCTTTCTCCCTTGG
CCTCCCCAGCCAACTTTTTACAGCAGACTGAGGTCCAAATTCCTTCTAACCTAGAAGGACTATTTGTGAACTTACTGCCT
CCCCTGCTGCAAGAGGACTGTCTCCTGAGCCTTGGGGAGGAGGAAGGCATCAGTGATACCTTTGATGCTGATGATTTGGA
AAAGCTTCCACTGATGGAAGACTTC

Alignment

ORF - retro_pabe_2137 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.3 %
• Parental protein coverage: 51.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGCSLSEDGGMLAQCQGLSKEVTELSQEEKKLDELIQSCTLDLKLLTEDSENQRLAYVTYQDIRKISGLK
          .G.SLSED.GMLAQCQGLSKE.T.LSQEEKKLDELIQSCTLDLKLLT.DSENQRLAY..YQ.I.K.SGLK
Retrocopy VGYSLSEDEGMLAQCQGLSKEATKLSQEEKKLDELIQSCTLDLKLLTTDSENQRLAYIAYQNI*KLSGLK

Parental  DQTVI-VVKAPPETRLEVPDSIESLQIHLASTQGPIEVYLCPEETETHSPMKTNNQD-HNGNIPKPASKD
          DQTVI.VVKAPPE.RLE...SIESLQ..LASTQGPIEVY.CPEE.ETH.P.KTNNQD.HNGNI.KP.SKD
Retrocopy DQTVI>VVKAPPEIRLEALYSIESLQTYLASTQGPIEVYSCPEEMETHNPVKTNNQD>HNGNISKPNSKD

Parental  LASTNSGHSDCSISMGNLSPLASPANLLQQTEDQIPSNLEGPFVNLLPPLLQEDYLLSLGEEEGISDLFD
          L.STNSGHSD.SISM.NLSPLASPAN.LQQTE.QIPSNLEG.FVNLLPPLLQED.LLSLGEEEGISD.FD
Retrocopy LDSTNSGHSDWSISMANLSPLASPANFLQQTEVQIPSNLEGLFVNLLPPLLQEDCLLSLGEEEGISDTFD

Parental  AYDLEKLPLVEDF
          A.DLEKLPL.EDF
Retrocopy ADDLEKLPLMEDF

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	0.06 RPM	4.26 RPM
SRP007412_cerebellum	0.24 RPM	1.70 RPM
SRP007412_heart	0.00 RPM	1.66 RPM
SRP007412_kidney	0.03 RPM	2.65 RPM
SRP007412_liver	0.00 RPM	1.65 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2137 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2137 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2137 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1731
Gorilla gorilla	retro_ggor_1796

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021045	1 retrocopy	retro_btau_1523,
Choloepus hoffmanni	ENSCHOG00000008679	2 retrocopies	retro_chof_416, retro_chof_871,
Homo sapiens	ENSG00000112242	1 retrocopy	retro_hsap_1749,
Gorilla gorilla	ENSGGOG00000011022	2 retrocopies	retro_ggor_1796, retro_ggor_2254,
Macaca mulatta	ENSMMUG00000017649	1 retrocopy	retro_mmul_955,
Pongo abelii	ENSPPYG00000012646	1 retrocopy	retro_pabe_1,
Pongo abelii	ENSPPYG00000016269	2 retrocopies	retro_pabe_1447, retro_pabe_2137 ,
Pan troglodytes	ENSPTRG00000023584	2 retrocopies	retro_ptro_1217, retro_ptro_1731,
Tupaia belangeri	ENSTBEG00000000171	1 retrocopy	retro_tbel_4457,