Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgagtatgcaaccatttcaattgatccttatataggtgcgggaagcacatggtacatgcatatcctctactagtatcatcatttgctagtggttataagaaattattgtattacatactttcttttctatctttgagcatattttgatgtactattgtttattcatatgagtattcatgcagAGTAATCCTGTTGCGAGATGGCATATATGTCAAGGTTCAATTAACAGCATTGCATTCTCAAATGATGGGGCACACTTGGCAACTGTTGGAAGAGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G53390.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA03G33740.1 (Glycine max), 3'ss of exon 6
gtatgtgagtatgcaaccatttcaattgatccttatataggtgcgggaagcacatggtacatgcatatcctctactagtatcatcatttgctagtggttataagaaattattgtattacatactttcttttctatctttgagcatattttgatgtac---tattgtttattcatatgagtattcat----gcagAGTAATCCTGTTGCGAGATGGCATATATGTCAAGGTTCAATTAACAGCATTGCATTCTCAAATGATGGGGCACACTTGGCAACTGTTGGAAGAGATG
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----------------------------------------------------------------------------------------------tggatgaaatgatgaattctacaattggccctcctgtagaatattttgcattattatatctatactttttttttaataaaacaagtattggtctttgcagAGTAATCCTATAGCCAGATGGCATATATGCCAGGGTTCAATTAATAGTATTTCTTTCTCAATGGATGGGGCATACTTAGCAACTGTTGGACGAGATG
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G36480.1 (Glycine max), 3'ss of exon 6
gtatgtgagtatgcaaccatttcaattgatccttatataggtgcgggaagcacatggtacatgcatatcctctactagtatcatcatttgctagtggttataagaaattattgtattacatacttt-cttttctatctttgagcatattttgatgtactattgtttattcatatgagtattcatgcagAGTAATCCTGTTGCGAGATGGCATATATGTCAAGGTTCAATTAACAGCATTGCATTCTCAAATGATGGGGCACACTTGGCAACTGTTGGAAGAGATG
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--------------------------------------------------------------------------------ggatgaaatgatgaattctacaattggcacttctgtagaatattttgcgttactatatct----ataattt--tcttttaaaaaaaagaaatattggtctt--tgcagAGTAATCCTATAGCGAGATGGCATATATGCCAGGGTTCAATTAATAGTATTTCTTTCTCGATGGATGGGGCATTCTTAGCAACTGTTGGGCGAGATG
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G20240.1 (Glycine max), 3'ss of exon 7
gtatgtgagtatgcaaccatttcaattgatccttatataggtgcgggaagcacatggtacatgcatatcctctactagtatcatcatttgctagtggttataagaaattattgtattacatactttcttttctatctttgagcatattttgatgtactattgtttattcatatgagtattcatgcagAGTAATCCTGTTGCGAGATGGCATATATGTCAAGGTTCAATTAACAGCATTGCATTCTCAAATGATGGGGCACACTTGGCAACTGTTGGAAGAGATG
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--------------------------------------------------------------------------ttaatttgtatataggatgg--gttctagg---tttttctgttatggagaatttcttgtgttctct------ctttcatcttttttgcccttttaatattgacttt--tgcagAGTAATCCAATAGCCAGATGGCATATATGCCAGGGTTCAATTGACAGTATTTCTTTCTCAACTGATGGGACTTACATAGCTACTGTTGGACGAGATG
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G05890.1 (Glycine max), 3'ss of exon 7
gtatgtgagtatgcaaccatttcaattgatccttatataggtgcgggaagcacatggtacatgcatatcctctactagtatcatcatttgctagtggttataagaaattattgtattacatactttcttttctatctttgagcatattttgatgtactattgtttattcatatgagtattcatgcagAGTAATCCTGTTGCGAGATGGCATATATGTCAAGGTTCAATTAACAGCATTGCATTCTCAAATGATGGGGCACACTTGGCAACTGTTGGAAGAGATG
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------------------------------------------------------------------------------tggcttaatttgtataggatggtcccaggtttttctgttttggagaatttcttgtgttctc-------tcttcatctttgttccccttttaatattggcttt--tgcagAGTAATCCAATAGCCAGATGGCATATATGCCAGGGTTCAATCAACAGTATTTCTTTCTCAACCGATGGGACTTACATAGCAACTGTTGGACGGGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatctttgagcatattttgatgtactattgtttattcatatgagtattcatgcagAGTAATCCTGTTGCGAGATGGCATATATGTCAAGGTTCAATTAACAGCATTGCATTCTCAAATGATGGGGCACACTTGGCAACTGTTGGAAGAGATG
ttttgat putative branch site (score: 4)
tattgtttattcatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgagtatgcaaccatttcaattgatccttatataggtgcgggaagcacatggtacatgcatatcctctactagtatcatcatttgctagtggttataagaaattattgtattacatactttcttttctatctttgagcatattttgatgtactattgtttattcatatgagtattcatgcagAGTAATCCTGTTGCGAGATGGCATATATGTCAAGGTTCAATTAACAGCATTGCATTCTCAAATGATGGGGCACACTTGGCAACTGTTGGAAGAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG