RetrogeneDB ID: retro_pabe_842

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:52472955..52474522(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX23
• Ensembl ID: ENSPPYG00000004468
• Aliases: None
• Description: probable ATP-dependent RNA helicase DDX23 [Source:RefSeq peptide;Acc:NP_001125347]

Sequence

>retro_pabe_842
GGTGCAGGTGTTAGGGCAAGGCTTCATTGCAGGCATTGACCTCAAGAGCAGTCACATTTCTGTGGAGACCTAATGGAAAA
GGGCGAACCCTGGAAGAAAAGGAGCAGAAGGAGGCAAGACTCCGCAAACTTCATAAGAAGGAAGCCAAGCGCACTGGGAT
GATCCTCACTGGTCTCAGAAAAAGTTAGATGAGATGAGGGACAGGGACTGGTGGCTCTTCTGTGAGGGCTACAGCATCAC
CACCAAAGATGGCAAGATCCCCAATCCCATCCGATCCTGGAAAGACTCTTCTCTGCCCCCACACATCTTGGAGGTCATTG
ATAAGTGTGGCTACAAGGAATCAACACCTATCCAGTGTCAGGCAATTCCGATTGGACTACAGAATCGTGACATCATTGAT
GTGGCTGAGACTGGCAGCAGCAAGACAGCAGCCTTCCTCATCCCACTGCTGGTCTAGATCACCACACTTCCCAAAATTGA
CAGGATCGAAGAGTCAGACCAAGGCCCTTATGCCAACATCCTGGCTCCCACCCATAAGTTGGCTCAACAGATTGAGGAAG
AGACCATCAAGTTTGGGAAGCCACTAGATATCCAACTGTGGCTGTCATTGGTGGCATCTCCAGAGAAGACCGGGGCTTCA
GGCTGCGCATGGGTTGTGAGATTGTGATCACTACCCCTGGGCATTTGATTGATGTGCTGGAGAATCGCTACCTGGTGCTG
AGCTGCTGTACTACGTGGTTCTGGATGAGGCAGATAGGATGATTAACATGGGCTTTGAGCCAGATGTTCAGAAGATCCTG
GAGCACATGCCTGTCAGCAACCAGAAGCCGGACATGGATGAGGCTGAGGACCCTGAGAAGATGCTGGCCAACTTTGAGTC
AGGAAAACGTTAAGGACCACCAAAGTCATGTTCATGGCCACCATGCCCCCAGCAGTGGAGCGTCTGGCCAGGAGCTATCT
TCAGCGACCTGCTGTGGTGTACATTGACCCCGCAGGCAAGCCCCATGAGCGTGTGGAACAGGTCTTTCTCATGTCAGAGT
CAGAAAAGAGGAAAAAGCTGCTGGCAATCTTGAAGCAAGGCTTTGGCCCAGCCATCATTATTTTTGTCAACCAGAAGAAG
GGCTGTGACATCTTGGCCAAATCCCTGGAGAAGATGGGGTACAAGGCTTGCGCACTGCACAGTGGAAAAGGCCAGGAGCA
GCGAGAGTTTGCCTTGTCCAACCTCAAGGCTGGGGCCAAGGATATCTTGGTGGCTACAGATGTGACTGGTCGTGGTATTG
ACATCCAAGATGTGTCTATGGTTGTCAACTATGATATGGCCAAAAATATTGACGATTACAAACACCTCATTGACCGCACG
GGACGAGCAGGCAAGAGTGGGGTGGCCATCACCTTTCTCACAAAAGAGGACTCTGCGGTGTTCTATGAGCCGAAGCAAGC
CATCCTGGAAAGCAAGGACAGGAAGACAGTGTCTTCCTGTCCCCCCGAACTAGCCAACCACCCAGATGCCCAGCATAAGC
CAGGCACCATCCTCACCAAGAAGCGCCGGGAAGAGACCATCTTTGCC

Alignment

ORF - retro_pabe_842 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.66 %
• Parental protein coverage: 61.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GRGFIAGIDLKQQKREQSRFYGDLMEKR-RTLEEKEQEEARLRKLRKKEAKQ-RWDDRHWSQKKLDEMTD
          G.G..A.........EQS.F.GDLMEK..RTLEEKEQ.EARLRKL.KKEAK...WDD.HWSQKKLDEM.D
Retrocopy GAGVRARLHCRH*PQEQSHFCGDLMEKG<RTLEEKEQKEARLRKLHKKEAKR<HWDDPHWSQKKLDEMRD

Parental  RDWRIFREDYSITTKGGKIPNPIRSWKDSSLPPHILEVIDKCGYKEPTPIQRQAIPIGLQNRDIIGVAET
          RDW..F.E.YSITTK.GKIPNPIRSWKDSSLPPHILEVIDKCGYKE.TPIQ.QAIPIGLQNRDII.VAET
Retrocopy RDWWLFCEGYSITTKDGKIPNPIRSWKDSSLPPHILEVIDKCGYKESTPIQCQAIPIGLQNRDIIDVAET

Parental  GSGKTAAFLIPLLVWITTLPKIDRIEESDQGPYAIILAPTRELAQQIEEETIKFGKPLGIR-TVAVIGGI
          GS.KTAAFLIPLLV.ITTLPKIDRIEESDQGPYA.ILAPT..LAQQIEEETIKFGKPL.I..TVAVIGGI
Retrocopy GSSKTAAFLIPLLV*ITTLPKIDRIEESDQGPYANILAPTHKLAQQIEEETIKFGKPLDIQ<TVAVIGGI

Parental  SREDQGFRLRMGCEIVIATPGRLIDVLENRYLVLSRCT-YVVLDEADRMIDMGFEPDVQKILEHMPVSNQ
          SRED.GFRLRMGCEIVI.TPG.LIDVLENRYLVLS.CT.YVVLDEADRMI.MGFEPDVQKILEHMPVSNQ
Retrocopy SREDRGFRLRMGCEIVITTPGHLIDVLENRYLVLSCCT<YVVLDEADRMINMGFEPDVQKILEHMPVSNQ

Parental  KPDTDEAEDPEKMLANFESG-KHKYRQTVMFTATMPPAVERLARSYLRRPAVVYIGSAGKPHERVEQKVF
          KPD.DEAEDPEKMLANFESG.K......VMF.ATMPPAVERLARSYL.RPAVVYI..AGKPHERVEQ.VF
Retrocopy KPDMDEAEDPEKMLANFESG<KTLRTTKVMFMATMPPAVERLARSYLQRPAVVYIDPAGKPHERVEQ-VF

Parental  LMSESEKRKKLLAILEQGFDPPIIIFVNQKKGCDVLAKSLEKMGYNACTLHGGKGQEQREFALSNLKAGA
          LMSESEKRKKLLAIL.QGF.P.IIIFVNQKKGCD.LAKSLEKMGY.AC.LH.GKGQEQREFALSNLKAGA
Retrocopy LMSESEKRKKLLAILKQGFGPAIIIFVNQKKGCDILAKSLEKMGYKACALHSGKGQEQREFALSNLKAGA

Parental  KDILVATDVAGRGIDIQDVSMVVNYDMAKNIEDYIHRIGRTGRAGKSGVAITFLTKEDSAVFYELKQAIL
          KDILVATDV.GRGIDIQDVSMVVNYDMAKNI.DY.H.I.RTGRAGKSGVAITFLTKEDSAVFYE.KQAIL
Retrocopy KDILVATDVTGRGIDIQDVSMVVNYDMAKNIDDYKHLIDRTGRAGKSGVAITFLTKEDSAVFYEPKQAIL

Parental  ES----PVSSCPPELANHPDAQHKPGTILTKKRREETIFA
          ES.....VSSCPPELANHPDAQHKPGTILTKKRREETIFA
Retrocopy ESKDRKTVSSCPPELANHPDAQHKPGTILTKKRREETIFA

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	87.41 RPM
SRP007412_cerebellum	0.00 RPM	75.15 RPM
SRP007412_heart	0.00 RPM	33.75 RPM
SRP007412_kidney	0.00 RPM	75.48 RPM
SRP007412_liver	0.00 RPM	57.16 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_842 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_842 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_842 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000011033	2 retrocopies	retro_mluc_1089, retro_mluc_344,
Pongo abelii	ENSPPYG00000004468	1 retrocopy	retro_pabe_842 ,