RetrogeneDB ID: retro_ptro_1217

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:21469443..21470241(-)
• Located in intron of: ENSPTRG00000030902

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_1217
AAAACTCCAAAATCTACCTCAGAAAAAACACGGTAGGATAGTATCTTGATCTGCTCACCAAGAAGTTCATTCAGCTCCTG
AGCCAGTCACCCGATGGGGTCTTGGTTTTGAACAAGGCAGCGGAAGTGCTAAAAGTGCAAAATAGAAGGATTTATGATAT
CACCAACGCTCTGGAAGGCATCCACCTCATTAAGAAGAAGTCTAAAAATAACGTCCAGTGGATGGGTTGCAGTCTGTCTG
CGGATGGGGGCATGCTGACCCAGTGTCAAGGCCTGTCAAAAGAAATGACCAAGCTCACTCAGGAAGAGAAGAAATTAGAT
GAACTGATCCAAAGCTGCACCCTGGACCTCAAACTATTAACCGAGGATTCAGATCGTCAAAGGTTAGCTTATGTTACATA
TCAACATATTCGAAAAATTAGTGGCCTTAAAGACCAAACTGTTATAGTTGTGAAAGCCCCTCCAGAAATAAGATTTGAGT
GCCTGACTCAATAAGAGAGCCTACAAATACATTTGGCAGGTACCCAAGGGCCCATTGAGGTTTACTTATGTCCAGAAGAG
ACTGAAACACAGTCCAATGACAACAAACAACCAAGACCCCAATGGGAATATCCTTAAACCCACCTCGTTGGCTTCAACCA
ACTCAGGACATAGTGATTGCTCAATTTCTATGGGAAACCTTTCTCCTCTGGCCTCCCCAGCCAACCTCTTACAGCAGACT
GCGGACCAAATTCCTTCTAATCCTCTAGTATGACCATTTGTGAACTTACTGCCTCCCCTGCTGCAAGATGACCATTTG

Alignment

ORF - retro_ptro_1217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.95 %
• Parental protein coverage: 80.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RSPDSPKKKTRYDTSL-GLLTKKFIQLLSQSPDGVLDLNKAAEVLKVQKRRIYDITNVLEGIHLIKKKSK
          ..P.S...KTR.D..L..LLTKKFIQLLSQSPDGVL.LNKAAEVLKVQ.RRIYDITN.LEGIHLIKKKSK
Retrocopy KTPKSTSEKTR*DSIL<DLLTKKFIQLLSQSPDGVLVLNKAAEVLKVQNRRIYDITNALEGIHLIKKKSK

Parental  NNVQWMGCSLSEDGGMLAQCQGLSKEVTELSQEEKKLDELIQSCTLDLKLLTEDSENQRLAYVTYQDIRK
          NNVQWMGCSLS.DGGML.QCQGLSKE.T.L.QEEKKLDELIQSCTLDLKLLTEDS..QRLAYVTYQ.IRK
Retrocopy NNVQWMGCSLSADGGMLTQCQGLSKEMTKLTQEEKKLDELIQSCTLDLKLLTEDSDRQRLAYVTYQHIRK

Parental  ISGLKDQTVIVVKAPPETRLE-VPDSI-ESLQIHLASTQ-GPIEVYLCPEETETHSPMKTNNQDHNGNIP
          ISGLKDQTVIVVKAPPE.R.E.VPDSI.ESLQIHLA.TQ.GP............HSPM.TNNQD.NGNI.
Retrocopy ISGLKDQTVIVVKAPPEIRFE<VPDSI>ESLQIHLAGTQ>GPLR-FTYVQKRLKHSPMTTNNQDPNGNIL

Parental  KPASKDLASTNSGHSDCSISMGNLSPLASPANLLQQTEDQIPSN-LEGPFVNLLPPLLQEDYL
          KP.S..LASTNSGHSDCSISMGNLSPLASPANLLQQT.DQIPSN.L..PFVNLLPPLLQ.D.L
Retrocopy KPTS--LASTNSGHSDCSISMGNLSPLASPANLLQQTADQIPSNPLV*PFVNLLPPLLQDDHL

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	13.62 RPM
SRP007412_cerebellum	0.00 RPM	2.12 RPM
SRP007412_heart	0.06 RPM	9.62 RPM
SRP007412_kidney	0.08 RPM	13.83 RPM
SRP007412_liver	0.00 RPM	8.05 RPM
SRP007412_testis	0.21 RPM	8.43 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1217 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1217 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1217 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1749
Gorilla gorilla	retro_ggor_2254
Pongo abelii	retro_pabe_1447

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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,