Sequence
atgc intronic sequence ATGC exonic sequence...gcttgtcttgtgtagttctccttgaagtctactcaagttttgcaatatgctgatcttgaaaagcatttattaagtaatactcgatgcgatcatgtaacagATTGCAAGGGAGATTCGGCTGAGAGATATTGGCGGTATCATTGTGGTAGATTTCATCGACATGGCAGATGAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G04270.4 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G04270.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G38840.1 (Glycine max), 3'ss of exon 9
---gcttgtcttgtgtagttctccttgaagtctactcaagttttgcaatatgctgatcttgaaaagcatttattaagtaatactcgatgcgatcatgtaacagATTGCAAGGGAGATTCGGCTGAGAGATATTGGCGGTATCATTGTGGTAGATTTCATCGACATGGCAGATGAAT
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ttttattaagtaaaaaaaataattttgtgcctttgttttcttttgcaacat-taattcatgtaaagcggt-ataattttttaatagaaacaat-gtgttacagATTGCAAGGGAGTTGCGACTACGGGATATTGGAGGCATCATTGTGGTAGATTTCATTGATATGACAGATGAGG
upper sequence: AT2G04270.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA14G36910.1 (Glycine max), 3'ss of exon 10
gcttgtctt---gtgtagttctccttgaagtctactcaagttttgcaatatgctgatcttgaaaagcatttattaagtaatactcgatgcgatcatgtaacagATTGCAAGGGAGATTCGGCTGAGAGATATTGGCGGTATCATTGTGGTAGATTTCATCGACATGGCAGATGAAT
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ttttttctttaagtaaaaaaaatcttgtgcctttgttttcttttgcagcat-taattcatgtgaagcagt-gcaattttttaatagaaac-attgtgttacagATTGCAAGGGAGTTGCGACTACGGGATATTGGAGGCATCATTGTGGTAGATTTCATTGATATGACAGATGAGG
upper sequence: AT2G04270.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv12s0057g01320.t01 (Vitis vinifera), 3'ss of exon 9
gcttgtcttgtgtagttctccttgaagtctactcaagttttgcaatatgctgatcttgaaaagcatttattaagtaat--actcgatgcgatca-----tgtaacagATTGCAAGGGAGATTCGGCTGAGAGATATTGGCGGTATCATTGTGGTAGATTTCATCGACATGGCAGATGAAT
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-------tctagcagttatgctaaaatgctttagatattggattctagtctatccttttaaagctttaatgtactagagaactcactgaaaaaaaaaattgtttcagATTGCAAGGGAGTTACGACTGAGAGATATTGGCGGCATCATCGTAGTAGATTTCATTGATATGTTGGATGACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgctgatcttgaaaagcatttattaagtaatactcgatgcgatcatgtaacagATTGCAAGGGAGATTCGGCTGAGAGATATTGGCGGTATCATTGTGGTAGATTTCATCGACATGGCAGATGAAT
tgctgat putative branch site (score: 3)
aaaagcatttattaag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcttgtcttgtgtagttctccttgaagtctactcaagttttgcaatatgctgatcttgaaaagcatttattaagtaatactcgatgcgatcatgtaacagATTGCAAGGGAGATTCGGCTGAGAGATATTGGCGGTATCATTGTGGTAGATTTCATCGACATGGCAGATGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG