General information for g3809.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Amyloid-beta-like protein.
Parent gene
- The parent gene g3809 is located on chr_3: 28064662..28065912 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_3 | g3809 | g3809.t1 | TSS | g3809.t1 | 28044968 | 28044968 |
| chr_3 | g3809 | g3809.t1 | isoform | g3809.t1 | 28044991 | 28065912 |
| chr_3 | g3809 | g3809.t1 | exon | g3809.t1.exon1 | 28044991 | 28045116 |
| chr_3 | g3809 | g3809.t1 | cds | g3809.t1.CDS1 | 28044991 | 28045116 |
| chr_3 | g3809 | g3809.t1 | exon | g3809.t1.exon2 | 28045173 | 28046138 |
| chr_3 | g3809 | g3809.t1 | cds | g3809.t1.CDS2 | 28045173 | 28046138 |
| chr_3 | g3809 | g3809.t1 | exon | g3809.t1.exon3 | 28046698 | 28046868 |
| chr_3 | g3809 | g3809.t1 | cds | g3809.t1.CDS3 | 28046698 | 28046868 |
| chr_3 | g3809 | g3809.t1 | exon | g3809.t1.exon4 | 28058053 | 28058191 |
| chr_3 | g3809 | g3809.t1 | cds | g3809.t1.CDS4 | 28058053 | 28058191 |
| chr_3 | g3809 | g3809.t1 | exon | g3809.t1.exon5 | 28061376 | 28061597 |
| chr_3 | g3809 | g3809.t1 | cds | g3809.t1.CDS5 | 28061376 | 28061597 |
| chr_3 | g3809 | g3809.t1 | exon | g3809.t1.exon6 | 28063548 | 28063790 |
| chr_3 | g3809 | g3809.t1 | cds | g3809.t1.CDS6 | 28063548 | 28063790 |
| chr_3 | g3809 | g3809.t1 | exon | g3809.t1.exon7 | 28063921 | 28064099 |
| chr_3 | g3809 | g3809.t1 | cds | g3809.t1.CDS7 | 28063921 | 28064099 |
| chr_3 | g3809 | g3809.t1 | exon | g3809.t1.exon8 | 28064229 | 28064384 |
| chr_3 | g3809 | g3809.t1 | cds | g3809.t1.CDS8 | 28064229 | 28064384 |
| chr_3 | g3809 | g3809.t1 | exon | g3809.t1.exon9 | 28064458 | 28064607 |
| chr_3 | g3809 | g3809.t1 | cds | g3809.t1.CDS9 | 28064458 | 28064607 |
| chr_3 | g3809 | g3809.t1 | exon | g3809.t1.exon10 | 28064662 | 28065299 |
| chr_3 | g3809 | g3809.t1 | cds | g3809.t1.CDS10 | 28064662 | 28065299 |
| chr_3 | g3809 | g3809.t1 | exon | g3809.t1.exon11 | 28065361 | 28065502 |
| chr_3 | g3809 | g3809.t1 | cds | g3809.t1.CDS11 | 28065361 | 28065502 |
| chr_3 | g3809 | g3809.t1 | exon | g3809.t1.exon12 | 28065574 | 28065744 |
| chr_3 | g3809 | g3809.t1 | cds | g3809.t1.CDS12 | 28065574 | 28065744 |
| chr_3 | g3809 | g3809.t1 | exon | g3809.t1.exon13 | 28065817 | 28065912 |
| chr_3 | g3809 | g3809.t1 | cds | g3809.t1.CDS13 | 28065817 | 28065912 |
| chr_3 | g3809 | g3809.t1 | TTS | g3809.t1 | 28066015 | 28066015 |
Sequences
>g3809.t1 Gene=g3809 Length=3399
ATGGCAGAAGTAATAAAATGTCGTGCTGCTGTTTGCTGGGCAAAGAACGAAATTAAAATT
GAAGAAATTGAGGTTGCTCCGCCTAAGAAAAATGAAGTTCGCATTAAAGTTGTTGCTTCT
GGATTGTGTCATTCTGATATTTCTGGAATGAAGGGAAAATTTAATGATCAATTTCCAATA
ATATTGGGCCACGAAGGGTCTGGTATCGTTGAATCAATCGGTGAAGGTGTTGCAAATGTA
AAACCAGGCGATCATGTATTATTTGTCCTATGCCCGCAATGTGATGAATGTCGAGTTTGT
AAAAAAGGAAAAAATAATATTTGTTTTTCAAAAACATTTGGACGAAAAGATATGAGTGAT
GGAACTACAAGGTTTTCTTGTCGTGGTCAAGAAATCCATCATTTTATGAGAGCAGCTACT
TTCTCTCAATATACTGTAGTATCTGTTGATAATTGTGTGAAAATCAATGAAAATGCACCA
CTTGAAAAGGTTTGTTTGTTAGCTTGTGGTGTGCCCACTGGTTATGGAGCAGTCATAAAT
TCAGCAAAGGTCGAAGAAGGAAGCACATGTGCAATTTTTGGACTTGGTGCTATTGGACTT
TCAGCTGTTATGGGTTGTAGAGATTCTAAAGCAAGTCGAATTGTCGCAATTGATATAAAT
TCAGATAAATTCGAACTGGCTAAAGAATATGGTGCAACTGATTGTATCAATCCAAAAGAT
TTAGACACGCCAATTGAAAAATACTTGCAGAAAGAGTTCGATGGTGGTTTCGATTACACT
TTTGAATGTATTGGTCTTATTGAGACAATGACACAAGCTTGGGAATCAACATTTTTGGGT
CATGGTGAATGCATTATTATTGGAGTTGATGCCAAAGAAAAAATGCTTTCAATTTCTCCT
TTTGCCACTCTTTTTGGTAAAAAAATTCGAGGATCTGCCTTTGGCGGTTATAAAAGTGAA
GATTTACCAAAATTGGTTGAGAAATACATCAAAGGCGAATTGAATTTTGATGAAATGATT
ACACATAATTTGACATTGAATGATATCAAGAAAGCAATTGAATTACTTGAAAGTGGCAAA
TCTATAAGAAGTTGTTCATCACCACGCTGGGAGCCACAAATTTCGGTTTTATGTGAGCCA
GGACAACAGTATTTGCCACAATTTCTTTCGGAAGATGGTCGATGGACATCAGAATTAAGT
GTGAAAGTGCCAGGCGTTTCATGTTTACGCGATAAAATGGATTTGCTTGATTATTGCAAG
AAGGTTTATCCTGGACGTGATATAACGAATATTGTTGAGTCATCACATTATCAGAAAATT
GGTGGCTGGTGTAGACAAGGAGCGACAAATTTAGGAAAATGCAAGGGTGCACAGAGATGG
ATCAAACCTTTCCGTTGCTTGGAGGGACCTTTCCAGTCGGATGCACTTCTGGTACCAGAG
GGTTGCTTATTCGATCATATCCATAATGCGTCACGATGCTGGCCATTTGTTCGATGGAAT
CAAACTGGAGCCGCTGCTTGTCAGGAACGCAACATGCAAATGCGAAGCTTTGCAATGTTA
TTGCCATGTGGCATTTCACTCTTTTCGGGTGTCGAATTTGTCTGCTGTCCAAAACATTTC
AAAGTTGTTCCACCTAAGGTAAAGAAAACCGACTTGCCAATTTTGCCACCAGAGTCAGAG
ATTTTGCCATCATTGGATGATTCTGAAGATAATTTTTCTGATGACCTAGATGAAGATGAA
GATTTAGATGATCAAGATGAAATGGTTGCCGATGAGCCGCTTGAGACATTAGAAGAGGAA
GAAGATGAAGACGAATATGATTCAGATGAAGACACACCGACACTCGATTCTGAATTTCCA
AATGATGCAATTCCAATTAATGATTATGTCAACTTACAAACCACATCGCAGACACCTGAT
AAACCAATTTCGGAAATACCGATTTCTGTGAATGATGGCCAGAGCACTTCAATCCCAACA
CCTGATCCATACTTCACTCACTTTGATCCGCGAATAGAACATCAAAGCTATAAAGTAGGA
CTAGATGAAGCACAACAACGTTTGGAGGAAGCACATCGTGAAAAGGTGACTCGTGTCATG
AAAGATTGGTCTGATTTGGAGGAGCGCTATCAAGATATGCGCTTAGCCGATCCCAAATCA
GCTCAAAGTTTTAAGCAGAAGATGACGGCTCGATTCCAAGTAACTTCCGTTCAGGCACTT
GAAGAAGAAGGAAATGCAGAGAAACATCAATTAGCTGCTATGCATCAACAGCGAGTTTTA
GCTCACATTAATCAACGCAAACGTGAGGCAATGACATGTTATACACAAGCTCTAACTGAA
CTTCCACCAAATGGTCATCGTGTTGAAAAATGCTTACAAAAACTTCTTCGTGCTCTTCAT
AAGGATCGTGCACATGCATTGGCTCATTATCGTCATCTTTTGAGCTCAGGTGGAACAGGT
GGTCTTGAAGCTGCAGCACAAGAACGTCCACGCACATTGGAACGTTTGATTGATATTGAT
CGTGCCGTAAATCAATCAATGACAATGCTAAAACGTTATCCATCACTTTCAAAGAAACTT
TCACAACTTATGGAAGATTATATTCAAGCATTGCGTTCAAAGGACGATACACCTGGTCTT
TTACTTTCAATGACAGAAGAAGCAGAATCAGGAATTTTGGATAAATACCGTATTGAGATT
GAACGAAAAGTAAATGAAAAAGAACGACAGCGTGTTGCTGAAAAGCAACGTAAAGAACAA
CGTTCACAGGAGCGTGAAAAGATTCGAGAAGAAAAGATGCGTTTACAAGCAAAGAATGCT
GAAAAAGCTTATCGTGCACAACAAATGAAAGAGAAAGATCAACAACAAGATCATCAAGAA
CAAGAGACAAAGACAGAAGCTGCACAACAATCGTCCAAGGAGCAGACAAGTGAAGCTGCT
ATTGATGTTAAAGAAACAACTGTTGAATACACTGAAGAATCAGTTTATCTAACTTCACCA
ACATCATTGCCAACAGTTGATGATGCAGCTGTTCAACGAGCTGTTGAAGAAGTTGCTGCT
GCCGTTGCCCATCAAGAAACCGAGCCACAATTAAGTCATGCACGTGCTCATGATTTCGGA
CATGGAGAAGCTAGTTTCTCAGTTCGTCGTGAAATTTATGGAGGTCGTGAAGGTCGAAAT
GTCTATTTCACATTGGCATTTGCTGGTGTTGCATTAATGGCTGCTGTATTTGTTGGCGTT
GCAGTTGCAAAGTATCGTGCATCACGTTCACCACACGCTCAAGGATTTGTTGAGGTCGAT
CAGACGGTTGCTGTTCCAGTTACACCAGAGGAACGACACGTAGCAAATATGCAAATTAAT
GGTTATGAAAATCCCACATACAAGTACTTTACAGAGTAA
>g3809.t1 Gene=g3809 Length=1132
MAEVIKCRAAVCWAKNEIKIEEIEVAPPKKNEVRIKVVASGLCHSDISGMKGKFNDQFPI
ILGHEGSGIVESIGEGVANVKPGDHVLFVLCPQCDECRVCKKGKNNICFSKTFGRKDMSD
GTTRFSCRGQEIHHFMRAATFSQYTVVSVDNCVKINENAPLEKVCLLACGVPTGYGAVIN
SAKVEEGSTCAIFGLGAIGLSAVMGCRDSKASRIVAIDINSDKFELAKEYGATDCINPKD
LDTPIEKYLQKEFDGGFDYTFECIGLIETMTQAWESTFLGHGECIIIGVDAKEKMLSISP
FATLFGKKIRGSAFGGYKSEDLPKLVEKYIKGELNFDEMITHNLTLNDIKKAIELLESGK
SIRSCSSPRWEPQISVLCEPGQQYLPQFLSEDGRWTSELSVKVPGVSCLRDKMDLLDYCK
KVYPGRDITNIVESSHYQKIGGWCRQGATNLGKCKGAQRWIKPFRCLEGPFQSDALLVPE
GCLFDHIHNASRCWPFVRWNQTGAAACQERNMQMRSFAMLLPCGISLFSGVEFVCCPKHF
KVVPPKVKKTDLPILPPESEILPSLDDSEDNFSDDLDEDEDLDDQDEMVADEPLETLEEE
EDEDEYDSDEDTPTLDSEFPNDAIPINDYVNLQTTSQTPDKPISEIPISVNDGQSTSIPT
PDPYFTHFDPRIEHQSYKVGLDEAQQRLEEAHREKVTRVMKDWSDLEERYQDMRLADPKS
AQSFKQKMTARFQVTSVQALEEEGNAEKHQLAAMHQQRVLAHINQRKREAMTCYTQALTE
LPPNGHRVEKCLQKLLRALHKDRAHALAHYRHLLSSGGTGGLEAAAQERPRTLERLIDID
RAVNQSMTMLKRYPSLSKKLSQLMEDYIQALRSKDDTPGLLLSMTEEAESGILDKYRIEI
ERKVNEKERQRVAEKQRKEQRSQEREKIREEKMRLQAKNAEKAYRAQQMKEKDQQQDHQE
QETKTEAAQQSSKEQTSEAAIDVKETTVEYTEESVYLTSPTSLPTVDDAAVQRAVEEVAA
AVAHQETEPQLSHARAHDFGHGEASFSVRREIYGGREGRNVYFTLAFAGVALMAAVFVGV
AVAKYRASRSPHAQGFVEVDQTVAVPVTPEERHVANMQINGYENPTYKYFTE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g3809.t1 | Coils | Coil | Coil | 674 | 694 | - |
| 24 | g3809.t1 | Coils | Coil | Coil | 737 | 757 | - |
| 25 | g3809.t1 | Coils | Coil | Coil | 893 | 941 | - |
| 22 | g3809.t1 | Gene3D | G3DSA:3.90.180.10 | - | 16 | 362 | 2.3E-128 |
| 17 | g3809.t1 | Gene3D | G3DSA:3.40.50.720 | - | 174 | 312 | 2.3E-128 |
| 21 | g3809.t1 | Gene3D | G3DSA:3.90.570.10 | - | 363 | 472 | 7.1E-33 |
| 18 | g3809.t1 | Gene3D | G3DSA:3.30.1490.140 | Amyloid beta a4 protein copper binding domain | 480 | 538 | 2.9E-24 |
| 20 | g3809.t1 | Gene3D | G3DSA:1.20.120.770 | - | 651 | 879 | 4.3E-81 |
| 19 | g3809.t1 | Gene3D | G3DSA:2.30.29.30 | - | 1107 | 1132 | 2.3E-7 |
| 35 | g3809.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 592 | 623 | - |
| 37 | g3809.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 592 | 616 | - |
| 34 | g3809.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 906 | 984 | - |
| 36 | g3809.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 906 | 964 | - |
| 7 | g3809.t1 | PANTHER | PTHR23103:SF15 | AMYLOID-BETA-LIKE PROTEIN | 361 | 1130 | 1.4E-250 |
| 8 | g3809.t1 | PANTHER | PTHR23103 | ALZHEIMER’S DISEASE BETA-AMYLOID RELATED | 361 | 1130 | 1.4E-250 |
| 9 | g3809.t1 | PRINTS | PR00203 | Amyloid A4 protein precursor signature | 526 | 544 | 6.5E-9 |
| 10 | g3809.t1 | PRINTS | PR00203 | Amyloid A4 protein precursor signature | 1110 | 1132 | 6.5E-9 |
| 6 | g3809.t1 | Pfam | PF08240 | Alcohol dehydrogenase GroES-like domain | 31 | 155 | 3.7E-24 |
| 3 | g3809.t1 | Pfam | PF00107 | Zinc-binding dehydrogenase | 197 | 327 | 2.8E-20 |
| 2 | g3809.t1 | Pfam | PF02177 | Amyloid A4 N-terminal heparin-binding | 371 | 480 | 6.0E-32 |
| 5 | g3809.t1 | Pfam | PF12924 | Copper-binding of amyloid precursor, CuBD | 481 | 537 | 3.3E-22 |
| 1 | g3809.t1 | Pfam | PF12925 | E2 domain of amyloid precursor protein | 656 | 850 | 2.1E-73 |
| 4 | g3809.t1 | Pfam | PF10515 | Beta-amyloid precursor protein C-terminus | 1076 | 1130 | 1.0E-23 |
| 27 | g3809.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 1060 | - |
| 28 | g3809.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1061 | 1083 | - |
| 26 | g3809.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1084 | 1132 | - |
| 31 | g3809.t1 | ProSitePatterns | PS00059 | Zinc-containing alcohol dehydrogenases signature. | 63 | 77 | - |
| 33 | g3809.t1 | ProSitePatterns | PS00319 | Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. | 530 | 537 | - |
| 32 | g3809.t1 | ProSitePatterns | PS00320 | Amyloid precursor protein (APP) intracellular domain signature. | 1121 | 1128 | - |
| 39 | g3809.t1 | ProSiteProfiles | PS51869 | Amyloid precursor protein (APP) E1 domain profile. | 368 | 538 | 34.289 |
| 38 | g3809.t1 | ProSiteProfiles | PS51870 | Amyloid precursor protein (APP) E2 domain profile. | 660 | 867 | 88.675 |
| 30 | g3809.t1 | SMART | SM00006 | A4_EXTRA_3 | 364 | 537 | 3.2E-106 |
| 15 | g3809.t1 | SUPERFAMILY | SSF50129 | GroES-like | 3 | 182 | 7.91E-63 |
| 12 | g3809.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 160 | 332 | 7.07E-41 |
| 14 | g3809.t1 | SUPERFAMILY | SSF50129 | GroES-like | 318 | 365 | 1.41E-7 |
| 16 | g3809.t1 | SUPERFAMILY | SSF56491 | A heparin-binding domain | 369 | 472 | 1.07E-30 |
| 11 | g3809.t1 | SUPERFAMILY | SSF89811 | Amyloid beta a4 protein copper binding domain (domain 2) | 473 | 538 | 1.31E-26 |
| 13 | g3809.t1 | SUPERFAMILY | SSF109843 | CAPPD, an extracellular domain of amyloid beta A4 protein | 661 | 867 | 2.35E-70 |
| 29 | g3809.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1061 | 1083 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0046914 | transition metal ion binding | MF |
| GO:0016021 | integral component of membrane | CC |
| GO:0008270 | zinc ion binding | MF |
| GO:0008201 | heparin binding | MF |
| GO:0055114 | NA | NA |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K04520 (amyloid beta A4 protein)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
