Sequence
atgc intronic sequence ATGC exonic sequencegtgagatttttagcttttcacacaccatgtcactaatgaggtacattggttatcaattatgaaaaaaatatcagtggcggtatccattaagctaaagagcttttggtgtgctataataatcacttgatgcatcctaattttttttctgaagtccagATATTGGACAGGTGTGGGGTTGGGGTTATGGAGGAGAAGGACAGCTTGGATTGGGCTCTCGTGTACGTCTAGTCTCCTCTCCTCATCCTATTCCATGCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G55580.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 5
gtgagatttttagcttttcacacaccatgtcactaatgaggtacattggttatcaattatgaaaaaaatatcagtggcggtatccattaagctaaagagcttttggtgtgctataataatcacttgatgcatcctaattttttttctgaag-tccagATATTGGACAGGTGTGGGGTTGGGGTTATGGAGGAGAAGGACAGCTTGGATTGGGCTCTCGTGTACGTCTAGTCTCCTCTCCTCATCCTATTCCATGCAT
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---------------------------------------------------------------------gtaacctgcatatgtcattatgacactga-catttgccctataaggatatttactgactaaaa--tattttttcctccgaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
upper sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G03870.1 (Glycine max), 3'ss of exon 5
------gtgagatttttagct-tttcacacaccatgtcactaatgaggtacattggtt--atcaattatg-aaaaaaatatcagt---ggcggtatccattaagctaaagagcttttggtgtgctataataatcacttgatgcatcctaattttttttctgaagtccagATATTGGACAGGTGTGGGGTTGGGGTTATGGAGGAGAAGGACAGCTTGGATTGGGCTCTCGTGTACGTCTAGTCTCCTCTCCTCATCCTATTCCATGCAT
||| | | || ||| || | | ||| ||| | || || | || ||| | || | | || || | | || | || || | | | ||| || | || | || || ||||||| | | || | ||||||| |||||||||||||||||||| ||||| || ||||| |||||||| ||||| ||| | |||| | || ||||||||||||| |||| || ||
gtattgactttattatgaactatttgtcaacctaggtctaaaattttatctgttattttcgtatatgatgtgataatcttttggttgaagcagaactttttgtgttatggaagatcagttatgcaatctaagacatgtcattgattgtaattttctgt--gagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
upper sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 5
--------------gtgagatttttagcttttcacacaccatgtcactaatgaggtacattggttatcaattatgaaaaaaatatcagtg--gcggtatccattaagctaaagagcttttggtgtgctataataatcacttgatgcatcctaattttttttctgaagtccagATATTGGACAGGTGTGGGGTTGGGGTTATGGAGGAGAAGGACAGCTTGGATTGGGCTCTCGTGTACGTCTAGTCTCCTCTCCTCATCCTATTCCATGCAT
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gtattgactttattatgggctatttgtcaacctaggtctaaaattttatctatgctattttcgt-atataatatgataatcttttggttgaagcataactttttgtgctatggaagatcagttatgcattcgaagacatgtcattgattgtaattttctgg--aagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
upper sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv13s0019g02280.t01 (Vitis vinifera), 3'ss of exon 5
--------gtgagatttttagcttttcacacaccatgtcactaatgaggtaca-ttggttatcaattatgaaaaaaatatcagtggcggtatccattaagctaaagagcttttggtgtgctat-------aataatca-cttgatgcatcctaattttttttctgaagtccagATATTGGACAGGTGTGGGGTTGGGGTTATGGAGGAGAAGGACAGCTTGGATTGGGCTCTCGTGTACGTCTAGTCTCCTCTCCTCATCCTATTCCATGCAT
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gtaaatccatgaaatcttggattgttgtccctaagcctcagttttaattcatagttctttttctgttgtggttatgcaacataggctggtactcagtatgactagaagccatggaagttctattttgtaaagcaacaaacttaatgttttcta-ttgttcccccaagtttcagATGTTGGACAGGTGTGGGGTTGGGGCTATGGGGGTGAGGGGCAACTAGGTTTGGGTTCCCGGATACGTATGGTATCCTCTCCTCATCCTGTGCCTTGTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttggtgtgctataataatcacttgatgcatcctaattttttttctgaagtccagATATTGGACAGGTGTGGGGTTGGGGTTATGGAGGAGAAGGACAGCTTGGATTGGGCTCTCGTGTACGTCTAGTCTCCTCTCCTCATCCTATTCCATGCAT
tcctaat putative branch site (score: 2)
tcctaattttttttct CT-rich tract
taattttttttctgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagatttttagcttttcacacaccatgtcactaatgaggtacattggttatcaattatgaaaaaaatatcagtggcggtatccattaagctaaagagcttttggtgtgctataataatcacttgatgcatcctaattttttttctgaagtccagATATTGGACAGGTGTGGGGTTGGGGTTATGGAGGAGAAGGACAGCTTGGATTGGGCTCTCGTGTACGTCTAGTCTCCTCTCCTCATCCTATTCCATGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC