Sequence
atgc intronic sequence ATGC exonic sequence...acttattcccaagttgtcttcattgtcatagttccatctatatgtatgaagcttttcgttttttggatgaatgttagctgatatgaatttctcaacgcagTCCCCAGGTAACAATAGCCACTGCTATATTTTTCTGTCACCGATTCTTCCTTCGTCAATCACATGCGAAAAATGACAGACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G19560.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G19560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G308570_T02 (Zea mays), 3'ss of exon 10
acttattcccaagttgtcttcattgtcatagttccatctatatgtatgaagcttttcgttttttggatgaatgttag-ctgat----atgaatttctcaacgcagTCCCCAGGTAACAATAGCCACTGCTATATTTTTCTGTCACCGATTCTTCCTTCGTCAATCACATGCGAAAAATGACAGACAG
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----gcctgcatgttactgcacgttttatgatgtcttgtttgagt-tgaaatcttttatatatgcaatttttattcttctaatgccaactaactccataatgtagGCCTCAAGTGACAATTGCTACTGCTATAGTGTTCTGTCATCGGTTTTTTCTTCGTCAATCTCATGCGAAAAATGACAGACGG
upper sequence: AT4G19560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: AC233979.1_FGT009 (Zea mays), 3'ss of exon 1
acttattcccaagttgtcttcattgtcatagttccatctatatgtatgaagcttttcgttttttggatgaatgttagctgat----atgaatttctcaacgcagTCCCCAGGTAACAATAGCCACTGCTATATTTTTCTGTCACCGATTCTTCCTTCGTCAATCACATGCGAAAAATGACAGACAG
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---tgcctgcatgctactgcacgggttgtgatatcttgtttgagt-tgaaaccttttttatatgtaatttttttcttctaatgctgatgaactttgtaatgtagACCTCAAGTGACAATTGCTACTGCTATAGTGTTCTGTCATCGGTTCTTTCTTCGTCAATCGCATGCCAAAAATGACAGACGG
upper sequence: AT4G19560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G115670_T01 (Zea mays), 3'ss of exon 1
----acttattcccaagttgtcttcattgtcatagttccatcta-tatgtatgaagcttttcgttttttggatgaatgttagctgatatgaatttctcaacgcagTCCCCAGGTAACAATAGCCACTGCTATATTTTTCTGTCACCGATTCTTCCTTCGTCAATCACATGCGAAAAATGACAGACAG
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tggaacttttttatgttttaaatggactg-cattgt--catcaaatatgttggaagtcttttagctcatccttttctcatagtcatt--ggttcgctgtttttagGCCCCAAGTGACGATTGCTACAGCTACGGTATTCTGTCACCGTTTTTTCCTTCGTCAATCCCATGCAAAGAATGATAGACGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgaagcttttcgttttttggatgaatgttagctgatatgaatttctcaacgcagTCCCCAGGTAACAATAGCCACTGCTATATTTTTCTGTCACCGATTCTTCCTTCGTCAATCACATGCGAAAAATGACAGACAG
agctgat putative branch site (score: 4)
tttctc putative PPT
atatgaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acttattcccaagttgtcttcattgtcatagttccatctatatgtatgaagcttttcgttttttggatgaatgttagctgatatgaatttctcaacgcagTCCCCAGGTAACAATAGCCACTGCTATATTTTTCTGTCACCGATTCTTCCTTCGTCAATCACATGCGAAAAATGACAGACAG
- - - - ccaagtt
- - - - - - - - - - - - - - - - -ccatcta