Sequence
atgc intronic sequence ATGC exonic sequencegtaagaatcatgaatcccctcctttaatcttcttaaaatccgatttgtgtactgacgatgaccgggttttttcgttatagGCCATCAAACGCGATAGTTCATTTGCGAGCAAGGTGAAGAAAATTGTTATTCTTGGTGGAGCTTTCTTTTCTTTGGGAAATGTCAATCCTGCAGCTGAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G36310.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G36310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G085960_T01 (Zea mays), 3'ss of exon 4
-----gtaagaatcatg-----aatcccctcctttaatcttcttaaaatccgatttgtgtactgacgatgaccgggttttttcgttatagGCCATCAAACGCGATAGTTCATTTGCGAGCAAGGTGAAGAAAATTGTTATTCTTGGTGGAGCTTTCTTTTCTTTGGGAAATGTCAATCCTGCAGCTGAGG
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gtatgttcaggatcgtaggattaaacctatttgttgtgctgtctatgctgcgctatatgttacgactaagtgtctctgttcttgct-tagGCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTACTGGGTGGAGCTTTCTTCGTGGCTGGAAATGTCAACCCTGCTGCTGAAG
upper sequence: AT2G36310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G015344_T02 (Zea mays), 3'ss of exon 4
-----gtaagaatcatg-----aatcccctcctttaatcttcttaaaatccgatttgtgtactga--cgatgaccgggttttttcgttatagGCCATCAAACGCGATAGTTCATTTGCGAGCAAGGTGAAGAAAATTGTTATTCTTGGTGGAGCTTTCTTTTCTTTGGGAAATGTCAATCCTGCAGCTGAGG
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gtatgttcaggatcataggactaaacctatttatcgtgctgtttatgctgtgctatatgttataagtcagtgtctctgttctttgctta--gGCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTACTGGGTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAG
upper sequence: AT2G36310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G37830.1 (Glycine max), 3'ss of exon 4
-------------------gtaagaatcatgaatcccctccttta-atcttc---ttaaaatccgatttgtgtactgacgatgaccgggtt-ttttcgttat-agGCCATCAAACGCGATAGTTCATTTGCGAGCAAGGTGAAGAAAATTGTTATTCTTGGTGGAGCTTTCTTTTCTTTGGGAAATGTCAATCCTGCAGCTGAGG
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gtaagttgtacattgctgtattgtattctatggtcctgccctttataacttcaaattatagttccctacgtttgttgatt-tgacagtgtcacttccattattagGCAATCAAACGAGATTCTGCGTTTGCAAGCAAAGTGAAGAGAATAGTTATTCTTGGTGGTGCATTCTTTGCCTTGGGGAATGTGAATCCTGCTGCAGAAG
upper sequence: AT2G36310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0007g03690.t01 (Vitis vinifera), 3'ss of exon 4
-------------gtaagaatcatgaatcccctcctttaatcttc-----ttaaaatccgatttgtgtac-----tgacgatgaccgggttttttcgtta--tagGCCATCAAACGCGATAGTTCATTTGCGAGCAAGGTGAAGAAAATTGTTATTCTTGGTGGAGCTTTCTTTTCTTTGGGAAATGTCAATCCTGCAGCTGAGG
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gtaagttgcggtatcctgtcctttcagttcaattctgtgattttcatggtctgagttctgcaatgcataccattctggtcacacaaatgtatttttattgattagGCTATTAAAAGGGACTCGTCCTTTGCGAGCAAGGTGAAGAAGGTGGTCGTACTTGGTGGTGCTTTCTTTGCACTGGGAAATGTCAATCCTGCTGCCGAAGMapped 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|116442244|gb|EG484836.1|EG484836EST: CGGGTGAAGTCACCATTCTCGCCCTCGGACCTCTAACCAACCTGGCATTA GCCATCAAACGCGATAGTTCATTTGCGAGCAAGGTGAAGAAAATTGTTATT
genomic: CGGGTGAAGTCACCATTCTCGCCCTCGGACCTCTAACCAACCTGGCATTAgtaagaatca ... ttcgttatagGCCATCAAACGCGATAGTTCATTTGCGAGCAAGGTGAAGAAAATTGTTATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcttcttaaaatccgatttgtgtactgacgatgaccgggttttttcgttatagGCCATCAAACGCGATAGTTCATTTGCGAGCAAGGTGAAGAAAATTGTTATTCTTGGTGGAGCTTTCTTTTCTTTGGGAAATGTCAATCCTGCAGCTGAGG
tactgac putative branch site (score: 1)
ttttttcgtt putative PPT
tcttaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaatcatgaatcccctcctttaatcttcttaaaatccgatttgtgtactgacgatgaccgggttttttcgttatagGCCATCAAACGCGATAGTTCATTTGCGAGCAAGGTGAAGAAAATTGTTATTCTTGGTGGAGCTTTCTTTTCTTTGGGAAATGTCAATCCTGCAGCTGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA