RetrogeneDB ID: retro_ggor_1201

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 15:39057943..39059736(-)
• 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_1201
ATGTCTCACCTGCTGATGAAACTCCTGAGCAAGAACATCAAGAAGCGGTACCTCAAAATGCACACCGGAGCCTAAAGTTG
CCGGGGGCCTCAAATCTGACCCTATCAGAAATTCAAAACGGAGGTGTGTCTGAAGAAACGATGGGAGGTGGAAAGGTTAA
AAAAATCAAAACATTCTGTGCATGTGGGGTTATCAGAAGCTCAAGATAGAGATGTGTCTCAAGAAACAGTGGAAAATGTA
AAAGTTCAAAAATCTCCCCAGAAATCCACTGTATTAACAAACGGAGAGACAGCAATGCAGTCTCCCAATTCAGAATCAAA
AAAGAAAAAGAAGAAAAAGAGAAAAATGGTGAATGATGCAGGCCTGATGCAAAAAAAGGCAAAAACTGAAAACAAAGGGG
AATCTAAAGAAGAAAGTGTCAAGACTCCCAAAGAAACAGAAAATAATCTGGAGAAGCCAGATAATGAGGAAGATAACCAT
GAGGTGCCCAGCCTGCGCCTGAGACTGACAGGAGCTTTTGAGGATACTTCATTTGCTTCTCTATCTAATCTTGTCAATGA
AAACACTTTGAAGGCAATAAAAGAAATGAGCTTTACAAACATGACTGAAATTCAGCATAAAAGTATCAGATCACTCCTGG
AAGGCAGGGATCTTCTAGCAGCTGCAAAAACAGGCAGTGGTAAACCCTGGCTTTTCTCATTCCTGCAGTTGAACTCACTG
TTAAGTTAAAGTTCATGCCCACGAATAGACCAGGGGTCTTTATTCTCTCACCTACTAGATAACTAGCCATGCAAATTTTT
GGTGGTCTTAAGGAGCTAACACTCACCACATGCATACCTATGGGTTGATAATGGGTGGCGGTAACACATCGGCTGAAGCA
CAGAAACTTGCTAATGGGATTAACATCACTGTGGCCACACCAGGCCATCTGCTTGACTATATGCAGAATACACCAGGGTT
TATGTATAAAAACCTACAATATTTGGTTATTGATGAAGCTGATAGAATCTTGGATCTTGGGTTTGAAGAGGAATTAAAGC
AAATTATTAAACTTTTGCCAACAGGCATACACACTATGCTCTTATCTGCCACCCAAACTCGAAAAGTTGAAGACCTGGCA
AGGATTTCTCTGAAAAAAGGAGCCATTGTATGTTGGCGATGATGATAAAGCTAATGCAACAGTGGATGGTCTTGAGCAGG
GATACGTTGTTTGTCCCTCTGAAAAAAGATTCCTTCTGCCCTTTGCTGTCCTTAAGAAGAACCAAAAGAAGAAGGTTATG
GTCTTCTTTTCATCTTGTATGTCTGTGAAATACCACTATGAGTTGCTAAATTACATGGATTTGCCCATCTTGGCCATTCA
TGGAAAGCAAAAGCAAAATAAGGGTACAACCACATTCTTCCAGTTCTGCAAAGCAGATTCAGGAATACTATTATGTATGG
ATGTGGCAGCAAGAGGACTGGACATTCCTGAAGTCGACTGGATTGTTCAGCATGACCCTCTGGATGACCCTAAGGAATAT
ATTCATCGTGTAAGCAGAACAGCCAGAGGTCTAAATGGGAGAGGGCATGCCTTGCTCATTTTGTGCCCAGAAGAAATGGG
GTTCCTTCACTACTTGAAACAATCCAAGTTTCCATTAAGTGAATTTGACTTTTCCTGGTCTAAAATTTCTGACATTCAGT
CTCAGGTTGAGAAATTAATTGAAAAGAACTACTTTCTTCATAAGACAGCCCAGGAAGCATATAAGTCATACACACGAGCC
TATGATTCCCATTCTCTAAAACAGATCTTTAAT

Alignment

ORF - retro_ggor_1201 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.72 %
• Parental protein coverage: 89.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSHLPMKLLRKKIEKRNLKLR-QRNLKLQGASNLTLSETQNGDVSEETMGSRKVKK-SKQKPMNVGLSET
          MSHL.MKLL.K.I.KR.LK....R.LKL.GASNLTLSE.QNG.VSEETMG..KVKK.SK.....VGLSE.
Retrocopy MSHLLMKLLSKNIKKRYLKMH<HRSLKLPGASNLTLSEIQNGGVSEETMGGGKVKK>SKHS-VHVGLSEA

Parental  QNGDVSQEAVENIKVKKSPQKSTVLTNEEAAMQSSNSESKKKKKKKRKMVNDAEPAKDTKKAKTENKGKS
          Q..DVSQE.VEN.KV.KSPQKSTVLTN.E.AMQS.NSE...........VNDA...............K.
Retrocopy QDRDVSQETVENVKVQKSPQKSTVLTNGETAMQSPNSEXXXXXXXXXXXVNDAGLMXXXXXXXXXXESKE

Parental  EEESAETPKETENNVEKPDNDEDESEVPSLPLGLTGAFEDTSFASLCNLVNENTLKAIKEMGFTNMTEIQ
          E..S..TPKETENN.EKPDN.ED..EVPSL.L.LTGAFEDTSFASL.NLVNENTLKAIKEM.FTNMTEIQ
Retrocopy E--SVKTPKETENNLEKPDNEEDNHEVPSLRLRLTGAFEDTSFASLSNLVNENTLKAIKEMSFTNMTEIQ

Parental  HKSIRPLLEGRDLLAAAKTGSGK-TLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELM
          HKSIR.LLEGRDLLAAAKTGSGK.TLAFLIPAVEL.VKL.FMP.N..GV.ILSPTR.LAMQ.FG.LKEL.
Retrocopy HKSIRSLLEGRDLLAAAKTGSGK<TLAFLIPAVELTVKLKFMPTNRPGVFILSPTR*LAMQIFGGLKELT

Parental  -THHVHTYGLIMGGSNRSAEAQKLANGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFE
          .THH.HTYGLIMGG.N.SAEAQKLANGINI.VATPG.LLD.MQNTPGFMYKNLQ.LVIDEADRILD.GFE
Retrocopy <THHMHTYGLIMGGGNTSAEAQKLANGINITVATPGHLLDYMQNTPGFMYKNLQYLVIDEADRILDLGFE

Parental  EELKQIIKLLPTRRQTMLFSATQTRKVEDLARISL-KKEPLYVGVDDDKANATVDGLEQGYVVCPSEKRF
          EELKQIIKLLPT...TML.SATQTRKVEDLARISL.KKEPLYVG.DDDKANATVDGLEQGYVVCPSEKRF
Retrocopy EELKQIIKLLPTGIHTMLLSATQTRKVEDLARISL>KKEPLYVG-DDDKANATVDGLEQGYVVCPSEKRF

Parental  LLLFTFLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIHGKQKQNKRTTTFFQFCNADSGTLLCTD
          LL.F..LKKN.KKK.MVFFSSCMSVKYHYELLNY.DLP.LAIHGKQKQNK.TTTFFQFC.ADSG.LLC.D
Retrocopy LLPFAVLKKNQKKKVMVFFSSCMSVKYHYELLNYMDLPILAIHGKQKQNKGTTTFFQFCKADSGILLCMD

Parental  VAARGLDIPEVDWIVQYDPPDDPKEYIHRVGRTARGLNGRGHALLILRPEELGFLRYLKQSKVPLSEFDF
          VAARGLDIPEVDWIVQ.DP.DDPKEYIHRV.RTARGLNGRGHALLIL.PEE.GFL.YLKQSK.PLSEFDF
Retrocopy VAARGLDIPEVDWIVQHDPLDDPKEYIHRVSRTARGLNGRGHALLILCPEEMGFLHYLKQSKFPLSEFDF

Parental  SWSKISDIQSQLEKLIEKNYFLHKSAQEAYKSYIRAYDSHSLKQIFN
          SWSKISDIQSQ.EKLIEKNYFLHK.AQEAYKSY.RAYDSHSLKQIFN
Retrocopy SWSKISDIQSQVEKLIEKNYFLHKTAQEAYKSYTRAYDSHSLKQIFN

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	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_1201 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1201 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1579
Pan troglodytes	retro_ptro_1064
Pongo abelii	retro_pabe_1301
Callithrix jacchus	retro_cjac_753

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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,