RetrogeneDB ID: retro_ptro_1041

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:28565037..28566502(-)
• Located in intron of: ENSPTRG00000006863

Retrocopy information

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

Parental gene information

• Parental gene symbol: DEPDC1
• Ensembl ID: ENSPTRG00000000847
• Aliases: None
• Description: None

Sequence

>retro_ptro_1041
CAGTCTTCAAAATTCCTTCACTTAAACAATTTGAATTCCTTCAAATCAACTGAGTGCCTTCTTCTCAGTCTGCTTCATAG
AGAAAAAAAAAATAAAGAAGAATCAGATTCTACTGAGAGACTACAGATAAGCAATCCAGGATTTCAAGAAAGATGTGCTA
AGAAAATGCAGCTAGTTAATTTAAGAAACAGAAGAGTGAGTGCTAATGACATAATGGGAGGAAGTTGTCATAATTTAATA
GGGTTAAGTAGTATGCATGATCTATCCTCTAACAGCAAACCAAGGTGCTATTCTTTGGAAGGAATTGTAGATGTGTCAGG
GAATTCAAGTAAAGAGGCATCCAGTGTCTTTCATCAATCTTTTCCGAACATAGAAGGACAAAATAATAAACTGTTTTTAG
AGTCTAAGCCCAAACAGGAATTCCTGTTGAATCTTCATTCAGAGGAAAATATTCAAAAGCCATTCAGTGCTGGTTTTAAG
AGAACCTCTACTTTGATTGTTCAAGACCAAGAGGAGTTGTGTAATGGGAAATGCAAGTCAGAACAGCTTTGTAGGTCTCA
GAGTTTGCTTTTAACAAGTAGTACAAGAAGGAATAGTTATTATCAATACACCAGTGGCTGAAATTACCATGAAACCAAAT
GTTGGACAAGGCAGCACAAGTGTGCAAACAGCTATGGAAAGTGAACTTGGAGAGTCTAGTGCCACAATCAATAAAAGACT
CTGCAAAAGTACAATAGAACTTTCAGAAGATTCTTTACTTCCAGCTTCTTCTGTGTTGACTGGCACACAAAGTTTGCTGC
AACCTCATTTAGAGAGGGTTGCCATCGATGCTCTACAGTTATGTTGTTTGTTATTTCCCCCACCAAATCATAGAAAGCTT
CAACTTTTAATGCGTATGATTTCCCGAATGAGTCAAAATGTTGATATGCCCAAACTTCATGATGCAATGGGTGCGAGATC
ACTGTTGATACATACCTTTTCTCAATGTGTGTTATGCTGTGCTGAAGAAGTGGACCTTGATGAGCTTCTTGCTGGAAGAT
TAGTTTCTTTCTTAATGGATCATGATCAGGAAATTCTTCAAGTACCCTCTTACTTGCAGACTGCAGTGGAAAAACATCTT
GACTACTTAAAAAGGGGACATATTGAAAGTCCTGGAGGTGGACTATTTGCTCCTTTGCCAACTTACTCATACGGTAAGCA
GATTAGTGCTCAGGAGTTTGATGAGCAAAAAATTTCTACCTCTCAAGCTGCAATTGCAGAACTTTTAGAAAATATTGTTA
AAAACAGGAGTTTACCTCTAAAGGAGAAAAGAAAAAAACTAAAATAGTTTCAGAAGGAATATCCTTTGATATATCAGAAA
AGATTTCCAACCATGGAGAGTGAAGCAGCACTTTTTGGTGACAAACCTACAATCAAGCAACCAATGCTGATTTTAAGAAA
ACCAAAGTTCTGTAGTCTAAGATAC

Alignment

ORF - retro_ptro_1041 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.02 %
• Parental protein coverage: 59.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QSSKFLHLNNLNSFKSTECLLLSLLHREKN-KEESDSTERLQISNPGFQERCAKKMQLVNLRNRRVSAND
          QSSKFLHLNNLNSFKSTECLLLSLLHR....KEESDSTERLQISNPGFQERCAKKMQLVNLRNRRVSAND
Retrocopy QSSKFLHLNNLNSFKSTECLLLSLLHRXXXXKEESDSTERLQISNPGFQERCAKKMQLVNLRNRRVSAND

Parental  IMGGSCHNLIGLSNMHDLSSNSKPRCCSLEGIVDVPGNSSKEASSVFHQSFPNIEGQNNKLFLESKPKQE
          IMGGSCHNLIGLS.MHDLSSNSKPRC.SLEGIVDV.GNSSKEASSVFHQSFPNIEGQNNKLFLESKPKQE
Retrocopy IMGGSCHNLIGLSSMHDLSSNSKPRCYSLEGIVDVSGNSSKEASSVFHQSFPNIEGQNNKLFLESKPKQE

Parental  FLLNLHSEETIQKPFSAGFKRNSTLTVQDQEELYNGKCKSKQLCRSQSLLLRSSTRRNSY-INTPVAEII
          FLLNLHSEE.IQKPFSAGFKR.STL.VQDQEEL.NGKCKS.QLCRSQSLLL.SSTRRNSY.INTPVAEI.
Retrocopy FLLNLHSEENIQKPFSAGFKRTSTLIVQDQEELCNGKCKSEQLCRSQSLLLTSSTRRNSY>INTPVAEIT

Parental  MKPNVGQGSTSVQTAMESELGESSATINKRLCKSTIELSENSLLPASSMLTGTQSLLQPHLERVAIDALQ
          MKPNVGQGSTSVQTAMESELGESSATINKRLCKSTIELSE.SLLPASS.LTGTQSLLQPHLERVAIDALQ
Retrocopy MKPNVGQGSTSVQTAMESELGESSATINKRLCKSTIELSEDSLLPASSVLTGTQSLLQPHLERVAIDALQ

Parental  LCCLLLPPPNRRKLQLLMRMISRMSQNVDMPELHDAMGTRSLMIHTFSRCVLCCAEEVDLDELLAGRLVS
          LCCLL.PPPN.RKLQLLMRMISRMSQNVDMP.LHDAMG.RSL.IHTFS.CVLCCAEEVDLDELLAGRLVS
Retrocopy LCCLLFPPPNHRKLQLLMRMISRMSQNVDMPKLHDAMGARSLLIHTFSQCVLCCAEEVDLDELLAGRLVS

Parental  FLMDHHQEILQVPSYLQTAVEKHLDYLKKGHIENPGDGLFAPLPTYSYCKQISAQEFDEQKVSTSQAAIA
          FLMDH.QEILQVPSYLQTAVEKHLDYLK.GHIE.PG.GLFAPLPTYSY.KQISAQEFDEQK.STSQAAIA
Retrocopy FLMDHDQEILQVPSYLQTAVEKHLDYLKRGHIESPGGGLFAPLPTYSYGKQISAQEFDEQKISTSQAAIA

Parental  ELLENIIKNRSLPLKEKRKKLKQFQKEYPLIYQKRFPTTESEAALFGDKPTIKQPMLILRKPKFRSLRY
          ELLENI.KNRSLPLKE.......FQKEYPLIYQKRFPT.ESEAALFGDKPTIKQPMLILRKPKF.SLRY
Retrocopy ELLENIVKNRSLPLKEXXXXXX*FQKEYPLIYQKRFPTMESEAALFGDKPTIKQPMLILRKPKFCSLRY

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	0.05 RPM	0.11 RPM
SRP007412_cerebellum	0.04 RPM	0.00 RPM
SRP007412_heart	0.03 RPM	0.06 RPM
SRP007412_kidney	0.05 RPM	0.03 RPM
SRP007412_liver	0.00 RPM	0.16 RPM
SRP007412_testis	0.00 RPM	38.89 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1041 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1041 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1041 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1545
Gorilla gorilla	retro_ggor_1176

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013839	1 retrocopy	retro_cpor_735,
Homo sapiens	ENSG00000024526	2 retrocopies	retro_hsap_1545, retro_hsap_4206,
Gorilla gorilla	ENSGGOG00000016316	1 retrocopy	retro_ggor_1176,
Macaca mulatta	ENSMMUG00000017766	1 retrocopy	retro_mmul_1176,
Mus musculus	ENSMUSG00000028175	1 retrocopy	retro_mmus_3028,
Nomascus leucogenys	ENSNLEG00000009334	1 retrocopy	retro_nleu_2931,
Otolemur garnettii	ENSOGAG00000000934	1 retrocopy	retro_ogar_1907,
Pongo abelii	ENSPPYG00000001248	1 retrocopy	retro_pabe_3441,
Pan troglodytes	ENSPTRG00000000847	2 retrocopies	retro_ptro_1041 , retro_ptro_2855,