Sequence
atgc intronic sequence ATGC exonic sequencegtttttttttaatctctaaaatcttatattagactctctttttttcttaaccctatatcctatattagactcttaattctcatcattgttgttaatcttatccttaactaagagtaattgttgtgccagGATTGCAAAGGAATGGGAAAAGCTGCAGATTAAGGTGGATTAATTACCTAAGACCAGGACTAAAGAGGGGGTCGTTTAGTGAAGAAGAAGAAGAGACCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G52260.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G52260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G38110.1 (Glycine max), 3'ss of exon 1
gtttttttttaatctctaaaatcttatattagactctctttttttcttaaccctatatcctatattagactcttaattctcatcattgttgttaatcttatccttaactaagagtaattgttgtgccagGATTGCAAAGGAATGGGAAAAGCTGCAGATTAAGGTGGATTAATTACCTAAGACCAGGACTAAAGAGGGGGTCGTTTAGTGAAGAAGAAGAAGAGACCAT
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---------------------gctggtaataaacaaagtgttatagtcaaacc---atcaggtattta--tataattttttaaaaattttacctgac--actgttggggcaaatacatttatgtgc-agGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGAAAGTTCAGCAAACAGGAAGAGGAGACAAT
upper sequence: AT5G52260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G29710.1 (Glycine max), 3'ss of exon 1
gtttttttttaatctctaaaatcttatattagactctctttttttcttaaccctatatcctatattagactcttaattctcatcattgttgttaatcttatccttaactaagagtaattgttgtgccagGATTGCAAAGGAATGGGAAAAGCTGCAGATTAAGGTGGATTAATTACCTAAGACCAGGACTAAAGAGGGGGTCGTTTAGTGAAGAAGAAGAAGAGACCAT
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--------------------agctggtaataaacaaaagtgttatagtcaacc---atcgggcattta--tatcattttttaaatttttacctgacattgt--tggggcaaatacatttgt-gtac-agGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGGAAATTCAGCAAACAGGAAGAGGAGACAAT
upper sequence: AT5G52260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G25590.1 (Glycine max), 3'ss of exon 1
gtttttttttaatctctaaaatcttatattagactctctttttttcttaaccctatatcctatattagactcttaattctcatcattgttgttaatcttatccttaactaagagtaattgttgtgccagGATTGCAAAGGAATGGGAAAAGCTGCAGATTAAGGTGGATTAATTACCTAAGACCAGGACTAAAGAGGGGGTCGTTTAGTGAAGAAGAAGAAGAGACCAT
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--------------------actttttattattccttatttatgtagtattc--atatcatgtg---agtttgtatttatttgatttgatgttgagttgctaactaactacacttaaatat----ctagGCTTGCAAAGAAATGGGAAGAGCTGCAGACTAAGGTGGATTAACTACTTGAGGCCAGGATTGAAGAGAGGGGTGTTCAGCAAACATGAGAAAGATACAAT
upper sequence: AT5G52260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv16s0050g00050.t01 (Vitis vinifera), 3'ss of exon 1
gtttttttttaatctctaaaatcttatattagactctctttttttcttaaccctatatcctatattagactcttaattctcatcattgttgttaatcttatccttaactaagagtaattgttgtgc----cagGATTGCAAAGGAATGGGAAAAGCTGCAGATTAAGGTGGATTAATTACCTAAGACCAGGACTAAAGAGGGGGTCGTTTAGTGAAGAAGAAGAAGAGACCAT
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------------------------------atgttcttttagtgccattgttgcatgttacataccatatgatcacatgttggt-ctagcattaatatg--ccttgattctttgaccttgtggtgcattgcagGTTTGCAAAGGAATGGAAAGAGCTGCAGATTAAGGTGGATTAACTACTTAAGACCAGGATTAAAACGCGGGATGTTTACGATCGAGGAGGAAGAGACGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattctcatcattgttgttaatcttatccttaactaagagtaattgttgtgccagGATTGCAAAGGAATGGGAAAAGCTGCAGATTAAGGTGGATTAATTACCTAAGACCAGGACTAAAGAGGGGGTCGTTTAGTGAAGAAGAAGAAGAGACCAT
ccttaac putative branch site (score: 3)
ttaatcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttttttaatctctaaaatcttatattagactctctttttttcttaaccctatatcctatattagactcttaattctcatcattgttgttaatcttatccttaactaagagtaattgttgtgccagGATTGCAAAGGAATGGGAAAAGCTGCAGATTAAGGTGGATTAATTACCTAAGACCAGGACTAAAGAGGGGGTCGTTTAGTGAAGAAGAAGAAGAGACCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA