Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttgatcagattctcaggtctggtaactggttgagatatgttaataatgttagctaacttatggtttaaatgttaagGTTTGTGATGACCGGCACTCGGAAATCATCCCTTGCTTAGATAGGAATTTCATCTACCAAATGAGGTTGAAGCTTGATCTCTCTTTAATGGAACATTATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G04430.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G04430.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 2
gtaagtttg-atcagattctcaggtctggtaactggttgag-atatgttaataatgttagctaacttatggtttaaatgttaagGTTTGTGATGACCGGCACTCGGAAATCATCCCTTGCTTAGATAGGAATTTCATCTACCAAATGAGGTTGAAGCTTGATCTCTCTTTAATGGAACATTATG
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gtaagttcccaacgcgtgaccagcccttttctcttgtggattgtctgttcatgatttaaattgtttgttttcttggttgcttagGTGTGTGATGACCGGCACTCTGAACTGATCCCCTGCTTGGATAGGAACTTGATATATCAAATGAGGCTGAAGCTGGATTTAAACCTGATGGAGCACTATG
upper sequence: AT1G04430.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G107629_T03 (Zea mays), 3'ss of exon 3
gtaagtttgatcagattctcaggtctggtaactggttgag-atatgttaataatgttagctaacttatggtttaaatgttaagGTTTGTGATGACCGGCACTCGGAAATCATCCCTTGCTTAGATAGGAATTTCATCTACCAAATGAGGTTGAAGCTTGATCTCTCTTTAATGGAACATTATG
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gtaagtcccaacgagtgatcagtccttttcttttgtggattgtctattcatgattgtaagtgtttttta--ttgggtgtttagGTGTGTGATGACCGGCACTCTGAGCTGATCCCCTGCTTGGATCGGAACTTGATATATCAAATGAGGCTGAAGCTGGATTTAAACCTGATGGAGCACTATG
upper sequence: AT1G04430.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------------------gtaagtttgatcag---attctcaggtctggtaactggttgagatatgttaataatgttagctaacttatggtttaaatgttaagGTTTGTGATGACCGGCACTCGGAAATCATCCCTTGCTTAGATAGGAATTTCATCTACCAAATGAGGTTGAAGCTTGATCTCTCTTTAATGGAACATTATG
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gtaagtttctagtagctgagctggaatcagcaccagtactagcctcctcttctctttgacactttgacttgtttatttttgcttcttatattcagttttcttttattgatggtgtcatgtttctgct--tctgattttgaagGTTTGTGATGATCGGCATTCTGAATTAATTCCCTGCCTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTGGATCTTTCTTTGATGGAGCACTATGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|116486105|gb|EG528697.1|EG528697EST: ATTCTGTGGCTAATGCAGAAGACAGTCTTGTTGTCGCCAAAAGTTTTCCT GTTTGTGATGACCGGCACTCGGAAATCATCCCTTGCTTAGATAGGAATTTC
genomic: ATTCTGTGGCTAATGCAGAAGACAGTCTTGTTGTCGCCAAAAGTTTTCCTgtaagtttga ... aaatgttaagGTTTGTGATGACCGGCACTCGGAAATCATCCCTTGCTTAGATAGGAATTTC
EST:
gi|116486106|gb|EG528698.1|EG528698EST: ATTCTGTGGCTAATGCAGAAGACAGTCTTGTTGTCGCCAAAAGTTTTCCT GTTTGTGATGACCGGCACTCGGAAATCATCCCTTGCTTAGATAGGAATTTC
genomic: ATTCTGTGGCTAATGCAGAAGACAGTCTTGTTGTCGCCAAAAGTTTTCCTgtaagtttga ... aaatgttaagGTTTGTGATGACCGGCACTCGGAAATCATCCCTTGCTTAGATAGGAATTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaactggttgagatatgttaataatgttagctaacttatggtttaaatgttaagGTTTGTGATGACCGGCACTCGGAAATCATCCCTTGCTTAGATAGGAATTTCATCTACCAAATGAGGTTGAAGCTTGATCTCTCTTTAATGGAACATTATG
agctaac putative branch site (score: 2)
atatgttaataatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttgatcagattctcaggtctggtaactggttgagatatgttaataatgttagctaacttatggtttaaatgttaagGTTTGTGATGACCGGCACTCGGAAATCATCCCTTGCTTAGATAGGAATTTCATCTACCAAATGAGGTTGAAGCTTGATCTCTCTTTAATGGAACATTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC