RetrogeneDB ID: | retro_pabe_3572 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | Un:10987684..10988837(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | AGGF1 | ||
| Ensembl ID: | ENSPPYG00000015574 | ||
| Aliases: | None | ||
| Description: | angiogenic factor with G patch and FHA domains 1 [Source:HGNC Symbol;Acc:24684] |
Retrocopy-Parental alignment summary:
>retro_pabe_3572
GAGGAAAAGGATTTGAATTCAGAGGATCCAAAAGCCTTCAGTGTTGAACATACAAGCTGCAATGGGAAAGACAATTTTAC
AAATGTGAAAGAAAGGCCAAAATAGGCATTCATCACAAAAATAATCCCCCAAAAGTCACTGTTCCAATTAGTGGAAATAC
TATGGACTCTCCTTTTAATGAAAACATGTCAATTCAACTTTATTTAAAGATGAGAAAGTCGCAGACAGTGATAGTGAATC
AGAAGAAGGTGAAATCACAGACTCTCAGACCGAGGGTAGTTATGATGAAGACATTACCAGTGAAGGCAATACAACTGCAA
AAGATACTGAAGAGAGAGATGAGGAATAACTGTGGCCCCCATGTATAAGAGTAATTGTCATTAAATCACCCCTGTTACAG
ACAGGATCACTCTTCATCATTACTGCTGTAAAACCTGCTACAATTGAAAGAGAAAATGATATGGAGCATACTCTTCGAAT
CCCTGCAGTTGGTGTCAGTAAGTTTCACGCACAAATTTATTTTGACCATGACTTACAAAGTTGTGTCCTTTTGTATCGGG
CAGTCAAAATGTAACAATTGTTAATGAAAAACGGATTATTCAGCTGAAAACTAAATGTGACCCTTATGTGCTTGAGCATG
GAGATAAAGCAAAAATTGGAGAGACTGTGTTATCTTATTATATTCACCCTGGCAGTAATAGCTATGTTGGATGTGAACCA
GTGCAGGTTAGATCTCACCTTTCCTTGGTAAGAAAGATGAATCATTTGTTGGTCCAACATTAACTAAGAAGGAAAGGAGT
TGGAAAGAAGAAAAGGATTTTAGAAATATATCAGTAAAATATGCTTTACAGAATACAGACTACAAAGATGATAAGATATT
GGAGAATCTAAAATATAAAGATAGAGTTGTAAAACATAAGGAACAGATTGGAAGTGAAGGAAATTTCCAAAGAGATGATG
CTCCTGCATCTGTTCATTCTGAAATTACTGATAGTGACAAAGGTCACAAGATGTTGAAGAAGATATGTTGAAAACATTAG
TAGGCCTGGGGAAGGATGGTGGGAGAATATAAACTCCAATACAGCTTCAACTTTGGCAAACACAAGCAGGATTGGAGACA
GACAAACCATCCTCAATTAAAGAGGCTCACCTT
ORF - retro_pabe_3572 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.08 % |
| Parental protein coverage: | 54.06 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | EEKDLNSEDQKTFSVEHTSCSEEENFANMK-KKAKIGIHHKNSPPKVTVPTSGNTIESPLHENIS-KSTS |
| EEKDLNSED.K.FSVEHTSC....NF.N.K..KAKIGIHHKN.PPKVTVP.SGNT..SP..EN.S..ST. | |
| Retrocopy | EEKDLNSEDPKAFSVEHTSCNGKDNFTNVK<RKAKIGIHHKNNPPKVTVPISGNTMDSPFNENMS<NSTL |
| Parental | FRDEKIMETDSEPEEGEITDSQTEDSYDEDITSEGNVTAEDSEDEDEDKIWPPCIRVIVIRSPVLQIGSL |
| F.DEK....DSE.EEGEITDSQTE.SYDEDITSEGN.TA.D.E..DE...WPPCIRVIVI.SP.LQ.GSL | |
| Retrocopy | FKDEKVADSDSESEEGEITDSQTEGSYDEDITSEGNTTAKDTEERDEE*LWPPCIRVIVIKSPLLQTGSL |
| Parental | FIITAVNPATIGREKDMEHTLRIPEVGVSKFHAEIYFDRDLQSYVLVDQ-GSQNGTIVNGKQILQPKTKC |
| FIITAV.PATI.RE.DMEHTLRIP.VGVSKFHA.IYFD.DLQS.VL....GSQN.TIVN.K.I.Q.KTKC | |
| Retrocopy | FIITAVKPATIERENDMEHTLRIPAVGVSKFHAQIYFDHDLQSCVLLYR<GSQNVTIVNEKRIIQLKTKC |
| Parental | DPYVLEHGDEVKIGETVLSFHIHPGSDTCDGCEPGQVRAHLR-LDKKDESFVGPTLSKEEKELERRKELK |
| DPYVLEHGD..KIGETVLS..IHPGS....GCEP.QVR.HL..L.KKDESFVGPTL.K.E......K... | |
| Retrocopy | DPYVLEHGDKAKIGETVLSYYIHPGSNSYVGCEPVQVRSHLS<LGKKDESFVGPTLTKKERSWKEEKDFR |
| Parental | KIRVKYGLQNTEYEDEKTLKNPKYKDRAGKRREQVGSEGTFQRDDAPASVHSEITDSNKGRKMLEKMGWK |
| .I.VKY.LQNT.Y.D.K.L.N.KYKDR..K..EQ.GSEG.FQRDDAPASVHSEITDS.KG.KML.K...K | |
| Retrocopy | NISVKYALQNTDYKDDKILENLKYKDRVVKHKEQIGSEGNFQRDDAPASVHSEITDSDKGHKMLKKIC*K |
| Parental | KGEGLGK-DGGGMKTPIQLQLRRTHAGLGTGKPSSIEDIHL |
| .....G..DGG...TPIQLQL..T.AGL.T.KPSSI...HL | |
| Retrocopy | H**AWGR<DGGRI*TPIQLQLWQTQAGLETDKPSSIKEAHL |
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 .00 RPM | 37 .04 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 36 .48 RPM |
| SRP007412_heart | 0 .00 RPM | 11 .74 RPM |
| SRP007412_kidney | 0 .07 RPM | 21 .78 RPM |
| SRP007412_liver | 0 .00 RPM | 13 .25 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3572 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3572 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3572 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pongo abelii | ENSPPYG00000015574 | 1 retrocopy |
retro_pabe_3572 ,
|
| Pan troglodytes | ENSPTRG00000017008 | 1 retrocopy |