Sequence
atgc intronic sequence ATGC exonic sequence...aaatgcaaatggcttggattcttcttcgttacagttataatgctcttacagaacattactcatatgtagttgatggcattgattacattggatgttgcagGGGATGATTACAAGATTAAAGTTTGGAACTACAAAACTCACAGGTGTCTTTTCACTCTTCTCGGGCATCTTGATTATATCCGCACTGTCCAATTTCACCA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G21390.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g50340.1 (Oryza sativa), 3'ss of exon 1
aaatgcaaatggcttggattcttcttcgttacagttataatgctcttacagaacattactca-tatgtagttgatggcattgattacattggatgttgcagGGGATGATTACAAGATTAAAGTTTGGAACTACAAAACTCACAGGTGTCTTTTCACTCTTCTCGGGCATCTTGATTATATCCGCACTGTCCAATTTCACCA
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-catactggtgtccggtcgtattgctcggtggactaatatgattgggatgcggaatggttgaacttctgaactattctaagatttctgtgatgcattgcagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCTTCACACTTCACGGGCACCTTGACTATATTCGCACCGTGCAATTCCACCA
upper sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g04110.2 (Oryza sativa), 3'ss of exon 1
aaatgcaaatggcttggattcttcttcgttacagtta-----taatgctcttacagaacattactcatatgtagttgatggcattgattacattggatgttgcagGGGATGATTACAAGATTAAAGTTTGGAACTACAAAACTCACAGGTGTCTTTTCACTCTTCTCGGGCATCTTGATTATATCCGCACTGTCCAATTTCACCA
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-----tgttccgcctggttgtatttctgggatagctgtgggctaatacgattgggatatggaattgttgaatcgtagattctaagatttctgtgatgcattgcagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCTTCACACTTCATGGGCACCTTGACTACATTCGCACCGTGCAATTCCACCA
upper sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G04290.2 (Glycine max), 3'ss of exon 1
aaatgcaaatggcttggattcttcttcgttacagttataatgctcttacagaacattactcat-atgtagttgatggcatt-gattacattggatgtt-----gcagGGGATGATTACAAGATTAAAGTTTGGAACTACAAAACTCACAGGTGTCTTTTCACTCTTCTCGGGCATCTTGATTATATCCGCACTGTCCAATTTCACCA
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-------ggtggagaagattttgatgtgctatgtacatcatgtgaaaggggagggttttgctttatacaatttacagcttttgactatattttgtttcttgggacagGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGTTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACTGTGCAATTTCATCA
upper sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G12080.1 (Glycine max), 3'ss of exon 1
aaatgcaaatggcttggattcttcttcgttacagttataatgctcttacagaacattactca-tatgtagttgatggcattgattacattggatgttgcagGGGATGATTACAAGATTAAAGTTTGGAACTACAAAACTCACAGGTGTCTTTTCACTCTTCTCGGGCATCTTGATTATATCCGCACTGTCCAATTTCACCA
| | | || || | || || | || | | | ||| || | | || | || | | || || || |||||||||||||||||||||| ||||||||||| || | || ||||| | ||||||||||| || || |||||||||||||| || || |||||||| ||
gtacattggtataataagttatttattgtc-catgtggaaggggagggctttgctttatacaatttacagcttattgactatatattgtttcttgggacagGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGCTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACCGTGCAATTTCATCA
upper sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S135_34V6.1 (Physcomitrella patens), 3'ss of exon 1
aaatgcaaatggcttggattcttcttcgttacagttataatgctcttacagaacattactcatatgtagttgatggc-attgattaca----ttggatgttgcagGGGATGATTACAAGATTAAAGTTTGGAACTACAAAACTCACAGGTGTCTTTTCACTCTTCTCGGGCATCTTGATTATATCCGCACTGTCCAATTTCACCA
| | | || | ||| || | | | | || | || || || || | | | | | | | | ||| | ||||||||||||||||||||| || || ||||||||||| | | | ||||| |||||| | | || || || ||||| ||||| || || ||||| || ||
-----ttattatgcctggttttacttggtgggattccctaggttcgtgtgatcttttcatcgtacctatataaagtttaataactgtaggaattgcaaaatgcagGGGATGATTACAAGATAAAGGTATGGAACTACAAGATGCGGCGATGTCTGTTCACTTTGTTGGGTCACCTCGATTACATCCGGACGGTACAATTCCATCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacagaacattactcatatgtagttgatggcattgattacattggatgttgcagGGGATGATTACAAGATTAAAGTTTGGAACTACAAAACTCACAGGTGTCTTTTCACTCTTCTCGGGCATCTTGATTATATCCGCACTGTCCAATTTCACCA
attgatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatgcaaatggcttggattcttcttcgttacagttataatgctcttacagaacattactcatatgtagttgatggcattgattacattggatgttgcagGGGATGATTACAAGATTAAAGTTTGGAACTACAAAACTCACAGGTGTCTTTTCACTCTTCTCGGGCATCTTGATTATATCCGCACTGTCCAATTTCACCA
- atgcaaa
- - - - - ggcttgg
- - - - - - - - - - cttcttc
- - - - - - - - - - - - - - - - - - - - - - - - cagaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -actcata