Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttgattaatacactttcactctctaatccatattatgagtgtttcttaatttattaatgttcatatatacagATAAGATACAGAAGAGAATCCCCACTGGTTCTAAAAGGAATCAGCTGCACATTTGAAGGAGGACACAAGATTGGAATTGTTGGCCGAACCGGTAGTGGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G59140.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G59140.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G37160.1 (Glycine max), 3'ss of exon 7
-------------------gtaagtttgattaatacactttcactctctaatc---catattatgagtgtttcttaatttattaatgttcatatatacagATAAGATACAGAAGAGAATCCCCACTGGTTCTAAAAGGAATCAGCTGCACATTTGAAGGAGGACACAAGATTGGAATTGTTGGCCGAACCGGTAGTGGGA
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gtatttgttactattgttagtcaggtttcacaatgtcctgaaaacttgtagttgaacactcgaacagaagcatataatttacttcttgatatcaaaacagATACGTTATAGGCCTGATGCGCCACTAGTACTTCGTGGAATCACATGCACATTTGAAGGAGGCCACAAGATTGGTATTGTTGGCAGAACAGGCAGTGGAA
upper sequence: AT3G59140.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G28890.1 (Glycine max), 3'ss of exon 15
----------------------gtaagtttg--attaatacactttcactctctaatccatattatgagtgtttcttaatttattaatgttcatatatacagATAAGATACAGAAGAGAATCCCCACTGGTTCTAAAAGGAATCAGCTGCACATTTGAAGGAGGACACAAGATTGGAATTGTTGGCCGAACCGGTAGTGGGA
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gtatttgtctaattgcatactttaaaatttgcaacatatataatattaaaaagcatgggagttcaaatgaaatgcataattttgtggtctataccaaaacagATAAGATATAGGCCTGAAGGGCCACTTGTACTCCATGGCATCACTTGCACATTTGAAGGAGGGCACAAGATTGGTATTGTTGGCAGGACAGGCAGTGGGA
upper sequence: AT3G59140.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G30490.1 (Glycine max), 3'ss of exon 9
---------------gtaagtttgatt----aatacactttcactctctaatc---catattatgagtgtttcttaatttattaatgttcatatatacagATAAGATACAGAAGAGAATCCCCACTGGTTCTAAAAGGAATCAGCTGCACATTTGAAGGAGGACACAAGATTGGAATTGTTGGCCGAACCGGTAGTGGGA
||| || || ||| || | || | || | | | |||||| || | | || | ||||||| | ||||| || | ||||| || || ||||||| ||||||||||||||||| ||||| ||||| ||||||||| |||| || ||||| |
gtaattgttactgttttaaaactggttgcacaatgtcctgaaaaatggtagttaaacacttgaactgaagctcttaagttgcttcttgatatcaaaacagATACGTTACAGGCCTGATGCACCACTAGTACTTCGTGGAATCACATGCACATTTGAAGGAGGTCACAAAATTGGTATTGTTGGCAGAACAGGCAGTGGAA
upper sequence: AT3G59140.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G37150.1 (Glycine max), 3'ss of exon 8
--------gtaagtttgattaatacactttcactctctaatccatattatgagtgtttcttaatttattaatgttcata-tatacagATAAGATACAGAAGAGAATCCCCACTGGTTCTAAAAGGAATCAGCTGCACATTTGAAGGAGGACACAAGATTGGAATTGTTGGCCGAACCGGTAGTGGGA
| | | | | ||| | | | | | || | || | | || |||| ||| || ||||||||| ||| | || | ||||| || ||| || |||| ||||||||||||||||| ||||||||||| |||||||| |||| || ||||| |
gtaataaaatgaactaactgcaagtgattttaaaattttggtgagttgatcactgaagtgcatgatttttttgttgataataaacagATAAGGTACCGGCCTGATGCGCCACTAGTACTACGTGGGATCACATGCACATTTGAAGGAGGGCACAAGATTGGTGTTGTTGGCAGAACAGGCAGTGGAA
upper sequence: AT3G59140.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G28910.1 (Glycine max), 3'ss of exon 9
----------------gtaagtttgattaatacactttcactctctaatccatattatgagt--gtttcttaatttattaatgttcatatatacagATAAGATACAGAAGAGAATCCCCACTGGTTCTAAAAGGAATCAGCTGCACATTTGAAGGAGGACACAAGATTGGAATTGTTGGCCGAACCGGTAGTGGGA
|| | ||| | ||| | | || | |||| | |||||| | | | | | ||||||| ||||||| || ||||| | || | ||||||| |||||||| ||| |||||||||||||||||||||||| | || || ||||| |
gtaattggtacttatttaaaatgtgagtcataatgctcataaaaatggtcattgaaatgaactgaatatataatttgtatgtttataccaagacagATACGATACAGGCTCGATGGACCACTTATACTCCATGGAATCACATGCACATTCAAAGCAGGACACAAGATTGGAATTGTTGGAAGGACAGGCAGTGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actctctaatccatattatgagtgtttcttaatttattaatgttcatatatacagATAAGATACAGAAGAGAATCCCCACTGGTTCTAAAAGGAATCAGCTGCACATTTGAAGGAGGACACAAGATTGGAATTGTTGGCCGAACCGGTAGTGGGA
tattaat putative branch site (score: 2)
tgtttcttaatttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttgattaatacactttcactctctaatccatattatgagtgtttcttaatttattaatgttcatatatacagATAAGATACAGAAGAGAATCCCCACTGGTTCTAAAAGGAATCAGCTGCACATTTGAAGGAGGACACAAGATTGGAATTGTTGGCCGAACCGGTAGTGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA