RetrogeneDB ID: retro_pabe_1301

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:56771450..56773253(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX18
• Ensembl ID: ENSPPYG00000012796
• Aliases: None
• Description: ATP-dependent RNA helicase DDX18 [Source:RefSeq peptide;Acc:NP_001126280]

Sequence

>retro_pabe_1301
ATGTCTCACCTGCTGATGAAACTCCTGAGCAAGAAGATCAAGAAGCAGAACCTCAAAATGCACAACAGATCCTAAAGTTG
CCGGGGGCCTCAAATCTGACCCTATCAGAAACTCAAAACAGAGATGTGTCTGAAGAAACAGTGGGAGGTGGAAAGGTTAA
AAAAATCAAAACGTTCTATGAATGTGGGGTTATCAGAAGCTCAAGATGGAGATGTGTCTCAAGAAACAGTGGAAAATGTA
AAAGTTCAAAAATCTCCCCAGAAATCCACTGTATTAACAAATGGAGAGACAGCAATGCAGTCTCCCAATGCAGAATCAAA
AAAGAAAAAGAAGAAAAAGAGAAAAATGGTAAATGATGCTGGGCCTGATGCGAAAAAAAAAAAAAAAGCAAAAACTGAAA
ACAAAAGGGAATCTAAAGAAGAAAGTGCCGAGACTCCCAAAGAAACAGAAAATAATGTGGAGAAGCCAGATAATGAGGAA
GATGATAGTGAGGTGCCCAGCCTGCCCCTGAGACTGACAGGAGCTTTTGAGGATACTTCATTTGCTTCTCTATCTAATCT
TGTCAATGAAAATACTTTGAAGGCAATAAAAGAAATGGGCTTTACGAACATGACTGAAATTCAGCATAAAAGTATCAGAC
CACTCCTGGAAGGCAGAGATCTTCTAGCAGCTGCAAAAACAGGCAGTGGTAAACTCTGGCTTTTCTCATTACTGCAGTTG
AACTCACAGTTAAGTTAAAGTTCATGCCCACGAATAGACCAGGGGTCTTTATTCTCTCACCTACTAGAGAACTAGCCATG
CAAATTTTTGGTGTTCTTAAGGAGCTAATGGCTCACCACATGCATACCTATGGGTTGATAATGGGTGGCGGTAACACATA
TGCTGAAGCACAGAAACTTGCTAATGGGATCAACATCATTGTGGCCACACCAGGCCGTCTGCTTGACTATATGCAGAATA
TACCAGGGTTTATATATAAAAACCTACAATGTTTGGTTATTAATGAAGCTGATAGAATCTTGGATGTTGGGTTTGAAGAG
GAATTAAAGCAAATTATTAAACTTTTGCCAACATGCAGACACACTATGCTCTTATCTGCCACCCTAACTCGAAAAGTTGA
AGACCTGGCAAGGATTTCTCTGAAAAAAGTAGCCATTGTGTGTTGGCGGTGATGATAAAGCTAATACAACAGTGGATGGT
CTTGAGCAGGGATACGTTGTTTGTCCCTCTGAAAAAAGATTCCTTCTGCCCTTTACTGTCCTTAAGAAGAACCGAAAGAA
GAAGGTTATGGTCTTCTTTTCATCTTGCATATCTGTGAAATATCACTATGAGTTGCCAAACTACGTGGATTTGCCCATCT
TGGCCATTCATGGAAAGCAAAAGCAAAATAAGGGTACGACCACATTCTTCCAGTTCTGCAACGCAGATTCAGGAATACTA
TTATGTATGGATGTGGCAGCAAGAGGACTGGACATTCCTGAAGTCAACTGGATTGTTCAGCATGACCCTCTGCATGACCC
TAAGGAATATATTCATCGTGTAAGCAGAACAGCCAGAGGTCTAAATGGGAGAGGTCATGCCTTGCTCATTTTGTGCCCAG
AAGAAATGGGGTTCCTTCACTACTTGAAACAATCCAAGTTTCCATTAAGTGAATTTGACTTTTCCTGGTCTAAAATTTCT
GACATTCAGTCTCAGCTTAAGAAATTGATTGAAAAGAACTACTTTCTTCATAAGTCAGGCCAGGAAGCGTATGAGTCATA
CACACGAACCTATGATTCCCATTCTCTGAAACAGATCTTTAAT

Alignment

ORF - retro_pabe_1301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.38 %
• Parental protein coverage: 96. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSHLPMKLLRKKIEKRNLKLRQRN-LKLQGASNLTLSETQNGDVSEETMGSRKVKK-SKQKPMNVGLSET
          MSHL.MKLL.KKI.K.NLK...R..LKL.GASNLTLSETQN.DVSEET.G..KVKK.SK...MNVGLSE.
Retrocopy MSHLLMKLLSKKIKKQNLKMHNRS<LKLPGASNLTLSETQNRDVSEETVGGGKVKK>SKRS-MNVGLSEA

Parental  QNGDMSQEAVENIKVKKSPQKSTVLTNGEAAMQSPNSESKKKKKKKRKMVNDAEPDTKKAKTENKGQPEE
          Q.GD.SQE.VEN.KV.KSPQKSTVLTNGE.AMQSPN.E...........VNDA.PD.............E
Retrocopy QDGDVSQETVENVKVQKSPQKSTVLTNGETAMQSPNAEXXXXXXXXXXXVNDAGPDAXXXXXXXXXXXXE

Parental  ESAE---TPKETENNVEKPDNDEDESEVPSLPLGLTGAFEDTSFASLCNLVNENTLKAIKEMGFTNMTEI
          ...E...TPKETENNVEKPDN.ED.SEVPSLPL.LTGAFEDTSFASL.NLVNENTLKAIKEMGFTNMTEI
Retrocopy SKEESAETPKETENNVEKPDNEEDDSEVPSLPLRLTGAFEDTSFASLSNLVNENTLKAIKEMGFTNMTEI

Parental  QHKSIRPLLEGRDLLAAAKTGSGK-TLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKEL
          QHKSIRPLLEGRDLLAAAKTGSGK.TLAFLI.AVEL.VKL.FMP.N..GV.ILSPTRELAMQ.FGVLKEL
Retrocopy QHKSIRPLLEGRDLLAAAKTGSGK<TLAFLITAVELTVKLKFMPTNRPGVFILSPTRELAMQIFGVLKEL

Parental  MTHHVHTYGLIMGGSNRSAEAQKLANGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFE
          M.HH.HTYGLIMGG.N..AEAQKLANGINIIVATPGRLLD.MQN.PGF.YKNLQCLVI.EADRILDVGFE
Retrocopy MAHHMHTYGLIMGGGNTYAEAQKLANGINIIVATPGRLLDYMQNIPGFIYKNLQCLVINEADRILDVGFE

Parental  EELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKE-PLYVGVDDDKANATVDGLEQGYVVCPSEKRF
          EELKQIIKLLPT.R.TML.SAT.TRKVEDLARISLKK..PL.VG..DDKAN.TVDGLEQGYVVCPSEKRF
Retrocopy EELKQIIKLLPTCRHTMLLSATLTRKVEDLARISLKKV>PLCVG-GDDKANTTVDGLEQGYVVCPSEKRF

Parental  LLLFTFLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIHGKQKQNKRTTTFFQFCNADSGTLLCTD
          LL.FT.LKKNRKKK.MVFFSSC.SVKYHYEL.NY.DLP.LAIHGKQKQNK.TTTFFQFCNADSG.LLC.D
Retrocopy LLPFTVLKKNRKKKVMVFFSSCISVKYHYELPNYVDLPILAIHGKQKQNKGTTTFFQFCNADSGILLCMD

Parental  VAARGLDIPEVDWIVQYDPPDDPKEYIHRVGRTARGLNGRGHALLILRPEELGFLRYLKQSKVPLSEFDF
          VAARGLDIPEV.WIVQ.DP..DPKEYIHRV.RTARGLNGRGHALLIL.PEE.GFL.YLKQSK.PLSEFDF
Retrocopy VAARGLDIPEVNWIVQHDPLHDPKEYIHRVSRTARGLNGRGHALLILCPEEMGFLHYLKQSKFPLSEFDF

Parental  SWSKISDIQSQLEKLIEKNYFLHKSAQEAYKSYIRAYDSHSLKQIFN
          SWSKISDIQSQL.KLIEKNYFLHKS.QEAY.SY.R.YDSHSLKQIFN
Retrocopy SWSKISDIQSQLKKLIEKNYFLHKSGQEAYESYTRTYDSHSLKQIFN

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	13.66 RPM
SRP007412_cerebellum	0.00 RPM	14.23 RPM
SRP007412_heart	0.00 RPM	8.22 RPM
SRP007412_kidney	0.00 RPM	10.61 RPM
SRP007412_liver	0.00 RPM	12.06 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1301 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1301 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1301 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1579
Pan troglodytes	retro_ptro_1064
Gorilla gorilla	retro_ggor_1201
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,