RetrogeneDB ID: retro_ptro_1731

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:200645970..200646634(-)
• Located in intron of: ENSPTRG00000012761

Retrocopy information

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

Parental gene information

• Parental gene symbol: E2F3
• Ensembl ID: ENSPTRG00000023584
• Aliases: None
• Description: E2F transcription factor 3 [Source:HGNC Symbol;Acc:3115]

Sequence

>retro_ptro_1731
GTGGGCTACAGTCTGTCTGAGGATGAGGACATGCTGGCCCAATGTCAACGCCTGTCAAAAGAAGCAACCGAGCTCAGTCA
GGAAGAGAAAAAATTAGATGAACTGATCCAAAGCTATACCCTGGACCTCAAACTATTAACCACAGATTCAGAGAATCAAA
GGTTAGCTTATGTTACGTATCAAGATATTTGAAAACTTAGTGGTCTTAAAGACCAAACGGTTATAAGTTGTGAAAGCCCC
TCCAGAAACAAGACTTGAAGCACTTTACTCAATAGAGAGCCTACAGATATATTTGGCAAGTACCCAAGGACCAATTGAGG
TTTACTCCTGTCCAGAAGAGATGGAAACACACAATCCAGTGAAAACAAACAACCAAGACCACAATGGGAATATCTCTAAA
CCCAATTCCAAAGACTTGGATTCAACCAACACAGGACATGGCGATTGGTCAATTTCTATGGCAAACCTTTCTCCCTTGGC
CTCCCCAGCCAACTTTTTACAGCAGACTGAGGACCAAATTCCTTCTAACCTAGAAGGACCATTTGTGAACTTACTGCCTC
TCCTGCTGCAGGAGGACTGTCTCCTGAGCCTTGGGGAGGAGGAAGGCATCAGTGATATCTTTGATGCTGATGATTTGGAA
AAGCTTCCACTGGTGGAAGACTTC

Alignment

ORF - retro_ptro_1731 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.04 %
• Parental protein coverage: 66.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGCSLSEDGGMLAQCQGLSKEVTELSQEEKKLDELIQSCTLDLKLLTEDSENQRLAYVTYQDIRKISGLK
          .G.SLSED..MLAQCQ.LSKE.TELSQEEKKLDELIQS.TLDLKLLT.DSENQRLAYVTYQDI.K.SGLK
Retrocopy VGYSLSEDEDMLAQCQRLSKEATELSQEEKKLDELIQSYTLDLKLLTTDSENQRLAYVTYQDI*KLSGLK

Parental  DQTVI-VVKAPPETRLEVPDSIESLQIHLASTQGPIEVYLCPEETETHSPMKTNNQDHNGNIPKPASKDL
          DQTVI.VVKAPPETRLE...SIESLQI.LASTQGPIEVY.CPEE.ETH.P.KTNNQDHNGNI.KP.SKDL
Retrocopy DQTVI>VVKAPPETRLEALYSIESLQIYLASTQGPIEVYSCPEEMETHNPVKTNNQDHNGNISKPNSKDL

Parental  ASTNSGHSDCSISMGNLSPLASPANLLQQTEDQIPSNLEGPFVNLLPPLLQEDYLLSLGEEEGISDLFDA
          .STN.GH.D.SISM.NLSPLASPAN.LQQTEDQIPSNLEGPFVNLLP.LLQED.LLSLGEEEGISD.FDA
Retrocopy DSTNTGHGDWSISMANLSPLASPANFLQQTEDQIPSNLEGPFVNLLPLLLQEDCLLSLGEEEGISDIFDA

Parental  YDLEKLPLVEDF
          .DLEKLPLVEDF
Retrocopy DDLEKLPLVEDF

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	0.27 RPM	13.62 RPM
SRP007412_cerebellum	0.00 RPM	2.12 RPM
SRP007412_heart	0.03 RPM	9.62 RPM
SRP007412_kidney	0.18 RPM	13.83 RPM
SRP007412_liver	0.00 RPM	8.05 RPM
SRP007412_testis	0.00 RPM	8.43 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1731 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1731 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1731 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1796
Pongo abelii	retro_pabe_2137

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 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	ENSPPYG00000016269	2 retrocopies	retro_pabe_1447, retro_pabe_2137,
Pan troglodytes	ENSPTRG00000011661	2 retrocopies	retro_ptro_1484, retro_ptro_3272,
Pan troglodytes	ENSPTRG00000023584	2 retrocopies	retro_ptro_1217, retro_ptro_1731 ,
Tupaia belangeri	ENSTBEG00000000171	1 retrocopy	retro_tbel_4457,