Sequence
atgc intronic sequence ATGC exonic sequencegtatcttaagtttcaacctttttgatagacaagcctctactttttatgcaacctttaaaatcttacacaattgtgattacatttcagCCTGTGATACTTGATTATCTTGCTAGCAAGTCAATTTCCTCTGAGGATTTGGTAGTGGTTTCTCCTGATGTTGGTGGAGTAGCCAGGGCACGTGCATTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G32380.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g03540.1 (Oryza sativa), 3'ss of exon 4
------------gtatcttaagtttcaacctttttgatagacaagcctctactttttatgcaacctttaaaatcttacacaattgtgattacatttcagCCTGTGATACTTGATTATCTTGCTAGCAAGTCAATTTCCTCTGAGGATTTGGTAGTGGTTTCTCCTGATGTTGGTGGAGTAGCCAGGGCACGTGCATTTG
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gtatgcactgatgcatgttgactgataactgcttgcatgt----gatttcatttatgattataactttgtctttctttttgattctttgatctgtcaagCCTGTGATTCTTGATTACCTCGCCAGCAAGACAATATGTTCAGATGACCTGGTGGTGGTGTCTCCGGATGTTGGAGGTGTTGCCAGGGCACGTGCTTTTG
upper sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G038791_T01 (Zea mays), 3'ss of exon 4
------------------gtatcttaagtt--tcaacctttttgatagacaagcctctactttttatgcaacctt--taaaatcttacacaattgtgattacat------ttcagCCTGTGATACTTGATTATCTTGCTAGCAAGTCAATTTCCTCTGAGGATTTGGTAGTGGTTTCTCCTGATGTTGGTGGAGTAGCCAGGGCACGTGCATTTG
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gtatatgtactgaagcatgctacttaaatctattaattcctttaagacttagtgtttatgatggtattcatccttcttataattgttttctatttttcctgtttgatccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTGGTAGTTGTATCTCCTGATGTTGGAGGTGTTGCCAGGGCACGTGCCTTTG
upper sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 4
gtatcttaagtttcaaccttt--ttgatagacaagcctctactttttatgcaacctttaa-aatcttacacaattgtgat-tacatttcagCCTGTGATACTTGATTATCTTGCTAGCAAGTCAATTTCCTCTGAGGATTTGGTAGTGGTTTCTCCTGATGTTGGTGGAGTAGCCAGGGCACGTGCATTTG
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gtaattaatttttaagccattgtttgatccttat-ctttttctgactccatatcactgaatgaaattac-tgtttgttttgtgcacacaagCCTGTGATTCTTGATTATCTTGCCAGCAAGACAATTTGTTGTAATGATTTGGTAGTGGTCTCACCTGATGTTGGAGGAGTTGCAAGAGCACGTGCTTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcctctactttttatgcaacctttaaaatcttacacaattgtgattacatttcagCCTGTGATACTTGATTATCTTGCTAGCAAGTCAATTTCCTCTGAGGATTTGGTAGTGGTTTCTCCTGATGTTGGTGGAGTAGCCAGGGCACGTGCATTTG
atcttac putative branch site (score: 3)
tttaaaatcttaca TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcttaagtttcaacctttttgatagacaagcctctactttttatgcaacctttaaaatcttacacaattgtgattacatttcagCCTGTGATACTTGATTATCTTGCTAGCAAGTCAATTTCCTCTGAGGATTTGGTAGTGGTTTCTCCTGATGTTGGTGGAGTAGCCAGGGCACGTGCATTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG