Sequence
atgc intronic sequence ATGC exonic sequencegtgaagttgaataaacgactttttacaaatccgagatgaagctgctaccttgtagttgaagattcatttgaggatgatcatgtttttacggaagtttcagATTTAGGACAGATTTGGGGTTGGGGATATGGAGGCGAAGGTCAACTAGGATTGGGTTCCCGGATTAAAATGGTGTCATCTCCTCATCTAATACCTTGCCT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G53830.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G53830.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g62810.4 (Oryza sativa), 3'ss of exon 4
gtgaagttgaataaacgactttttacaaatccgagatgaagctgc-taccttgtagttgaagattcatttgaggatgatc--atgtttttacggaagtttcagATTTAGGACAGATTTGGGGTTGGGGATATGGAGGCGAAGGTCAACTAGGATTGGGTTCCCGGATTAAAATGGTGTCATCTCCTCATCTAATACCTTGCCT
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----------gtagcctacattttgcactaacactatggcactacatttgctgggctagggaactttgctgattaaaactaaatgttttctcgaaagCTTCAGATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCC------
upper sequence: AT3G53830.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g62810.3 (Oryza sativa), 3'ss of exon 2
gtgaagttgaataaacgactttttacaaatccgagatgaagctgc-taccttgtagttgaagattcatttgaggatgatc--atgtttttacggaagtttcagATTTAGGACAGATTTGGGGTTGGGGATATGGAGGCGAAGGTCAACTAGGATTGGGTTCCCGGATTAAAATGGTGTCATCTCCTCATCTAATACCTTGCCT
|| | || |||| || | ||| || | | || | | | | ||| | | ||||||| || ||| |||||||||||| || | ||||||||||| |||||||| ||||| |||||||| ||||||| | || | || || ||||| |||| || || ||| |
----------gtagcctacattttgcactaacactatggcactacatttgctgggctagggaactttgctgattaaaactaaatgttttctcgaaagcttcagATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCCGTGCAT
upper sequence: AT3G53830.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 5
gtgaagttgaataaacgactttttacaaatccgagatgaagctgctaccttgtagttgaagattcatttgaggatgatcatgtttttacggaagtttcagATTTAGGACAGATTTGGGGTTGGGGATATGGAGGCGAAGGTCAACTAGGATTGGGTTCCCGGATTAAAATGGTGTCATCTCCTCATCTAATACCTTGCCT
|| | | | ||| | | || || | || | || | | ||| | | || | || | ||| | ||| |||||||||||| ||| | |||||||||||||||||||| ||||| |||||||| |||||||| | || || || || ||||| |||| |||| ||| |
-----gtaacctgcatatgtcattatgacactgacat-------ttgccctataa--ggatatttact-gactaaaatattttttcctccgaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
upper sequence: AT3G53830.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G302245_T01 (Zea mays), 3'ss of exon 3
gtgaagttgaataaacgactttttacaaatccgagatgaagctgctaccttgtagttgaagattcatttgaggatgatcatgtttttacggaagtttcagATTTAGGACAGATTTGGGGTTGGGGATATGGAGGCGAAGGTCAACTAGGATTGGGTTCCCGGATTAAAATGGTGTCATCTCCTCATCTAATACCTTGCCT
||| | | ||| || ||| | | || |||| || | ||| | | || | || |||||| | || ||| |||||||||||| ||| | |||||||||||||||||||| ||||| |||||||| |||| || | || || || || ||||| |||| |||| ||| |
----------gtaatctgcatttgtcattatgacactgacatt--ttccctgta--tggatatttact-gactaaaat-atgtttcttcg-aagcttcagATTTAGGTCAGGTATGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTCTGGGCTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
upper sequence: AT3G53830.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G40600.1 (Glycine max), 3'ss of exon 7
--------gtgaagttgaataa-acgactttttaca---aatccgagatgaagctgct---accttgtagttgaagattcatttgaggatg-atcatgtttttacggaagttt-cagATTTAGGACAGATTTGGGGTTGGGGATATGGAGGCGAAGGTCAACTAGGATTGGGTTCCCGGATTAAAATGGTGTCATCTCCTCATCTAATACCTTGCCT
|| ||| || | ||| || ||| |||||| | || | | || |||| ||||| ||||||| ||||||| ||||| | |||||| | ||||||||||| |||||||| ||||| || |||||||||||||| ||| | || ||||| ||||| |||||||| ||||
gttggctcttgtggttacattatgtagttttgtaggttcaatgaagtatgaagatatggaaggtttttgatgtaaagcaagacacctgatgcatcatatttttaccgaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGCTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGGGTAAAGATGGTATCATCCCCTCATCTTATAC-------
upper sequence: AT3G53830.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G16400.1 (Glycine max), 3'ss of exon 6
--------gtgaagttgaataa-acgactttttaca---aatccgagatgaagct---gctaccttgtagttgaagattcatttgaggatg-atcatgtttttacggaagttt-cagATTTAGGACAGATTTGGGGTTGGGGATATGGAGGCGAAGGTCAACTAGGATTGGGTTCCCGGATTAAAATGGTGTCATCTCCTCATCTAATACCTTGCCT
|| ||| || | | ||| || ||| |||||| | | | || | | || |||| ||||| ||||||| |||||| ||||| | |||||| | ||||||||||| |||||||| ||||| || |||||||||||||| || | || ||||| ||||| |||||||| ||||
gttgcctcttgtggttacattatatagttttgtaggttcaatgaagtatgaagataaggatggtttttgatgtaaagcaagacacctgatgcatcatatttttaccaaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGTTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGAGTAAAGATGGTATCATCCCCTCATCTTATAC-------
upper sequence: AT3G53830.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0007g00930.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------------------------------gtgaagttgaataaacgactttttacaaatccgagatgaagctgctaccttgtagttgaagattcatttgaggatgatcatgt--ttttacggaagtttcagATTTAGGACAGATTTGGGGTTGGGGATATGGAGGCGAAGGTCAACTAGGATTGGGTTCCCGGATTAAAATGGTGTCATCTCCTCATCTAATACCTTGCCT
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gtaaattctccatcccctgggtcactgcagcccacacaagccacagttttcaggtgtagcaatttcttctttgtggttacactatatagtttt-gtaggtc--atttgaag-tacgaagctatggaagatctttaatgtaaagcaagacacctaatttaacaaaagtttcagATATGGGACAGGTGTGGGGTTGGGGCTATGGAGGCGAAGGGCAGCTAGGTTTGGGTTCTCGGACAAAGCTGGTGTCTTCTCCTCATCTCATACCTTGCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taccttgtagttgaagattcatttgaggatgatcatgtttttacggaagtttcagATTTAGGACAGATTTGGGGTTGGGGATATGGAGGCGAAGGTCAACTAGGATTGGGTTCCCGGATTAAAATGGTGTCATCTCCTCATCTAATACCTTGCCT
atgttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaagttgaataaacgactttttacaaatccgagatgaagctgctaccttgtagttgaagattcatttgaggatgatcatgtttttacggaagtttcagATTTAGGACAGATTTGGGGTTGGGGATATGGAGGCGAAGGTCAACTAGGATTGGGTTCCCGGATTAAAATGGTGTCATCTCCTCATCTAATACCTTGCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC