Sequence
atgc intronic sequence ATGC exonic sequencegtatccttactaatttctagtattaaatcttgataccttggcctttgaatggattcttcttctatgttaaaaaatactagagaacacttgatttttgattgcattgctgttatgggaattaaggagaaaaatatttaaatagatttgttcctgtttaaccttaagtcacgtgcagAGATCTTAATCACTCGAACCAGTATGTTGTAGGACTTGCTCTCTGTGCTTTAGGGAATATTTGTTCAGCAGAAATGGCCCGTGATCTTGCGCCAGAAGTA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G23900.1 |
intron # | 3 |
splice site | 3' |
intron type | U12 (go to U12 genes for details) |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G23900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g07090.2 (Oryza sativa), 3'ss of exon 2
gtatccttactaatttctagtattaaatcttgataccttggcctttgaatggattcttcttctatgttaaaaaatactagagaacacttgatttttgattgcattgctgttatgggaattaaggagaaaaatatttaaatagatttgttcctgtttaaccttaagtcacgtgcagAGATCTTAATCACTCGAACCAGTATGTTGTAGGACTTGCTCTCTGTGCTTTAGGGAATATTTGTTCAGCAGAAATGGCCCGTGATCTTGCGCCAGAAGTA
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-------------------------------------------------------------------------gtatccacccatactatacttatgctc-catatctgttttgatttttctt-agaatgctatgttctgctttgagcatttggtagtacttaa--cgcggacagAGATCTTAACCACTCGAACCAGTTCATTGTGGGGCTTGCACTCTGTGCTCTTGGCAACATTTGCTCCGCTGAAATGGCGCGTGATCTGTCACCTGAGGTG
upper sequence: AT1G23900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G030144_T01 (Zea mays), 3'ss of exon 2
gtatccttactaatttctagtattaaatcttgataccttggcctttgaatggattcttcttctatgttaaaaaatactagagaacacttgatttttgattgcattgctgttatgggaattaaggagaaaaatatttaaatagat-----ttgttcctgtttaaccttaagtcacgtg--cagAGATCTTAATCACTCGAACCAGTATGTTGTAGGACTTGCTCTCTGTGCTTTAGGGAATATTTGTTCAGCAGAAATGGCCCGTGATCTTGCGCCAGAAGTA
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----------------------------------------------------------------------------------------------------gtatccaccctgtctgcacttaacagttgtgtttgttgattgttatgcgttgtttctgattgtaattacttaacgtgggcagAGATCTTAACCACTCAAACCAGTTCATTGTTGGTCTTGCACTCTGTGCCCTTGGCAATATATGTTCTGCTGAAATGGCGCGTGATCTTGCTCCTGAAGTG
upper sequence: AT1G23900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G18490.1 (Glycine max), 3'ss of exon 3
gtatccttactaatttctagtattaaatcttgataccttggcctttgaatggattcttcttctatgttaaaaaatactagagaacacttgatttttgattgcattgctgttatgggaattaaggagaaaaatatttaaatagatttgttcctgtttaaccttaagtcacgtgcagAGATCTTAATCACTCGAACCAGTATGTTGTAGGACTTGCTCTCTGTGCTTTAGGGAATATTTGTTCAGCAGAAATGGCCCGTGATCTTGCGCCAGAAGTA
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--------------------------------------------------------gtttcatttgtttttgtgttcctca-atttttagattccattttacaaatatgcta-gggagctagcaatattgatgatggga--gatgggttataaa--aaccttagctaagtcacagAGATCTTAATCACACGAATCAATATATAGTGGGACTTGCTCTTTGTGCTTTAGGAAATATTTGTTCAGCTGAAATGGCTCATGATCTTGCGCCAGAGGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaggagaaaaatatttaaatagatttgttcctgtttaaccttaagtcacgtgcagAGATCTTAATCACTCGAACCAGTATGTTGTAGGACTTGCTCTCTGTGCTTTAGGGAATATTTGTTCAGCAGAAATGGCCCGTGATCTTGCGCCAGAAGTA
aaccttaag putative branch site
aaaaatatttaaatag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatccttactaatttctagtattaaatcttgataccttggcctttgaatggattcttcttctatgttaaaaaatactagagaacacttgatttttgattgcattgctgttatgggaattaaggagaaaaatatttaaatagatttgttcctgtttaaccttaagtcacgtgcagAGATCTTAATCACTCGAACCAGTATGTTGTAGGACTTGCTCTCTGTGCTTTAGGGAATATTTGTTCAGCAGAAATGGCCCGTGATCTTGCGCCAGAAGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT