Sequence
atgc intronic sequence ATGC exonic sequence...gtgtgagtgaagaaattgggatatagatctggtttgcgtttaggaccctgccatgtcatcttccaacatatataactacaacatataatttcatggacagGTGAAAGTCCCAACTCGAGTCAATGGGTCGGAGTACACGGAGTATGTTGGTGTTGGTGCTAGGTTTGGCCCAACCTTGGAATCTAAGGAGAAACATGCTA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01650.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01650.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g51430.1 (Oryza sativa), 3'ss of exon 1
gtgtgagtgaagaaattgggatatagatc-tggtttgcgtttaggaccctgccatgtcatc--ttccaacatatataactacaacatataatttcatggac--agGTGAAAGTCCCAACTCGAGTCAATGGGTCGGAGTACACGGAGTATGTTGGTGTTGGTGCTAGGTTTGGCCCAACCTTGGAATCTAAGGAGAAACATGCTA
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-----cctgtacaatgtgaaacataaattatgttgtacttgcataattttcttttctggtcagtactctctctgatcattttgtcttctgtcccattaaattaagGTCAAAGTGCAAAGTTGGGTCAACGGCAAAGAGGATGATGAGTATGTTGGTGTTGGTGCTCGGTTTGGCCCGCAAATAGTGTCCAAGGAGAAACATGCAA
upper sequence: AT1G01650.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G01100.2 (Glycine max), 3'ss of exon 1
-gtgtgagtgaagaaattgggatatagatctggtttgcgtttaggaccctgccatgtcatctt--ccaacatatataactacaacatataatttcatggacagGTGAAAGTCCCAACTCGAGTCAATGGGTCGGAGTACACGGAGTATGTTGGTGTTGGTGCTAGGTTTGGCCCAACCTTGGAATCTAAGGAGAAACATGCTA
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tatgcaggctatttctgttttcttaaattgtgaattgccatatatacatatgcatgcctttttatttaacagctttgatcaatttcttcacttctgt---tagGTAAAAGTCCCCACTTGGATTGATGGTGTGGAAAACAGTGAGTATGTTGGTGTTGGTGCAAGATTTGGCCCTACATTGGAATCAAAAGAAAAACGGGCCA
upper sequence: AT1G01650.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G39500.1 (Glycine max), 3'ss of exon 1
-----gtgtga-gtgaagaaattgggatatagatctggtttgcgtttaggaccctgccatgtcatcttccaacatatataactacaacatataatttcatggacagGTGAAAGTCCCAACTCGAGTCAATGGGTCGGAGTACACGGAGTATGTTGGTGTTGGTGCTAGGTTTGGCCCAACCTTGGAATCTAAGGAGAAACATGCTA
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ctaccatgtggcatgttgctgttgccttacaaaggttgatag-gtgtaaagtatgaataagttttttctcta-----acaacttcgaccaatttctcttttgttagGTTAAAGTCCCTACTTGGATTGATGGTGTGGAAAGCTTTGAGTATGTTGGCGTTGGTGCAAGATTTGGCCCTACATTAGAATCAAAAGAAAAACATGCTA
upper sequence: AT1G01650.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 1
gtgtgagtgaagaaattgggatatagatctggtttgcgttt-aggaccctgccatgtcatcttccaac----atatataactacaac----atataatttcatgg-acagGTGAAAGTCCCAACTCGAGTCAATGGGTCGGAGTACACGGAGTATGTTGGTGTTGGTGCTAGGTTTGGCCCAACCTTGGAATCTAAGGAGAAACATGCTA
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----------aggcatgaatatgttgagccatttcttgttttattaaccctttgttttattccacaaggagaatctgtaattgtactcataatccgctttgatttcatagGTAAAAGTACCAACTTGGGTTGATCATGAAGAAGGGAATGAATATGTTGGTGTTGGTGCTCGATTCGGTCCTACCTTGGAATCAAAAGAGAAACATGCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccctgccatgtcatcttccaacatatataactacaacatataatttcatggacagGTGAAAGTCCCAACTCGAGTCAATGGGTCGGAGTACACGGAGTATGTTGGTGTTGGTGCTAGGTTTGGCCCAACCTTGGAATCTAAGGAGAAACATGCTA
atataac putative branch site (score: 3)
aacatatataactaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgagtgaagaaattgggatatagatctggtttgcgtttaggaccctgccatgtcatcttccaacatatataactacaacatataatttcatggacagGTGAAAGTCCCAACTCGAGTCAATGGGTCGGAGTACACGGAGTATGTTGGTGTTGGTGCTAGGTTTGGCCCAACCTTGGAATCTAAGGAGAAACATGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - -aagaaat
- - - - - - - - - - - - - - - ggtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatata