RetrogeneDB ID: retro_ptro_2855

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:104645419..104647384(+)
• Located in intron of: ENSPTRG00000021226

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_2855
TTATCTCAGGAAAATTCCGAGAAAATAAAGCATGAAATAATCAATGAAGATCAAGAAAATGCAGTTGATAATAGAAAACT
AAGCCAGGAAGATGTTGAAGAAATTTGGAGATATGTTATTCTGATCTACCTGCAAGCCATTTTAGGTGTGCCATCCCTAG
AAGAAGTCATAAATCCAAAACAAGTAATTCCCCAATATATAATGTACAACATGGCCAATACAAGTAAACATGGAGTAGTT
ACACTACAAAACAAATCAGATGACCTCCCTCACTGGGTATTATCTGCCATGAAGTGCCTAGCAAATTGGCCAAGAAGTGA
TGATACGAATAATCCAACTTATGTTGGATTTGAACAAGATATATTCAGCACAATCACAGATTATTTTCTAGATCTCCTTG
AACCTCTCCTTACTTTTGAAATTACGAATTATTTGTGAACATTTTGGTTGTTTGTGGCTATGTCATAGTTTCAGATAGAT
CCAGTGGGATACATAGAATCCAAGATGATCCACAGTCTTAAAAATTCCTTCAGAGTTTGAATTCCTTCAAATCAATGGAG
TGCCTTCTTCTCAGTCTGCTTCATAGAGGAAAAAGAAGAATCAGATTCTACTGAGAGACTACGGATAAGCAATCCAGGAT
TTCAAGAAAGAAGTGCTAAGAAAATGCAGCTAGTTAATTTAAGAAACAGAGGAGTGAGTGCTAATGACATAATGGGAGGA
AGCTGTCATAATTTAATAGGGTTAAGTGGTATGCATGATCTGTCCTCTAATAGCAAACCAAGTTGCTGTTCTTTGGAAGG
AATTGTAGATGTGTCAGGGAATTCAAGTAAAGAGGCATCCAGTGTAAAGAGGCATCAATCTTTTCCAAACATAGAAGGAC
AAAATACTAAACTGTTTTTAGAGTCTAAGCCCTAACAGGAATTCCTGTTGAATCTTCGTTCAGAGGAAAATATTCAAAAG
CCATTCCGTGCTGGTTTTAAGAGAACCACTACTTTGACTGCTCAAGACCAAGAGGAGTTGTGTAATGGGAAATGCAAGTC
AAAACAGCTTTGTAGGTCTCAGAGTTTGCTTTTAAGAAGTAGTACAAGAAGGAATAGTTGTATCAATACACCAGTGGCTG
AAATGATCATGAAACCAAATGTTGGACAAAGCAGCACAAGTGTGCAAACAGCTATGCAAAGTGAACTCGGAGAGTCTAGT
GCTGCAATCAATAAAAGACTCTGCAAAAGTTCAATAGAATTTTCAGAAAATTCTTTACTTCCAGCTTCTTCTGTGTTGAC
TGGTACACGAAGTTTGCTGCAACCTCATTTAGAGAGGGTTGCCATCGATGCGCTACAATTGTGTCGTTTGTTACTTCTGC
CACCAAATTGTAGAAAGCTTCAACTTTTAATGCGTATGATTTCCCAAATGAGTCAAAATGTTGATATGCCCAAACTTCAT
GATGCAATGGGCATGAAATCACCGATGATACATACCTTTTCTCGATGTGTGCTATGCTGTGCTGAAAAAGTGGATCTTGA
TAAGCTTCTGGCTGGAAGATTAGTTTCTTTCTTACTGGATCATCATCAGGAAATTCTTCAAGTACCAACTTATTTACAGA
CTGCAGTGGAAAAACATCTTGAATACTTATAAAAGGGACATATTGAAAATCCTGGAGATGGACTATTTGTTCCTTTGCCA
ACTTATTCATACTGTAAGCAGATTAGTGCTCAGGACTTTGAAAAGCAAAAAGTTTCTACCTCTCAAGCTGCAATTACAGA
ACTTATAGAAAATGTTATTAAAAACAAGAGTTTACCTCTAAAGGAGAAAAGAAAAAAACTAAAACAGTTTCAGAAGGAAT
ACCCCTTGATATATCAGAAAAGATTTCCAACCACGGAGAGTGAAGCAGCACTTTTTGGTGACAAACCTACAATCAAGCAA
CCAATGCTGATTTTAAGAAAACCAAAGTTTTGTAGTCTAAGATAC

Alignment

ORF - retro_ptro_2855 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.84 %
• Parental protein coverage: 81.03 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LSQENGEKIKHEIINEDQENAIDNRELSQEDVEEVWRYVILIYLQTILGVPSLEEVINPKQVIPQYIMYN
          LSQEN.EKIKHEIINEDQENA.DNR.LSQEDVEE.WRYVILIYLQ.ILGVPSLEEVINPKQVIPQYIMYN
Retrocopy LSQENSEKIKHEIINEDQENAVDNRKLSQEDVEEIWRYVILIYLQAILGVPSLEEVINPKQVIPQYIMYN

Parental  MANTSKRGVVILQNKSDDLPHWVLSAMKCLANWPRSNDMNNPTYVGFERDVFRTIADYFLDLPEPLLTFE
          MANTSK.GVV.LQNKSDDLPHWVLSAMKCLANWPRS.D.NNPTYVGFE.D.F.TI.DYFLDL.EPLLTFE
Retrocopy MANTSKHGVVTLQNKSDDLPHWVLSAMKCLANWPRSDDTNNPTYVGFEQDIFSTITDYFLDLLEPLLTFE

Parental  Y-YELFVNILVVCGYITVSDRSSGIHKIQDDPQSSKFLHLNNLNSFKSTECLLLSLLHR-EKNKEESDST
          ..YELFVNILVVCGY..VSDRSSGIH.IQDDPQS.KF..L..LNSFKS.ECLLLSLLHR.EK....S..T
Retrocopy I<YELFVNILVVCGYVIVSDRSSGIHRIQDDPQS*KF--LQSLNSFKSMECLLLSLLHR>EKEESDS--T

Parental  ERLQISNPGFQERCAKKMQLVNLRNRRVSANDIMGGSCHNLIGLSNMHDLSSNSKPRCCSLEGIVDVPGN
          ERL.ISNPGFQER.AKKMQLVNLRNR.VSANDIMGGSCHNLIGLS.MHDLSSNSKP.CCSLEGIVDV.GN
Retrocopy ERLRISNPGFQERSAKKMQLVNLRNRGVSANDIMGGSCHNLIGLSGMHDLSSNSKPSCCSLEGIVDVSGN

Parental  SSKEASSV-FHQSFPNIEGQNNKLFLESKPKQEFLLNLHSEETIQKPFSAGFKRNSTLTVQDQEELYNGK
          SSKEASSV..HQSFPNIEGQN.KLFLESKP.QEFLLNL.SEE.IQKPF.AGFKR..TLT.QDQEEL.NGK
Retrocopy SSKEASSVKRHQSFPNIEGQNTKLFLESKP*QEFLLNLRSEENIQKPFRAGFKRTTTLTAQDQEELCNGK

Parental  CKSKQLCRSQSLLLRSSTRRNSYINTPVAEIIMKPNVGQGSTSVQTAMESELGESSATINKRLCKSTIEL
          CKSKQLCRSQSLLLRSSTRRNS.INTPVAE.IMKPNVGQ.STSVQTAM.SELGESSA.INKRLCKS.IE.
Retrocopy CKSKQLCRSQSLLLRSSTRRNSCINTPVAEMIMKPNVGQSSTSVQTAMQSELGESSAAINKRLCKSSIEF

Parental  SENSLLPASSMLTGTQSLLQPHLERVAIDALQLCCLLLPPPNRRKLQLLMRMISRMSQNVDMPELHDAMG
          SENSLLPASS.LTGT.SLLQPHLERVAIDALQLC.LLL.PPN.RKLQLLMRMIS.MSQNVDMP.LHDAMG
Retrocopy SENSLLPASSVLTGTRSLLQPHLERVAIDALQLCRLLLLPPNCRKLQLLMRMISQMSQNVDMPKLHDAMG

Parental  TRSLMIHTFSRCVLCCAEEVDLDELLAGRLVSFLMDHHQEILQVPSYLQTAVEKHLDYLKKGHIENPGDG
          ..S.MIHTFSRCVLCCAE.VDLD.LLAGRLVSFL.DHHQEILQVP.YLQTAVEKHL.YL.KGHIENPGDG
Retrocopy MKSPMIHTFSRCVLCCAEKVDLDKLLAGRLVSFLLDHHQEILQVPTYLQTAVEKHLEYL*KGHIENPGDG

Parental  LFAPLPTYSYCKQISAQEFDEQKVSTSQAAIAELLENIIKNRSLPLKEKRKKLKQFQKEYPLIYQKRFPT
          LF.PLPTYSYCKQISAQ.F..QKVSTSQAAI.EL.EN.IKN.SLPLKE......QFQKEYPLIYQKRFPT
Retrocopy LFVPLPTYSYCKQISAQDFEKQKVSTSQAAITELIENVIKNKSLPLKEXXXXXXQFQKEYPLIYQKRFPT

Parental  TESEAALFGDKPTIKQPMLILRKPKFRSLRY
          TESEAALFGDKPTIKQPMLILRKPKF.SLRY
Retrocopy TESEAALFGDKPTIKQPMLILRKPKFCSLRY

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	0.11 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.06 RPM
SRP007412_kidney	0.03 RPM	0.03 RPM
SRP007412_liver	0.03 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_2855 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2855 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2855 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4206
Macaca mulatta	retro_mmul_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 ,