Sequence
atgc intronic sequence ATGC exonic sequence...ggtttcatgttatgagaagctttcttcttctaataattttctggagcatcgtgattcttgatcatctcttactgtttaaatggtctggttatgaatacagCTCCAAAGGGGTTATTTCCTCCAGAGCCTGTACCATACAAGGGACCTAAGCTGAAAGTAGCCATTATAGGAGCTGGACTTGCAGGCATGTCGACTGCTGT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G04870.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G04870.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G37170.1 (Glycine max), 3'ss of exon 1
------------------------------------------------------------------------------------------------------ggtttcatgttatgagaagctttcttcttctaataattttctggagcatcgtgattcttgatcatctcttactgtttaaatggtctggttatgaatacagCTCCAAAGGGGTTATTTCCTCCAGAGCCTGTACCATACAAGGGACCTAAGCTGAAAGTAGCCATTATAGGAGCTGGACTTGCAGGCATGTCGACTGCTGT
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gtttgtaatttcaatttctcatcaattgtcgatgttacacttatattagcagtatctttttttccccttctctttatctattatttttttttcatttttgggagtgttggaataatttggaaattaaaggcatagttagtttggggagtgtcacaacgtttagataa----taattcttaaactgtaagtttgacatggcagCGCCAAAAGGGTTGTTTCCTCCGGAACCAGAACATTATCGAGGACCGAAGCTGAAAGTGGCAATTATTGGAGCTGGACTTGCAGGCATGTCAACTGCAGT
upper sequence: AT3G04870.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G30220.1 (Glycine max), 3'ss of exon 1
----------------------------------------------------------------ggtttcatgttatgagaagctttcttct-----tctaataattttctggagcatcgtgattcttgatcatctcttactgtttaaatggtctggttatgaatacagCTCCAAAGGGGTTATTTCCTCCAGAGCCTGTACCATACAAGGGACCTAAGCTGAAAGTAGCCATTATAGGAGCTGGACTTGCAGGCATGTCGACTGCTGT
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gtttgtaatttcagttcctgatcaattttcgatcttacacttatcttaccagtgtattcttttcttttttttaatctattgattttcgttctgggagtgttgtgtgtttgcgatgtgtcacaatgtttagacaataataatt-ctcatactgtaagtttgacatggcagCGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCAAAACTGAAAGTGGCAATTATTGGAGCTGGACTTGCAGGCATGTCAACTGCAGT
upper sequence: AT3G04870.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0030g01740.t01 (Vitis vinifera), 3'ss of exon 1
ggtttcatgttatgagaagctttcttcttctaataattttctggagcatcgtgattct------tgatcatct--cttactgtt--taaatggtctggttatgaatacagCTCCAAAGGGGTTATTTCCTCCAGAGCCTGTACCATACAAGGGACCTAAGCTGAAAGTAGCCATTATAGGAGCTGGACTTGCAGGCATGTCGACTGCTGT
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--------aatttttgtacctttttcctttcaatgtaagtttgaaatttagcagctctgaggtgttattattcgatttgcgattcttaaatgga-tgtttgcttgc-cagCTCCAAAAGGGTTGTTTCCACCAGAACCTGAACACTATAGGGGACCAAAGCTCAAGGTGGCTATCATTGGAGCTGGGCTTGCAGGCATGTCAACTGCAGTMapped 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|125016975|gb|EL089244.1|EL089244EST: TTCTTCACTCGACTCCGATGTTTCCGACATGAGTGTTAACG CTCCAAAGGGGTTATTTCCTCCAGAGCCTGTACCATACAAGGGACCTAAGC
genomic: TTCTTCACTCGACTCCGATGTTTCCGACATGAGTGTTAACGgtaattaacc ... atgaatacagCTCCAAAGGGGTTATTTCCTCCAGAGCCTGTACCATACAAGGGACCTAAGC
EST:
gi|125257223|gb|EL271308.1|EL271308EST: CTATGTTAATTCTTCACTCGACTCCGATGTTTCCGACATGAGTGTTAACG CTCCAAAGGGG
genomic: CTATGTTAATTCTTCACTCGACTCCGATGTTTCCGACATGAGTGTTAACGgtaattaacc ... atgaatacagCTCCAAAGGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatcgtgattcttgatcatctcttactgtttaaatggtctggttatgaatacagCTCCAAAGGGGTTATTTCCTCCAGAGCCTGTACCATACAAGGGACCTAAGCTGAAAGTAGCCATTATAGGAGCTGGACTTGCAGGCATGTCGACTGCTGT
ctcttac putative branch site (score: 3)
tgtttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtttcatgttatgagaagctttcttcttctaataattttctggagcatcgtgattcttgatcatctcttactgtttaaatggtctggttatgaatacagCTCCAAAGGGGTTATTTCCTCCAGAGCCTGTACCATACAAGGGACCTAAGCTGAAAGTAGCCATTATAGGAGCTGGACTTGCAGGCATGTCGACTGCTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - -cttcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtctgg