RetrogeneDB ID: retro_pabe_1128

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:70118014..70119872(+)
• Located in intron of: ENSPPYG00000005936

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_1128
ATGTCTCACCTGCTGATGAAACTCCTACACAAGAAGATCAAGAAGTGGAACCTCAAATTGTGGCAGCGGAACCTAAAGTT
GCAGGGGGCCTCAAATCTGATCCTGTCCGAAACTCAAAATAGAGATGTGTCTGAAGAAACAATGGGAGGTGGAAAGGTTA
AAAAATCAAAACATTCTATGAATGTGAGCTTATCAGATGCTCAAAATGGAAACGTGTCTCAAGAAGCAGTGGAAAATATA
AAAGTTAAAAAATCTCCCCAGAAATCCACTGTATTAACCAATGGAGATGCAGCAATGCAGTCTCCTAATTCAGAATCAAA
AAAGAAAAAGAGAAAAATGGTGAATGATGCTGAGTCTGATACAAAAAAAGCAAAAACTGAAAACAAAAGGGAATCTGAAG
AAGAAAGTGCCAAGACTCCTGAAGAAACAGAAAATAATGTTAAGAAGCCAGATGATGAAGATGACAGTGAGGTGCCCAGC
CTGCCCCTGGGACTGACAGGAGCTTTTGAGGATATTTCATTTGCTTCTTATGTAATCTTGTCAATGAAAACACTCTGAAG
GCAATAAAAGAAATGGGTTTTACAAACATGACTGAAATTCAGCATAAAAGTATCAGACCACCTTTGGAAGGCAGGGATCT
TCTTGCAGCTACAAAAACCGTCAGTGGTAAAACCCTGGCTTTTCTCATCCCTGCAGTTGAACTCATTGTTAAGTTAAATT
TCATGCCCAGGAATGGAACGGGCGTCCTTATTCTCTCACCTACTAGAGAACTAGCCATGCAAACTTTTGGTGTTCTTAAG
GAGCTAATGTCTCACCACATGCATACCTATGGGTTAATAATGGGTGGCAGTAATAGATCTGCTGAAGCACAGAAACTTGC
TAATGGGATCAACATCATTGTGGTCACACCAGGCTGTCTGCTGGACCATATGCAGAATATCCCACGGTTTATGTGTAAAA
ATCTGCAGTGTCTGGTTATCGATGAAGCTGATCGTATCTTGGATGTTGAGTTTGAAGAGGAATTAAAACAAATTATTAAA
CTTTTGCCAACACGTAGACAGACGATGCTCTTTTCTGCCATCCAAACTTGAAAAGTTGAAGGCCTGGCAAGGATTTCTCT
GAAAAAGGAGCCACTGTATGTTGGTGTTGATGATGATAAAGCTAATGCAACAGTGGATGGTCTTGAGCAGGGGTATGTTG
TTTGTCCTTCTGAAAAGAGATTCCTTCTACTCTTTACATTCCTTAAGAAGAACCAAAAAAAGAAGCTTATGGCCTTCTTT
TCATCTTGTATGTCCGTGAAATACCACTATGAGTTGCTGAACTACATTGATTTGCCCGTCTTGGCCATTCATGGAAAGCA
AAAGCAAAATAAGCATACAACCACATTCTTCCAGTTCTGCAATGCAGATTCAGGAACACTATTGTGTACAGATGTGGCAG
CAAGAGAACTGGACATTACTGAAGTCGACTAGATTGTTCAGTATGACCCTCCGGATGATCCTAAGGAATAATATTCATCG
TGTGGGCAGAACAGCCAGAGACCTAAATGGGAGAGGGCATGCCTTGCTCATTTTGCACCCAGAAGAATTGGGTTTTCTTC
ACTACTTGAAATGATCCAAGGTTCCATTAAGGGAATTTGACTTTTCCTGGTCTTAAATTTCTGACATTCATTCTCAGCTT
GAGAAATTGATTCAAAAGAACTACTTTTTTCATAAGTCAGCTCAGGAAGCATATAAATCATACATACAAGCCTACGATTC
CCATTCTCTGAAACAGATCTTTAATGTTTAATAACTTAAATTTGCCTCAAGTTGCTGTCATTGGTTTCAAGGTGCCTCCC
TTTGTTGATCTGAACGTC

Alignment

ORF - retro_pabe_1128 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSHLPMKLLRKKIEKRNLKLRQRNLKLQGASNLTLSETQNGDVSEETMGSRKVKKSKQKPMNVGLSETQN
          MSHL.MKLL.KKI.K.NLKL.QRNLKLQGASNL.LSETQN.DVSEETMG..KVKKSK...MNV.LS..QN
Retrocopy MSHLLMKLLHKKIKKWNLKLWQRNLKLQGASNLILSETQNRDVSEETMGGGKVKKSKHS-MNVSLSDAQN

Parental  GDMSQEAVENIKVKKSPQKSTVLTNGEAAMQSPNSESKKKKKKKRKMVNDAEPDTKKAKTENKGQPEEES
          G..SQEAVENIKVKKSPQKSTVLTNG.AAMQ...S............VNDAE.D............EEES
Retrocopy GNVSQEAVENIKVKKSPQKSTVLTNGDAAMQ---SPNSEXXXXXXXXVNDAESDXXXXXXXXXXESEEES

Parental  AETPKETENNVEKPDNDEDESEVPSLPLGLTGAFEDTSFAS-LCNLVNENTLKAIKEMGFTNMTEIQHKS
          A.TP.ETENNV.KPD.DED.SEVPSLPLGLTGAFED.SFAS.LCNLVNENTLKAIKEMGFTNMTEIQHKS
Retrocopy AKTPEETENNVKKPD-DEDDSEVPSLPLGLTGAFEDISFAS<LCNLVNENTLKAIKEMGFTNMTEIQHKS

Parental  IRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHV
          IRP.LEGRDLLAA.KT.SGKTLAFLIPAVELIVKL.FMPRNGTGVLILSPTRELAMQTFGVLKELM.HH.
Retrocopy IRPPLEGRDLLAATKTVSGKTLAFLIPAVELIVKLNFMPRNGTGVLILSPTRELAMQTFGVLKELMSHHM

Parental  HTYGLIMGGSNRSAEAQKLANGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQ
          HTYGLIMGGSNRSAEAQKLANGINIIV.TPG.LLDHMQN.P.FM.KNLQCLVIDEADRILDV.FEEELKQ
Retrocopy HTYGLIMGGSNRSAEAQKLANGINIIVVTPGCLLDHMQNIPRFMCKNLQCLVIDEADRILDVEFEEELKQ

Parental  IIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYVGVDDDKANATVDGLEQGYVVCPSEKRFLLLFTF
          IIKLLPTRRQTMLFSA.QT.KVE.LARISLKKEPLYVGVDDDKANATVDGLEQGYVVCPSEKRFLLLFTF
Retrocopy IIKLLPTRRQTMLFSAIQT*KVEGLARISLKKEPLYVGVDDDKANATVDGLEQGYVVCPSEKRFLLLFTF

Parental  LKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIHGKQKQNKRTTTFFQFCNADSGTLLCTDVAARGL
          LKKN.KKKLM.FFSSCMSVKYHYELLNYIDLPVLAIHGKQKQNK.TTTFFQFCNADSGTLLCTDVAAR.L
Retrocopy LKKNQKKKLMAFFSSCMSVKYHYELLNYIDLPVLAIHGKQKQNKHTTTFFQFCNADSGTLLCTDVAAREL

Parental  DIPEVDWIVQYDPPDDPKE-YIHRVGRTARGLNGRGHALLILRPEELGFLRYLKQSKVPLSEFDFSWSKI
          DI.EVD.IVQYDPPDDPKE..IHRVGRTAR.LNGRGHALLIL.PEELGFL.YLK.SKVPL.EFDFSWS.I
Retrocopy DITEVD*IVQYDPPDDPKE>NIHRVGRTARDLNGRGHALLILHPEELGFLHYLK*SKVPLREFDFSWS*I

Parental  SDIQSQLEKLIEKNYFLHKSAQEAYKSYIRAYDSHSLKQIFNV-NNLNLPQVALSFGFKVPPFVDLSI
          SDI.SQLEKLI.KNYF.HKSAQEAYKSYI.AYDSHSLKQIFNV.NNLNLPQVA...GFKVPPFVDL..
Retrocopy SDIHSQLEKLIQKNYFFHKSAQEAYKSYIQAYDSHSLKQIFNV>NNLNLPQVAV-IGFKVPPFVDLNV

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	0.06 RPM	13.66 RPM
SRP007412_cerebellum	0.00 RPM	14.23 RPM
SRP007412_heart	0.03 RPM	8.22 RPM
SRP007412_kidney	0.07 RPM	10.61 RPM
SRP007412_liver	0.09 RPM	12.06 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1128 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1128 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1128 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1361
Pan troglodytes	retro_ptro_933
Macaca mulatta	retro_mmul_2192

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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,