RetrogeneDB ID: retro_pabe_3816

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:136462527..136463806(-)
• Located in intron of: ENSPPYG00000020772

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX21
• Ensembl ID: ENSPPYG00000002389
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 21 [Source:HGNC Symbol;Acc:2744]

Sequence

>retro_pabe_3816
ATGCCGGGAAAACTCCATAGTAATGCTGGTTTGGAACCAGACACCACAATGAAAAAAGTGGAGACATTACGAAAGCAAAC
TGAGAAGAAAGAGAAAAAAGAGAAGTCAAAATCTAGTAAGACTGAAGAGACAGCAGAAGAGGAAGAAACTTTCCCCAAAG
CTAAACAAGTTAAAAAGAAAACAGAGCCTTCTGAAGTTGACATGAATTATCCTAAATCCAAAAAGGCAAAAAAGAAAGAG
GAGCCATCTCAAGATGACAGTTCTCCTAAAACCAAAAGTTTGAGAAAGAAAAAGGAGCCTATTGAAAAGAAAGTGGTTTC
TTCTAAAACCAAAAGTGATAAAAAATGAGGAGCCTTCTGAGGAAGAAATAGATGCTCTTAAGCCCAAGAAGATGAAGAAA
GAAAAGGAAATAAATGGAGAAACTGGAGAGAAAAGCCCCAAACTGAAGAATGGATTTCCTCATTCTGAACCTGACTGTGA
CCTCAATGAAGTTGCCAATGAAGAAAGTAACAGTGAGACAGAGTAGGAAATACGTGTGGAACAAAAAGAAGGCGCTTTCT
CTAATTGTCCCATATCTGAAGAAACTATTAAGCTTCTCAAAGGCTGAGAAGTGACCTTCCTATTTCCTATACAAGCAAAG
ACATTCCATCATGTTTACAGCAGGAAGGACTTAATTGCACAGGCGTGGACAGGAAGAACTGGGAAAACATTCTCCTTTGC
TATCCCTTTGATTGAGAAACTTCATGGGGAACTGTAAGACAGGAAGAGAGACCGTCCCCCTCAGGTACTGGTTCTTGCAC
CTACAAGAGAGTTGGCAAATCAAGTAAGCAAAGACTTCAGTGACATCACAAAAAGGCTATCAGTGGCTTGTTTTTATGGT
GGAACTCCCTATGGAGGTCAATTCGAATGCATGAGGAATGGGATTGATATCCTGGTTGGGACCCCAGGTCGTATCAAAGA
CCACATACAGAATGGCAAACTAGATCTCACCAAACTTAAGCATGTTTTCCTGGATGAAGTTGACCAGATGTTGGATATGG
GATTGCTGATCAAGTGGAAGAGATTTTAAGTGTGGCATACAAGAAAGATTCTGAAGACAATCACCAAACATTGCTTTTTT
TCTGCAACTGGCCCTCATTGGGTATTTAATGTTGCCAAGAAATACATGAAATCTGCATATGAACAGGTGGACCTGATTGG
TGAAAAGACTCAGAAAATGGCAAAAACTATAGAGCATCTGGCTATTAAGTGCCACTGGACTCAGAGGGCAGCAGCTATT

Alignment

ORF - retro_pabe_3816 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.54 %
• Parental protein coverage: 54.53 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPGKLRSDAGLESDTAMKKGETLRKQTEKKEKKEKPKSDKTEEIAEEEETVFPKAKQVKKKAEPSEVDMN
          MPGKL.S.AGLE.DT.MKK.ETLRKQTEKKEKKEK.KS.KTEE.AEEEET.FPKAKQVKKK.EPSEVDMN
Retrocopy MPGKLHSNAGLEPDTTMKKVETLRKQTEKKEKKEKSKSSKTEETAEEEET-FPKAKQVKKKTEPSEVDMN

Parental  SPKSKKAKKKEEPSQNDISPKTKSLRKKKEPIEKKVVSSKTKK-VTKNEEPFEEEIDAPKPKKMKKEKEM
          .PKSKKAKKKEEPSQ.D.SPKTKSLRKKKEPI..K.V.S...K.V.KNEEP.EEEIDA.KPKKMKKEKE.
Retrocopy YPKSKKAKKKEEPSQDDSSPKTKSLRKKKEPI-EKKVVSSKTK>VIKNEEPSEEEIDALKPKKMKKEKEI

Parental  NGETGEKSPKLKNGFPHPESDYNPSEAASEESNSEIEQEIPVEQKEGAFSNFPISEETIKLLKGRGVTFL
          NGETGEKSPKLKNGFPH.E.D....E.A.EESNSE.E.EI.VEQKEGAFSN.PISEETIKLLKG..VTFL
Retrocopy NGETGEKSPKLKNGFPHSEPDCDLNEVANEESNSETE*EIRVEQKEGAFSNCPISEETIKLLKG*EVTFL

Parental  FPIQAKTFHHVYSGKDLIAQARTG-TGKTFSFAIPLIEKLHGELQDRKRGRPPQVLVLAPTRELANQVSK
          FPIQAKTFHHVYS.KDLIAQA.TG.TGKTFSFAIPLIEKLHGEL.DRKR.RPPQVLVLAPTRELANQVSK
Retrocopy FPIQAKTFHHVYSRKDLIAQAWTGRTGKTFSFAIPLIEKLHGEL*DRKRDRPPQVLVLAPTRELANQVSK

Parental  DFSDITKKLSVACFYGGTPYGGQFERMRNGIDILVGTPGRIKDHIQNGKLDLTKLKHVVLDEVDQMLDM-
          DFSDITK.LSVACFYGGTPYGGQFE.MRNGIDILVGTPGRIKDHIQNGKLDLTKLKHV.LDEVDQMLDM.
Retrocopy DFSDITKRLSVACFYGGTPYGGQFECMRNGIDILVGTPGRIKDHIQNGKLDLTKLKHVFLDEVDQMLDM<

Parental  GFADQVEEILSVAYKKDSEDNPQTLL-FSATCPHWVFNVAKKYMKSTYEQVDLIGKKTQKTAITVEHLAI
          G.ADQVEEILSVAYKKDSEDN.QTLL.FSAT.PHWVFNVAKKYMKS.YEQVDLIG.KTQK.A.T.EHLAI
Retrocopy GIADQVEEILSVAYKKDSEDNHQTLL>FSATGPHWVFNVAKKYMKSAYEQVDLIGEKTQKMAKTIEHLAI

Parental  KCHWTQRAAVI
          KCHWTQRAA.I
Retrocopy KCHWTQRAAAI

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	20.68 RPM
SRP007412_cerebellum	0.00 RPM	23.35 RPM
SRP007412_heart	0.00 RPM	32.45 RPM
SRP007412_kidney	0.00 RPM	32.12 RPM
SRP007412_liver	0.00 RPM	29.13 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3816 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3816 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3816 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013791	2 retrocopies	retro_cfam_1024, retro_cfam_1925,
Callithrix jacchus	ENSCJAG00000012876	1 retrocopy	retro_cjac_1912,
Macropus eugenii	ENSMEUG00000010586	1 retrocopy	retro_meug_1383,
Microcebus murinus	ENSMICG00000015112	1 retrocopy	retro_mmur_95,
Mus musculus	ENSMUSG00000020075	2 retrocopies	retro_mmus_582, retro_mmus_662,
Procavia capensis	ENSPCAG00000016697	1 retrocopy	retro_pcap_346,
Pongo abelii	ENSPPYG00000002389	1 retrocopy	retro_pabe_3816 ,
Pongo abelii	ENSPPYG00000002390	3 retrocopies	retro_pabe_2007, retro_pabe_2369, retro_pabe_2418,
Pongo abelii	ENSPPYG00000016774	1 retrocopy	retro_pabe_39,
Tupaia belangeri	ENSTBEG00000002310	2 retrocopies	retro_tbel_1590, retro_tbel_4454,