RetrogeneDB ID: retro_pabe_3489

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:77223486..77224914(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX10
• Ensembl ID: ENSPPYG00000003849
• Aliases: None
• Description: probable ATP-dependent RNA helicase DDX10 [Source:RefSeq peptide;Acc:NP_001126807]

Sequence

>retro_pabe_3489
ACACGTATTCACAGAGGAGGTAGAACTGCCAGGTACAAAGAGGATGGTGAAAGTTTATTAATTTTGCTTGCCTCAGAAAA
AGCTATGGTGCAGCAGCTTCTTCAGAAGAAAGTACCTATGAAGGAAATCAAAATCAATCCAGAAAAACTTATAGATATCC
AGAAAACATTGGAATCTTTTTTAGCTGAAGATCAAGATTTAAAAGAAAGAGCTCAAAGGTGTTTCATCTCCGATATATGA
TCGGTATATCTGACGAAGGATAAAGAAGTATTTGATGTGAGCAAGTTACCTATACCTGAATATGCCCTGTCTCTTGGGCT
TGCTGTGGCACCACGCATAAGATTTCTTCAGAAAATGCAGAAACAACCCACCAAAGAATTGGTAATGAGCCAAGCCAATA
AAGTAATTGAGCCAAGGGCTCCCTCCCTCACCGATGACAAAGTGGAAGAATTTAGAGCCTTCTTCAATGAGAAAATGTCC
ATCCTTCAGAAAAGTGGAAAAAGACTCAAAGGGACAGAGCACAGACTGGCTAATGATACTAGTGACGAAGAACAGGAGGA
AGAGGAAGAAGATGAAGAAGAAATAGAAGAGAAACTGGCAAAAGCAAAAGGATCTCAAGCTCCATCTCTTCCTAACACCA
GTGAAGCAAAGAAGATCAAGGAAGTTCCTGTGTAGTTCCTGGACAGAGATGAGGAGGAAGAAAATGCTGATTTCTTGAAG
TTGAAGCAGCACAATGTGTTTGGATTTGACCTTAAAGAGGAGAAAATATGACAGAAGAAAGAACCTTCTAAATCCAGCAT
CAAGAAAAAAGTGGCCAAAGTTGCAGAAGCAAAAAAAGTAATGAAGAGAAATTTTAAAGCGAATAATAAGATAACATGTA
CTGATGAAGGGGAGTTGGTTCAGCAGTAGCCACAAATGCAGAAAGCTGCCATCAAGGATGCTGAGGAAGATGATGACACG
GGTGGTATCAACTTAAATAAAGCAAAGGGAAGACTTCTGGAAGAGGACAAATTTGACAAAGAAGAATATAGGAAGAAAAT
TAAGGCAAAGCATCGGGAGAAAAGACTGAAAGAAAGGGAAGCCAGAAGAGAAGCCAACAAGACACAAGCAAAGGCCAAAG
ATGAAGAGGAAGCCTTTCTGGATTGGAGTGATGATGATGATGATGATGGATTTGATCCAAGTACACTCCCAGATCCAGAT
AAGTACAGAAGCTCTGAAGATTCAGATAGTGAAGATATGGAAAATAAAATTAGTGATACCAAGAAGAAGTAGGGAATGAA
GAAGAGGAACAACAGTGAAGTAGAAGACGTGGGACCAACAAGTCGTAACAGAAAGAAGGCCAAGTGGGACACTTTAGAGC
CTTTGGATACTGGCCTGTCTCTAGCGGAGGATGAAGAGCTGGTGTTACATCTGCTAAGAAGTCAAAGC

Alignment

ORF - retro_pabe_3489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.5 %
• Parental protein coverage: 54.47 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TYIHRAGRTARYKEDGEALLILLPSEKAMVQQLLQKKVPVKEIKINPEKLIDVQKKLESILAQDQDLKER
          T.IHR.GRTARYKEDGE.LLILL.SEKAMVQQLLQKKVP.KEIKINPEKLID.QK.LES.LA.DQDLKER
Retrocopy TRIHRGGRTARYKEDGESLLILLASEKAMVQQLLQKKVPMKEIKINPEKLIDIQKTLESFLAEDQDLKER

Parental  AQRCFVSYIRSVYLMKDKEVFDVSKLPIPEYALSLGLAVAPRIRFLQKMQKQPTKELVMSQADKVIEPRA
          AQRCF.S.I.SVYL.KDKEVFDVSKLPIPEYALSLGLAVAPRIRFLQKMQKQPTKELVMSQA.KVIEPRA
Retrocopy AQRCFISDI*SVYLTKDKEVFDVSKLPIPEYALSLGLAVAPRIRFLQKMQKQPTKELVMSQANKVIEPRA

Parental  PSLTNDEVEEFRAYFNEKMSILQKGGKRLEGTEHRQDNDTGDEEQEEEEDDEEEVEEKLAKAKGSQAPSL
          PSLT.D.VEEFRA.FNEKMSILQK.GKRL.GTEHR..NDT.D................LAKAKGSQAPSL
Retrocopy PSLTDDKVEEFRAFFNEKMSILQKSGKRLKGTEHRLANDTSDXXXXXXXXXXXXXXXXLAKAKGSQAPSL

Parental  PNTSEAQKIKEVPTQFLDRDEEEEDADFLKVKRHNVFGLDLKEEKTLQKKEPSKSSIKKKVTKVAEAKKV
          PNTSEA.KIKEVP..FLDRDEEEE.ADFLK.K.HNVFG.DLKEEK..QKKEPSKSSIKKKV.KVAEAKKV
Retrocopy PNTSEAKKIKEVPV*FLDRDEEEENADFLKLKQHNVFGFDLKEEKI*QKKEPSKSSIKKKVAKVAEAKKV

Parental  MKRNFKVNKKITFTDEGELVQQWPQMQKSAIKDAEEDDDTGGINLDKAKERLQEEDKFDKEEYRKKIKAK
          MKRNFK.N.KIT.TDEGELVQQ.PQMQK.AIKDAEEDDDTGGINL.KAK.RL.EEDKFDKEEYRKKIKAK
Retrocopy MKRNFKANNKITCTDEGELVQQ*PQMQKAAIKDAEEDDDTGGINLNKAKGRLLEEDKFDKEEYRKKIKAK

Parental  HREKRLKEREARREANKRQAKAKDEEEAFLDW-SDDDDDGFDPSTLPDPDKYRSSEDSDSEDMENKISDT
          HREKRLKEREARREANK.QAKAKDEEEAFLDW........FDPSTLPDPDKYRSSEDSDSEDMENKISDT
Retrocopy HREKRLKEREARREANKTQAKAKDEEEAFLDWXXXXXXXXFDPSTLPDPDKYRSSEDSDSEDMENKISDT

Parental  KKKQGMKKRNNSEVEDIGPTSHNRKKAKWDPLEPLDTGLSLAEDEELVLHLLRSQS
          KKK.GMKKRNNSEVED.GPTS.NRKKAKWD.LEPLDTGLSLAEDEELVLHLLRSQS
Retrocopy KKK*GMKKRNNSEVEDVGPTSRNRKKAKWDTLEPLDTGLSLAEDEELVLHLLRSQS

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	24.27 RPM
SRP007412_cerebellum	0.00 RPM	22.86 RPM
SRP007412_heart	0.03 RPM	5.21 RPM
SRP007412_kidney	0.03 RPM	13.62 RPM
SRP007412_liver	0.00 RPM	13.65 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3489 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3489 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3489 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000178105	1 retrocopy	retro_hsap_4278,
Gorilla gorilla	ENSGGOG00000000271	1 retrocopy	retro_ggor_2862,
Pongo abelii	ENSPPYG00000003849	1 retrocopy	retro_pabe_3489 ,
Pan troglodytes	ENSPTRG00000004256	1 retrocopy	retro_ptro_2901,