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 summary: | ||
| Parental gene symbol: | DDX23 | ||
| Ensembl ID: | ENSPPYG00000004468 | ||
| Aliases: | None | ||
| Description: | probable ATP-dependent RNA helicase DDX23 [Source:RefSeq peptide;Acc:NP_001125347] |
Retrocopy-Parental alignment summary:
>retro_pabe_842
GGTGCAGGTGTTAGGGCAAGGCTTCATTGCAGGCATTGACCTCAAGAGCAGTCACATTTCTGTGGAGACCTAATGGAAAA
GGGCGAACCCTGGAAGAAAAGGAGCAGAAGGAGGCAAGACTCCGCAAACTTCATAAGAAGGAAGCCAAGCGCACTGGGAT
GATCCTCACTGGTCTCAGAAAAAGTTAGATGAGATGAGGGACAGGGACTGGTGGCTCTTCTGTGAGGGCTACAGCATCAC
CACCAAAGATGGCAAGATCCCCAATCCCATCCGATCCTGGAAAGACTCTTCTCTGCCCCCACACATCTTGGAGGTCATTG
ATAAGTGTGGCTACAAGGAATCAACACCTATCCAGTGTCAGGCAATTCCGATTGGACTACAGAATCGTGACATCATTGAT
GTGGCTGAGACTGGCAGCAGCAAGACAGCAGCCTTCCTCATCCCACTGCTGGTCTAGATCACCACACTTCCCAAAATTGA
CAGGATCGAAGAGTCAGACCAAGGCCCTTATGCCAACATCCTGGCTCCCACCCATAAGTTGGCTCAACAGATTGAGGAAG
AGACCATCAAGTTTGGGAAGCCACTAGATATCCAACTGTGGCTGTCATTGGTGGCATCTCCAGAGAAGACCGGGGCTTCA
GGCTGCGCATGGGTTGTGAGATTGTGATCACTACCCCTGGGCATTTGATTGATGTGCTGGAGAATCGCTACCTGGTGCTG
AGCTGCTGTACTACGTGGTTCTGGATGAGGCAGATAGGATGATTAACATGGGCTTTGAGCCAGATGTTCAGAAGATCCTG
GAGCACATGCCTGTCAGCAACCAGAAGCCGGACATGGATGAGGCTGAGGACCCTGAGAAGATGCTGGCCAACTTTGAGTC
AGGAAAACGTTAAGGACCACCAAAGTCATGTTCATGGCCACCATGCCCCCAGCAGTGGAGCGTCTGGCCAGGAGCTATCT
TCAGCGACCTGCTGTGGTGTACATTGACCCCGCAGGCAAGCCCCATGAGCGTGTGGAACAGGTCTTTCTCATGTCAGAGT
CAGAAAAGAGGAAAAAGCTGCTGGCAATCTTGAAGCAAGGCTTTGGCCCAGCCATCATTATTTTTGTCAACCAGAAGAAG
GGCTGTGACATCTTGGCCAAATCCCTGGAGAAGATGGGGTACAAGGCTTGCGCACTGCACAGTGGAAAAGGCCAGGAGCA
GCGAGAGTTTGCCTTGTCCAACCTCAAGGCTGGGGCCAAGGATATCTTGGTGGCTACAGATGTGACTGGTCGTGGTATTG
ACATCCAAGATGTGTCTATGGTTGTCAACTATGATATGGCCAAAAATATTGACGATTACAAACACCTCATTGACCGCACG
GGACGAGCAGGCAAGAGTGGGGTGGCCATCACCTTTCTCACAAAAGAGGACTCTGCGGTGTTCTATGAGCCGAAGCAAGC
CATCCTGGAAAGCAAGGACAGGAAGACAGTGTCTTCCTGTCCCCCCGAACTAGCCAACCACCCAGATGCCCAGCATAAGC
CAGGCACCATCCTCACCAAGAAGCGCCGGGAAGAGACCATCTTTGCC
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 |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
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 |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_842 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_842 was not experimentally validated.
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 | |
| Pongo abelii | ENSPPYG00000004468 | 1 retrocopy |
retro_pabe_842 ,
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