Gene loci information

Transcript annotation

  • This transcript has been annotated as Amyloid-beta-like protein.

Parent gene

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.t2 TSS g3809.t2 28044968 28044968
chr_3 g3809 g3809.t2 isoform g3809.t2 28044991 28065912
chr_3 g3809 g3809.t2 exon g3809.t2.exon1 28044991 28045116
chr_3 g3809 g3809.t2 cds g3809.t2.CDS1 28044991 28045116
chr_3 g3809 g3809.t2 exon g3809.t2.exon2 28045173 28046138
chr_3 g3809 g3809.t2 cds g3809.t2.CDS2 28045173 28046138
chr_3 g3809 g3809.t2 exon g3809.t2.exon3 28046698 28046868
chr_3 g3809 g3809.t2 cds g3809.t2.CDS3 28046698 28046868
chr_3 g3809 g3809.t2 exon g3809.t2.exon4 28058053 28058191
chr_3 g3809 g3809.t2 cds g3809.t2.CDS4 28058053 28058191
chr_3 g3809 g3809.t2 exon g3809.t2.exon5 28061376 28061597
chr_3 g3809 g3809.t2 cds g3809.t2.CDS5 28061376 28061597
chr_3 g3809 g3809.t2 exon g3809.t2.exon6 28063548 28063790
chr_3 g3809 g3809.t2 cds g3809.t2.CDS6 28063548 28063790
chr_3 g3809 g3809.t2 exon g3809.t2.exon7 28063921 28064087
chr_3 g3809 g3809.t2 cds g3809.t2.CDS7 28063921 28064087
chr_3 g3809 g3809.t2 exon g3809.t2.exon8 28064229 28064384
chr_3 g3809 g3809.t2 cds g3809.t2.CDS8 28064229 28064384
chr_3 g3809 g3809.t2 exon g3809.t2.exon9 28064458 28064607
chr_3 g3809 g3809.t2 cds g3809.t2.CDS9 28064458 28064607
chr_3 g3809 g3809.t2 exon g3809.t2.exon10 28064662 28065299
chr_3 g3809 g3809.t2 cds g3809.t2.CDS10 28064662 28065299
chr_3 g3809 g3809.t2 exon g3809.t2.exon11 28065361 28065502
chr_3 g3809 g3809.t2 cds g3809.t2.CDS11 28065361 28065502
chr_3 g3809 g3809.t2 exon g3809.t2.exon12 28065574 28065744
chr_3 g3809 g3809.t2 cds g3809.t2.CDS12 28065574 28065744
chr_3 g3809 g3809.t2 exon g3809.t2.exon13 28065817 28065912
chr_3 g3809 g3809.t2 cds g3809.t2.CDS13 28065817 28065912
chr_3 g3809 g3809.t2 TTS g3809.t2 28066015 28066015

Sequences

>g3809.t2 Gene=g3809 Length=3387
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
CCTGATCCATACTTCACTCACTTTGATCCGCGAATAGAACATCAAAGCTATAAAGAAGCA
CAACAACGTTTGGAGGAAGCACATCGTGAAAAGGTGACTCGTGTCATGAAAGATTGGTCT
GATTTGGAGGAGCGCTATCAAGATATGCGCTTAGCCGATCCCAAATCAGCTCAAAGTTTT
AAGCAGAAGATGACGGCTCGATTCCAAGTAACTTCCGTTCAGGCACTTGAAGAAGAAGGA
AATGCAGAGAAACATCAATTAGCTGCTATGCATCAACAGCGAGTTTTAGCTCACATTAAT
CAACGCAAACGTGAGGCAATGACATGTTATACACAAGCTCTAACTGAACTTCCACCAAAT
GGTCATCGTGTTGAAAAATGCTTACAAAAACTTCTTCGTGCTCTTCATAAGGATCGTGCA
CATGCATTGGCTCATTATCGTCATCTTTTGAGCTCAGGTGGAACAGGTGGTCTTGAAGCT
GCAGCACAAGAACGTCCACGCACATTGGAACGTTTGATTGATATTGATCGTGCCGTAAAT
CAATCAATGACAATGCTAAAACGTTATCCATCACTTTCAAAGAAACTTTCACAACTTATG
GAAGATTATATTCAAGCATTGCGTTCAAAGGACGATACACCTGGTCTTTTACTTTCAATG
ACAGAAGAAGCAGAATCAGGAATTTTGGATAAATACCGTATTGAGATTGAACGAAAAGTA
AATGAAAAAGAACGACAGCGTGTTGCTGAAAAGCAACGTAAAGAACAACGTTCACAGGAG
CGTGAAAAGATTCGAGAAGAAAAGATGCGTTTACAAGCAAAGAATGCTGAAAAAGCTTAT
CGTGCACAACAAATGAAAGAGAAAGATCAACAACAAGATCATCAAGAACAAGAGACAAAG
ACAGAAGCTGCACAACAATCGTCCAAGGAGCAGACAAGTGAAGCTGCTATTGATGTTAAA
GAAACAACTGTTGAATACACTGAAGAATCAGTTTATCTAACTTCACCAACATCATTGCCA
ACAGTTGATGATGCAGCTGTTCAACGAGCTGTTGAAGAAGTTGCTGCTGCCGTTGCCCAT
CAAGAAACCGAGCCACAATTAAGTCATGCACGTGCTCATGATTTCGGACATGGAGAAGCT
AGTTTCTCAGTTCGTCGTGAAATTTATGGAGGTCGTGAAGGTCGAAATGTCTATTTCACA
TTGGCATTTGCTGGTGTTGCATTAATGGCTGCTGTATTTGTTGGCGTTGCAGTTGCAAAG
TATCGTGCATCACGTTCACCACACGCTCAAGGATTTGTTGAGGTCGATCAGACGGTTGCT
GTTCCAGTTACACCAGAGGAACGACACGTAGCAAATATGCAAATTAATGGTTATGAAAAT
CCCACATACAAGTACTTTACAGAGTAA

>g3809.t2 Gene=g3809 Length=1128
MAEVIKCRAAVCWAKNEIKIEEIEVAPPKKNEVRIKVVASGLCHSDISGMKGKFNDQFPI
ILGHEGSGIVESIGEGVANVKPGDHVLFVLCPQCDECRVCKKGKNNICFSKTFGRKDMSD
GTTRFSCRGQEIHHFMRAATFSQYTVVSVDNCVKINENAPLEKVCLLACGVPTGYGAVIN
SAKVEEGSTCAIFGLGAIGLSAVMGCRDSKASRIVAIDINSDKFELAKEYGATDCINPKD
LDTPIEKYLQKEFDGGFDYTFECIGLIETMTQAWESTFLGHGECIIIGVDAKEKMLSISP
FATLFGKKIRGSAFGGYKSEDLPKLVEKYIKGELNFDEMITHNLTLNDIKKAIELLESGK
SIRSCSSPRWEPQISVLCEPGQQYLPQFLSEDGRWTSELSVKVPGVSCLRDKMDLLDYCK
KVYPGRDITNIVESSHYQKIGGWCRQGATNLGKCKGAQRWIKPFRCLEGPFQSDALLVPE
GCLFDHIHNASRCWPFVRWNQTGAAACQERNMQMRSFAMLLPCGISLFSGVEFVCCPKHF
KVVPPKVKKTDLPILPPESEILPSLDDSEDNFSDDLDEDEDLDDQDEMVADEPLETLEEE
EDEDEYDSDEDTPTLDSEFPNDAIPINDYVNLQTTSQTPDKPISEIPISVNDGQSTSIPT
PDPYFTHFDPRIEHQSYKEAQQRLEEAHREKVTRVMKDWSDLEERYQDMRLADPKSAQSF
KQKMTARFQVTSVQALEEEGNAEKHQLAAMHQQRVLAHINQRKREAMTCYTQALTELPPN
GHRVEKCLQKLLRALHKDRAHALAHYRHLLSSGGTGGLEAAAQERPRTLERLIDIDRAVN
QSMTMLKRYPSLSKKLSQLMEDYIQALRSKDDTPGLLLSMTEEAESGILDKYRIEIERKV
NEKERQRVAEKQRKEQRSQEREKIREEKMRLQAKNAEKAYRAQQMKEKDQQQDHQEQETK
TEAAQQSSKEQTSEAAIDVKETTVEYTEESVYLTSPTSLPTVDDAAVQRAVEEVAAAVAH
QETEPQLSHARAHDFGHGEASFSVRREIYGGREGRNVYFTLAFAGVALMAAVFVGVAVAK
YRASRSPHAQGFVEVDQTVAVPVTPEERHVANMQINGYENPTYKYFTE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g3809.t2 Coils Coil Coil 733 753 -
24 g3809.t2 Coils Coil Coil 889 937 -
22 g3809.t2 Gene3D G3DSA:3.90.180.10 - 16 362 2.3E-128
17 g3809.t2 Gene3D G3DSA:3.40.50.720 - 174 312 2.3E-128
21 g3809.t2 Gene3D G3DSA:3.90.570.10 - 363 472 7.0E-33
18 g3809.t2 Gene3D G3DSA:3.30.1490.140 Amyloid beta a4 protein copper binding domain 480 538 2.9E-24
20 g3809.t2 Gene3D G3DSA:1.20.120.770 - 651 875 8.0E-84
19 g3809.t2 Gene3D G3DSA:2.30.29.30 - 1103 1128 2.3E-7
35 g3809.t2 MobiDBLite mobidb-lite consensus disorder prediction 592 623 -
36 g3809.t2 MobiDBLite mobidb-lite consensus disorder prediction 592 616 -
33 g3809.t2 MobiDBLite mobidb-lite consensus disorder prediction 902 980 -
34 g3809.t2 MobiDBLite mobidb-lite consensus disorder prediction 902 960 -
7 g3809.t2 PANTHER PTHR23103:SF15 AMYLOID-BETA-LIKE PROTEIN 361 1126 2.4E-253
8 g3809.t2 PANTHER PTHR23103 ALZHEIMER’S DISEASE BETA-AMYLOID RELATED 361 1126 2.4E-253
9 g3809.t2 PRINTS PR00203 Amyloid A4 protein precursor signature 526 544 6.4E-9
10 g3809.t2 PRINTS PR00203 Amyloid A4 protein precursor signature 1106 1128 6.4E-9
6 g3809.t2 Pfam PF08240 Alcohol dehydrogenase GroES-like domain 31 155 3.7E-24
3 g3809.t2 Pfam PF00107 Zinc-binding dehydrogenase 197 327 2.8E-20
2 g3809.t2 Pfam PF02177 Amyloid A4 N-terminal heparin-binding 371 480 6.0E-32
5 g3809.t2 Pfam PF12924 Copper-binding of amyloid precursor, CuBD 481 537 3.2E-22
1 g3809.t2 Pfam PF12925 E2 domain of amyloid precursor protein 656 846 5.4E-76
4 g3809.t2 Pfam PF10515 Beta-amyloid precursor protein C-terminus 1072 1126 1.0E-23
26 g3809.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 1056 -
27 g3809.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 1057 1079 -
25 g3809.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1080 1128 -
30 g3809.t2 ProSitePatterns PS00059 Zinc-containing alcohol dehydrogenases signature. 63 77 -
32 g3809.t2 ProSitePatterns PS00319 Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. 530 537 -
31 g3809.t2 ProSitePatterns PS00320 Amyloid precursor protein (APP) intracellular domain signature. 1117 1124 -
38 g3809.t2 ProSiteProfiles PS51869 Amyloid precursor protein (APP) E1 domain profile. 368 538 34.289
37 g3809.t2 ProSiteProfiles PS51870 Amyloid precursor protein (APP) E2 domain profile. 660 863 95.765
29 g3809.t2 SMART SM00006 A4_EXTRA_3 364 537 3.2E-106
15 g3809.t2 SUPERFAMILY SSF50129 GroES-like 3 182 7.76E-63
12 g3809.t2 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 160 332 6.93E-41
14 g3809.t2 SUPERFAMILY SSF50129 GroES-like 318 365 1.39E-7
16 g3809.t2 SUPERFAMILY SSF56491 A heparin-binding domain 369 472 1.07E-30
11 g3809.t2 SUPERFAMILY SSF89811 Amyloid beta a4 protein copper binding domain (domain 2) 473 538 1.31E-26
13 g3809.t2 SUPERFAMILY SSF109843 CAPPD, an extracellular domain of amyloid beta A4 protein 661 863 4.71E-73
28 g3809.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 1057 1079 -

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

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.

Raw TPM values