RetrogeneDB ID: retro_ggor_1176

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 15:10145933..10147284(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DEPDC1
• Ensembl ID: ENSGGOG00000016316
• Aliases: None
• Description: None

Sequence

>retro_ggor_1176
TTGTTTCATTTCGTGGTAGTTGTTTGTGGCTACATAACAGTTTCAGATAGATCCAGTGGGATACATAAAATCCAAGATGA
TCCACAGTCTTCAAAATTCCTTCACTTAAACAATTTGAATTCCTTCAAATCAACTGAGTGCCTTCTTCTCAGTCTGCTTC
ATAGAGAAAAAAAAAACAAAGAAGAATCAGATTCTACTGAGAGACTACAGATAAGCAATCCAGGATTTCAAGAAAGATGT
GCTAAGAAAATGCAGCTAGTTAATTTAAGAAACAGAAGAGTGAGTGCTAATGACATAGTGGGAGGAAGTTGTCATAATTT
AATAGGGTTAAGTAATATGCATGATCTATCCTCTAACAGCAAACCAAGGTGCTATTCTTTGGAAGGAATTGTAGATGTGT
CAGGGAATTCAAGTAAAGAGGCATCCAGTGTCTTTCATCAATCTTTTCCGAACATAGAAGGACAAAATAATAAACTGTTT
TTAGAGTCTAAGCCCAAACAGGAATTCCTGTTGAATCTTCATTCAGAGGAAAATATTCAAAAGCCATTCAGTGCTGGTTT
TAAGAGAACCTCTACTTTGATTGTTCAAGACCAAGAGGAGTTGTGTAATGGGAAATGCAAGTCAGAACAGCTTTGTAGGT
CTCAGAGTTTGCTTTTAACAAGTAGTACAAGAAGGAATAGTTATTATCAATACACCAGTGGCTGAAATTACCATGAAACC
AAATGTTAGACAAGGCAGCACAAGTGTGCAAACAGCTATGGAAAGTGAACTTGGAGAGTCTAGTGCCACAATCAATAAAA
GACTCTGCAAAAGTACAATAGAACTTTCAGAAGATTGTTTACTTCCAGCTTCTTCTGTGTTGACTGGCACACAAAGTTTG
CTGCAACCTCATTTAGAGAGGGTTGCCATCAATGCTCTACAGTTATGTTGTTTGTTATTTCCCCCACCAAATCATAGAAA
GCTTCAACTTTTAATGCGTATGATTTCCCGAATGAGTCAAAATGTTGATATGCCCAAACTTCATGATGCAATGTGTGCAA
GATCACTGTTGATACATACCTTTTCTCAATGTGTGTTATGATGTGCTGAAGAAGTGGACCTTGATGAGCTTCTTGCTGGA
AGATTAGTTTCTTTCTTAATGGATCATGATCAGGAAATTCTTCAAGTACCCTCTTACTTGCAGACTGCAGTGGGAAAACA
TCTTGACTACTTAAAAAGGGGACATATTGAAAGTCCTGGAGATGGACTATTTGGTCCTTTGCCAACTTACTCATACAGTA
AGCAGATTAGTGCTCAGGAGTTTGATGAGCAAAAAATTTCTACCTCTCAAGCTGCAATTGCAGAACTTTTA

Alignment

ORF - retro_ggor_1176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.24 %
• Parental protein coverage: 62.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFVNILVVCGYITVSDRSSGIHKIQDDPQSSKFLHLNNLNSFKSTECLLLSLLHREKN-KEESDSTERLQ
          LF....VVCGYITVSDRSSGIHKIQDDPQSSKFLHLNNLNSFKSTECLLLSLLHR....KEESDSTERLQ
Retrocopy LFHFVVVVCGYITVSDRSSGIHKIQDDPQSSKFLHLNNLNSFKSTECLLLSLLHRXXXXKEESDSTERLQ

Parental  ISNPGFQERCAKKMQLVNLRNRRVSANDIMGGSCHNLIGLSNMHDLSSNSKPRCCSLEGIVDVSGNSSKE
          ISNPGFQERCAKKMQLVNLRNRRVSANDI.GGSCHNLIGLSNMHDLSSNSKPRC.SLEGIVDVSGNSSKE
Retrocopy ISNPGFQERCAKKMQLVNLRNRRVSANDIVGGSCHNLIGLSNMHDLSSNSKPRCYSLEGIVDVSGNSSKE

Parental  ASSVFHQSFPNIEGQNNKLFLESKPKQEFLLNLHSEENIQKPFSAGFKRTSTLTVQDQEELCNGKCKSKQ
          ASSVFHQSFPNIEGQNNKLFLESKPKQEFLLNLHSEENIQKPFSAGFKRTSTL.VQDQEELCNGKCKS.Q
Retrocopy ASSVFHQSFPNIEGQNNKLFLESKPKQEFLLNLHSEENIQKPFSAGFKRTSTLIVQDQEELCNGKCKSEQ

Parental  LCRSQSLLLRSSTRRNSY-INTPVAEIVMKPNVGQGSTSVQTAMERELGESSATINKRLCKSTIELSENS
          LCRSQSLLL.SSTRRNSY.INTPVAEI.MKPNV.QGSTSVQTAME.ELGESSATINKRLCKSTIELSE..
Retrocopy LCRSQSLLLTSSTRRNSY>INTPVAEITMKPNVRQGSTSVQTAMESELGESSATINKRLCKSTIELSEDC

Parental  LLPASSMLTGTQSLLQPHLERVAIDALQLCCLLLPPPNRRKLQLLMRMISRMSQNVDMPKLHDAMGTRSL
          LLPASS.LTGTQSLLQPHLERVAI.ALQLCCLL.PPPN.RKLQLLMRMISRMSQNVDMPKLHDAM..RSL
Retrocopy LLPASSVLTGTQSLLQPHLERVAINALQLCCLLFPPPNHRKLQLLMRMISRMSQNVDMPKLHDAMCARSL

Parental  MIHTFSRCVLCCAEEVDLDELLAGRLVSFLMDHHQEILQVPSYLQTAVEKHLDYLKKGHIENPGDGLFAP
          .IHTFS.CVL.CAEEVDLDELLAGRLVSFLMDH.QEILQVPSYLQTAV.KHLDYLK.GHIE.PGDGLF.P
Retrocopy LIHTFSQCVL*CAEEVDLDELLAGRLVSFLMDHDQEILQVPSYLQTAVGKHLDYLKRGHIESPGDGLFGP

Parental  LPTYSYCKQISAQEFDEQKVSTSQAAIAELL
          LPTYSY.KQISAQEFDEQK.STSQAAIAELL
Retrocopy LPTYSYSKQISAQEFDEQKISTSQAAIAELL

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	0.10 RPM	0.00 RPM
SRP007412_cerebellum	0.08 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	0.04 RPM
SRP007412_liver	0.00 RPM	0.05 RPM
SRP007412_testis	0.52 RPM	41.44 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1176 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1545
Pan troglodytes	retro_ptro_1041

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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,