RetrogeneDB ID: retro_ptro_1064

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:57235246..57237041(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX18
• Ensembl ID: ENSPTRG00000012391
• Aliases: None
• Description: None

Sequence

>retro_ptro_1064
ATGTCTTACCTGCTGATGAAACTCCTGAGCAAGAAGATCAAGAAGCAGAACCTCAAAATGCACAACAGAACCTAAAGTTG
CCGGGGGCCTCAAATCTGACCCTATCAGAAACTCAAAACGGAGGTGTGTCTGAAGAAACGATGGGAGGTGGAAAGGTTAA
AAAATCAAAACATTCTGTGAATGTGGGGTTATCAGAAGCTCAAGATGGAGATGTGTCTCAAGAAACAGTGGAAAATGTAA
AAGTTCAAAAATCTCCCCAGAAATCCACTGTATTAACAAACGGAGAGACAGCAATGCAGTCTCCCAATTCAGAATCAAAA
AAGAAAAAGAAGAAAAAGAGAAAAATGGTGAATGATTCTGGGCCTGATGCAAAAAAAAAAGCAAAAACTGAAAACAAAGG
GGAATCTAAAGAATAAAGTGCCAAGACTCCCAAAGAAACAGAAAATAATCTGGAGAAGCCAGATAATGAGGAAGATAACC
GTGAGGTGCCCAGCCTGCGCCTGAGACTGACAGGAGCTTTTGACGATACTTCATGTGCTTCTCTATCTAATCTTGTCAAT
GAAAACACTTTGAAGGCAATAAAAGAAATAAGCTTTACGAACATGACTGAAATTCAGCATAAAACTATCAGATCACTCCT
GGAAGGCAGGGATCTTCTAGCAGCTACAAAAACAGGCAGTGGTAAACCCTGGCTTTTCTCATTCCTGCAGTTGAACTCAC
TGTTAAGTTAAAGTTCATGCCCACGAATAGACCAGGGGTCTTTATTCTCTCACCTACTAGAGAACTAGCCATGCAAATTT
TTGGTGGTCTTAAGGAGCTAATACTCACCACATGCATACCTATGGGTTGATAATGGGTGGCGGTAACACATCTGCTGAAG
CACAGAAACTTGCTAATGGGATTAACATCATTGTGGCCACACCAGGCCGTCTGCTTGACTATATGCAGAATACACCAGGG
TTTATGTATAAAAACCTACAATATTTGGTTATTGATGAAGCTGATAGAATCTTGGATGTTGGGTTTGAAGAGGAATTAAA
GCAAATTATTAAACTTTTGCCAACATGCAGACACACTATGCTCTTATCTGCCACCCAAACTCAAAAAGTTGAAGACCTGG
CAAGGATTTCTCTGAAAAAAGGAGCCATTGTATGTTGGCGATGATGATAAAGCTAATGCAACAGTGGATGGTCTTGAGCA
GGAATACGTTGTTTGTCCCTCTGAAAAAAGATTCCTTCTGCCCTTTGCTGTCCTTAAGAAGAACCGAAAGAAGAAGGTTA
TGGTCTTCTTTTCATCTTGTATGTCTGTGAAATATCACTATGAGTTGCTAAATTACATGAATTTGCCCATCTTGGCCATT
CATGGAAAGCAAAAGCAAAATAAGGGTACAACCACATTCTTCCAGTTCTGCAAAGCAGATTCAGGAATACTATTGTGTAT
GGATGTGGCAGCAAGAGGACTGGACATTCCTGAAGTCGACTGGATTGTTCAGCATGACCCTCTGGATGACCCTAAGGAAT
ATATTCATCGTGTAAGCAGAACAGCCAGAGGTCTAAATGGGAGAGGGCATGCCTTGCTCATTTTGTGCCCAGAAGAAATG
GGGTTCCTTCACTACTTGAAACAATCCAAGTTTCCATTAAGTGAATTTGACTTTTCCTGGTCTAAAATTTCTGACATTCA
GTCTCAGCTTGAGAAATTAATTGGAAAGAACTACTTTCTTCATAAGGCAGCCCAGGAAGCATATAAGTCATACACACGAG
CCTAGGATTCCCATTCTCTAAAACAGATCTTTAAT

Alignment

ORF - retro_ptro_1064 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.16 %
• Parental protein coverage: 89.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSHLPMKLLRKKIEKRNLKLR-QRNLKLQGASNLTLSETQNGDVSEETMGSRKVKKSKQKPMNVGLSETQ
          MS.L.MKLL.KKI.K.NLK...Q.NLKL.GASNLTLSETQNG.VSEETMG..KVKKSK....NVGLSE.Q
Retrocopy MSYLLMKLLSKKIKKQNLKMH<QQNLKLPGASNLTLSETQNGGVSEETMGGGKVKKSKHS-VNVGLSEAQ

Parental  NGDVSQEAVENVKVKKSPQKSSVLTNGEAAMQSSNSESKKKKKKKRKMVNDAEPDTKKAKTENKGKSEEE
          .GDVSQE.VENVKV.KSPQKS.VLTNGE.AMQS.NSE...........VND..PD..............E
Retrocopy DGDVSQETVENVKVQKSPQKSTVLTNGETAMQSPNSEXXXXXXXXXXXVNDSGPDXXXXXXXXXXGESKE

Parental  -SAETPKETENNVDKPDNDEDESEVPNLPLGLTGAFEDTSFASLCNLVNENTLKAIKEMGFTNMTEIQHK
          .SA.TPKETENN..KPDN.ED..EVP.L.L.LTGAF.DTS.ASL.NLVNENTLKAIKE..FTNMTEIQHK
Retrocopy *SAKTPKETENNLEKPDNEEDNREVPSLRLRLTGAFDDTSCASLSNLVNENTLKAIKEISFTNMTEIQHK

Parental  SIRPLLEGRDLLAAAKTGSGK-TLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELM-T
          .IR.LLEGRDLLAA.KTGSGK.TLAFLIPAVEL.VKL.FMP.N..GV.ILSPTRELAMQ.FG.LKEL..T
Retrocopy TIRSLLEGRDLLAATKTGSGK<TLAFLIPAVELTVKLKFMPTNRPGVFILSPTRELAMQIFGGLKELI<T

Parental  HHVHTYGLIMGGSNRSAEAQKLANGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEE
          HH.HTYGLIMGG.N.SAEAQKLANGINIIVATPGRLLD.MQNTPGFMYKNLQ.LVIDEADRILDVGFEEE
Retrocopy HHMHTYGLIMGGGNTSAEAQKLANGINIIVATPGRLLDYMQNTPGFMYKNLQYLVIDEADRILDVGFEEE

Parental  LKQIIKLLPTRRQTMLFSATQTRKVEDLARISL-KKEPLYVGVDDDKANATVDGLEQGYVVCPSEKRFLL
          LKQIIKLLPT.R.TML.SATQT.KVEDLARISL.KKEPLYVG.DDDKANATVDGLEQ.YVVCPSEKRFLL
Retrocopy LKQIIKLLPTCRHTMLLSATQTQKVEDLARISL>KKEPLYVG-DDDKANATVDGLEQEYVVCPSEKRFLL

Parental  LFTFLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIHGKQKQNKRTTTFFQFCNADSGTLLCTDVA
          .F..LKKNRKKK.MVFFSSCMSVKYHYELLNY..LP.LAIHGKQKQNK.TTTFFQFC.ADSG.LLC.DVA
Retrocopy PFAVLKKNRKKKVMVFFSSCMSVKYHYELLNYMNLPILAIHGKQKQNKGTTTFFQFCKADSGILLCMDVA

Parental  ARGLDIPEVDWIVQYDPPDDPKEYIHRVGRTARGLNGRGHALLILRPEELGFLRYLKQSKVPLSEFDFSW
          ARGLDIPEVDWIVQ.DP.DDPKEYIHRV.RTARGLNGRGHALLIL.PEE.GFL.YLKQSK.PLSEFDFSW
Retrocopy ARGLDIPEVDWIVQHDPLDDPKEYIHRVSRTARGLNGRGHALLILCPEEMGFLHYLKQSKFPLSEFDFSW

Parental  SKISDIQSQLEKLIEKNYFLHKSAQEAYKSYIRAYDSHSLKQIFN
          SKISDIQSQLEKLI.KNYFLHK.AQEAYKSY.RA.DSHSLKQIFN
Retrocopy SKISDIQSQLEKLIGKNYFLHKAAQEAYKSYTRA*DSHSLKQIFN

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	0.04 RPM	18.52 RPM
SRP007412_cerebellum	0.00 RPM	42.48 RPM
SRP007412_heart	0.00 RPM	23.87 RPM
SRP007412_kidney	0.00 RPM	31.98 RPM
SRP007412_liver	0.00 RPM	26.09 RPM
SRP007412_testis	0.00 RPM	36.88 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1064 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1064 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1064 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1579
Gorilla gorilla	retro_ggor_1201
Pongo abelii	retro_pabe_1301
Callithrix jacchus	retro_cjac_753

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
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,