Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttggtgttaaggcgttttgtatttgatggctgctttctgataaagactagctctattttatgatttggtgttatcgatgttgatcgggattagttagtcccaaagttggagttaccaaccttctttcttagtttggtcactgtggtattcaacattttaagatctttctctatgtttcagAGACTGCACTAAAACTTGACACTTTAGTTGGTGATATTGAGGATGCTGTGATGTCTTCTTTGAATAAAAACTTAAGAACATCTCGGTCAAGTGGTTTTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G47700.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G47700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G47180.1 (Glycine max), 3'ss of exon 2
gtatgtttggtgttaaggcgttttgtatttgatggctgctttctgataaagactagctctattttatgatttggtgttatcgatgttgatcgggattagttagtcccaaagttggagttaccaaccttctttcttagtttggtcactgtggtattcaacattttaagatctttctctatgtttcagAGACTGCACTAAAACTTGACACTTTAGTTGGTGATATTGAGGATGCTGTGATGTCTTCTTTGAATAAAAACTTAAG--AACATCTCGGTCAAGTGGTTTTGA
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--------------------------------------------------------------------------tttcagtgatggttatcatactgtgtttg-------gtttgatttcttagg--tgttacct--tttggttaatgttgt-ttgattcttgaaactcctttgtttgtctttcagAGACAGCACTGAAACTTGATACTTTGGTTGGTGATATTGAGGATGCTGTATCATTTACCATGAGCAAGAACATAAGGAAACATTCTAGTCAAA--ATTCACA
upper sequence: AT3G47700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G25590.1 (Glycine max), 3'ss of exon 2
gtatgtttggtgttaaggcgttttgtatttgatggctgctttctgataaagactagctctattttatgatttggtgttatcgatgttgatcgggattagttagtcccaaagttggagttaccaaccttctttcttagtttggtcactgtggtattcaacattttaagatctttctctatgtttcagAGACTGCACTAAAACTTGACACTTTAGTTGGTGATATTGAGGATGCTGTGATGTCTTCTTTGAATAAAAACTTAAG--AACATCTCGGTCAAGTGGTTTTGA
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--------------------------------------------------------------------------tttcagtgatgattatcatactgtgtttggtttaatttcttaggtgtta--cctttttgtgaatgttgtt----tgattcttgaaactc------ctttgtttgtctttcagAGAAAGCACTGAAACTTGATACTTTGGTTGGTGATATTGAGGATGCTGTATCATTTACCATGAGCAAGAACATAAGGAAACATTCTAGTCAAA--ATTCACA
upper sequence: AT3G47700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv17s0000g05940.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtttggtgttaaggcgttttgtatttgatggctgctttctgataaagactagctctattttatgatttggtgttatcgatgttgatcgggattagttagtcccaaagttggagttaccaaccttctttcttagtttggtcactgtggtattcaacattttaagatctttctctatgtttcagAGACTGCACTAAAACTTGACACTTTAGTTGGTGATATTGAGGATGCTGTGATGTCTTCTTTGAATAAAAACTTAAGAA--CAT-CTCGGTCAAGTGGTTTTGA
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--------------------------------------------------------------gttacaagttattg----caatgcctattactgttaattctgatagtgactaaactttcca--cttcttttttt-ttctctccctatcgt--------ttttgcgat---------tctttcagAGACAGCATTAAAACTTGACAGTTTGGTTGGTGACATCGAAGATGCTGTATCTTCTACTATGAACAGAAATCTAAAGAAGCATGCTTCCACACACAGTTC--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttagtttggtcactgtggtattcaacattttaagatctttctctatgtttcagAGACTGCACTAAAACTTGACACTTTAGTTGGTGATATTGAGGATGCTGTGATGTCTTCTTTGAATAAAAACTTAAGAACATCTCGGTCAAGTGGTTTTGA
tctttctctatgtttc CT-rich tract
tattcaacattttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttggtgttaaggcgttttgtatttgatggctgctttctgataaagactagctctattttatgatttggtgttatcgatgttgatcgggattagttagtcccaaagttggagttaccaaccttctttcttagtttggtcactgtggtattcaacattttaagatctttctctatgtttcagAGACTGCACTAAAACTTGACACTTTAGTTGGTGATATTGAGGATGCTGTGATGTCTTCTTTGAATAAAAACTTAAGAACATCTCGGTCAAGTGGTTTTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC