RetrogeneDB ID: retro_ggor_535

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 10:104178923..104180526(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX18
• Ensembl ID: ENSGGOG00000028420
• Aliases: None
• Description: None

Sequence

>retro_ggor_535
GAAGGAGAATCTGAAGAATAAAGTGCCGAGACTCCTAAAGAAACAGAAAATAATGTGGAGAAGCTAGATAATGATGAAGA
TGACAGTGAGGTGCCCAGCCTGCTCCTGGGACTGACAGGAGCTTTTGAGGATACTTCATTTTCTTCTCTATGTAATCTTG
TCAATGAAAACACTCTGAAGGTAATAAAAGAAATGGGCTTTACAAACATGGCTGAAATTCAGCATAAAACTATCAGACCA
CTTCTGGAAGGCAGGGATCTTCTAGCAGCTGTAAAAACAGGCAGTGGTAAAACCTTGGCTGTTCTCATCCCTGCAGTTGA
ACTCGTTGTTAAGTTAAAGTTCATGCCCAGGAATGGAACAGGGGTCCTTATTCTCTCACCTACTAGACAACTAGCCATGC
AAACTTTTGGTGTTCTTAAAGAGCTAATGACTCACCATGTGCACACCTATGGGTTGATAATAGGTGGCAGTAACAGATCT
GCTGAAGCACAGAAACTTGCTAATGGGATCAACATCATTGTGGTCACACCAGGCCGTCTGCTGGACCATACGCAGAATAC
CCCAGGGTTTATGTATAAAAACCTGCAGGGTCTGGCTATTGATGAAGCTGATTGTATCTTGGACGTTGGGTTTGAAGATA
AATTAAAGCAAATTATTAAACTTTTGCCAACACGCAGGCAGACTATGCTCTTTTCTGCCACCTAAACTCGAAAAGTTGAG
GACCTGGCAAGGATTTCTCTGAAAAAGGAACCATTGTATGTTGGTGTTGATGAAGATAAAGCTAATGCAACTGTGGATGG
TCTTGAGCAGGGATACTTTGTTTGTCCCTCTGAAAAGAGATACCTTCTGCTCTTTATATTCCTTAAGAAGAACCGAAAGA
AGAAGCTCATGGTCTCCTTTTCAGCTTGTATGTCTGTGAAATACCCCTATGGGTTGCTGAAGTACATTGATTTGCTGTCT
TGGCCACTCATGGAAAGCAAAAGCAAAATAAGCATACAACCACATTCTTCTAGTTCTGCAACGCAGATTCAGGAACACTA
TTGTGTAAGGATGTGGCAGCAAGAGGACTGGACATTCCTGAAGTCAACTGGATTGTTCAGTATGACCCTCCAGATGACCC
TAAGGAATGTATTCATTGTGTGAGGAGAACAGCCAGAGGCCTAAATGGGGGAAGGCATGCCTTGTTCATTTTGCACCCAG
AAGAACTGGGTTTCCTTCACTACTTGAAACAATCCAAGGTTCCATTAAGTGAATTTGACTTTTCCTGATCTAAAATTTCT
GACATTCAGTCTCAGCTTGAGAAACTGATTGAAAAGAACTACTTTCTTCATAAGTCAGCCCAGGAAGCATATAAATCATA
CATACGAGCCTATGATTCCTATTCTCTGAAACAGATCTTTAACATTAATAACTTAAATTTGCCTCACATTGCTCTGTCAT
TTGGCTTCAAGTTGCCTCCCTTTGTTGATCTGAACATGAACAGCAATGAAGGCAAGCAGAAAAAGCAAGGAGGATTTGGC
TACCAGAAAACCAAGAAAGTTGAGAAGTCCATAATCTTTAAACACGTTAGCAAAAAGTCATCTGCAGCAGGCAGTTCCCT
CAC

Alignment

ORF - retro_ggor_535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.78 %
• Parental protein coverage: 80.06 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KGKSEEESAETPKETENNVEKPDNDEDESEVPSLPLGLTGAFEDTSFASLCNLVNENTLKAIKEMGFTNM
          .G.SEE.SAETPKETENNVEK.DNDED.SEVPSL.LGLTGAFEDTSF.SLCNLVNENTLK.IKEMGFTNM
Retrocopy EGESEE*SAETPKETENNVEKLDNDEDDSEVPSLLLGLTGAFEDTSFSSLCNLVNENTLKVIKEMGFTNM

Parental  TEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLK
          .EIQHK.IRPLLEGRDLLAA.KTGSGKTLA.LIPAVEL.VKL.FMPRNGTGVLILSPTR.LAMQTFGVLK
Retrocopy AEIQHKTIRPLLEGRDLLAAVKTGSGKTLAVLIPAVELVVKLKFMPRNGTGVLILSPTRQLAMQTFGVLK

Parental  ELMTHHVHTYGLIMGGSNRSAEAQKLANGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVG
          ELMTHHVHTYGLI.GGSNRSAEAQKLANGINIIV.TPGRLLDH.QNTPGFMYKNLQ.L.IDEAD.ILDVG
Retrocopy ELMTHHVHTYGLIIGGSNRSAEAQKLANGINIIVVTPGRLLDHTQNTPGFMYKNLQGLAIDEADCILDVG

Parental  FEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYVGVDDDKANATVDGLEQGYVVCPSEKR
          FE..LKQIIKLLPTRRQTMLFSAT.TRKVEDLARISLKKEPLYVGVD.DKANATVDGLEQGY.VCPSEKR
Retrocopy FEDKLKQIIKLLPTRRQTMLFSAT*TRKVEDLARISLKKEPLYVGVDEDKANATVDGLEQGYFVCPSEKR

Parental  FLLLFTFLKKNRKKKLMVFFSSCMSVKYHYELLNYIDL-PVLAIHGKQKQNKRTTTFFQFCNADSGTLLC
          .LLLF.FLKKNRKKKLMV.FS.CMSVKY.Y.LL.YIDL..VLA.HGKQKQNK.TTTFF.FCNADSGTLLC
Retrocopy YLLLFIFLKKNRKKKLMVSFSACMSVKYPYGLLKYIDL<AVLATHGKQKQNKHTTTFF*FCNADSGTLLC

Parental  TDVAARGLDIPEVDWIVQYDPPDDPKEYIHRVGRTARGLNGRGHALLILRPEELGFLRYLKQSKVPLSEF
          .DVAARGLDIPEV.WIVQYDPPDDPKE.IH.V.RTARGLNG..HAL.IL.PEELGFL.YLKQSKVPLSEF
Retrocopy KDVAARGLDIPEVNWIVQYDPPDDPKECIHCVRRTARGLNGGRHALFILHPEELGFLHYLKQSKVPLSEF

Parental  DFSWSKISDIQSQLEKLIEKNYFLHKSAQEAYKSYIRAYDSHSLKQIFNVNNLNLAQVALSFGFKVPPFV
          DFS.SKISDIQSQLEKLIEKNYFLHKSAQEAYKSYIRAYDS.SLKQIFN.NNLNL...ALSFGFK.PPFV
Retrocopy DFS*SKISDIQSQLEKLIEKNYFLHKSAQEAYKSYIRAYDSYSLKQIFNINNLNLPHIALSFGFKLPPFV

Parental  DLNVNSNEGKQKKRGGGGGFGYQKTKKVEKSKIFKHISRKSSD-SRQFSH
          DLN.NSNEGKQKK.GG...FGYQKTKKVEKS.IFKH.S.KSS..SRQF.H
Retrocopy DLNMNSNEGKQKKQGG---FGYQKTKKVEKSIIFKHVSKKSSA<SRQFPH

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	22.92 RPM
SRP007412_cerebellum	0.00 RPM	26.32 RPM
SRP007412_heart	0.00 RPM	4.88 RPM
SRP007412_kidney	0.00 RPM	34.92 RPM
SRP007412_liver	0.00 RPM	19.84 RPM
SRP007412_testis	0.00 RPM	43.82 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_535 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_535 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_608
Pan troglodytes	retro_ptro_448

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004950	2 retrocopies	retro_cfam_1404, retro_cfam_2116,
Echinops telfairi	ENSETEG00000017166	2 retrocopies	retro_etel_1919, retro_etel_297,
Homo sapiens	ENSG00000088205	6 retrocopies	retro_hsap_1361, retro_hsap_1579, retro_hsap_3223, retro_hsap_3561, retro_hsap_608, retro_hsap_834,
Gorilla gorilla	ENSGGOG00000028420	4 retrocopies	retro_ggor_1201, retro_ggor_2189, retro_ggor_2402, retro_ggor_535 ,
Microcebus murinus	ENSMICG00000017590	1 retrocopy	retro_mmur_1560,
Myotis lucifugus	ENSMLUG00000017607	1 retrocopy	retro_mluc_2279,
Macaca mulatta	ENSMMUG00000021343	1 retrocopy	retro_mmul_2192,
Monodelphis domestica	ENSMODG00000000533	1 retrocopy	retro_mdom_414,
Mus musculus	ENSMUSG00000001674	1 retrocopy	retro_mmus_2865,
Nomascus leucogenys	ENSNLEG00000011769	4 retrocopies	retro_nleu_1377, retro_nleu_1396, retro_nleu_266, retro_nleu_437,
Pongo abelii	ENSPPYG00000012796	4 retrocopies	retro_pabe_1128, retro_pabe_1301, retro_pabe_2670, retro_pabe_744,
Pan troglodytes	ENSPTRG00000012391	5 retrocopies	retro_ptro_1064, retro_ptro_2174, retro_ptro_2419, retro_ptro_448, retro_ptro_933,