Sequence
atgc intronic sequence ATGC exonic sequence...tctcgtcggaagctaaatcaggtgttcattggatctgatagctaggggagttcttgcaagtctcatattctttgttaacttttcttcttcttctttgcagATGAAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGATCCGCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08850.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 1
tctcgtcggaagctaaatcaggtgttcattggatctgatagctaggggagttcttgcaagtctcatattctttgttaacttttcttcttcttctt----tgcagATGAAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGATCCGCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGA
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----ctatatacttctatttgtatttctgttctttttattttcgggtgtactgttggatgttattgcttttatgctatttactaatagtgttttggtagtgcagATGAAAACTGGCTGTGTGGCACTTGTGTTGTGTTTAAACATTAGTGTTGATCCGCCGGATGTGATCAAAATCTCCCCTTGTGCAAGAAAGGAGTGCTGGA
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 1
-tctcgtcggaagctaaatcaggtgttcattggatctgatagc-taggggagttcttgcaagtctcatattctttgttaacttttcttcttcttctttgcagATGAAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGATCCGCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGA
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ttcctctaaaatgttctaatgattgtttctttaagatgcttatatattatatctttggtaagaagtatgctctattttaactcttaactttgtggt--gcagATGAAGACAGGATGTGTAGCTCTAGTATTATGTTTAAACATTAGTGTCGATCCACCAGATGTAATAAAGATATCCCCTTGTGCCAGAATGGAGTGCTGGA
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 1
tctcgtcggaa-gctaaatcaggtgttcattggatctgatagc-taggggagttcttgcaagtctcatattctttgttaacttttcttcttcttctttgcagATGAAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGATCCGCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGA
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tccctctaaaatgttctaatgattgtttctttaagatgcttatatgttatatctttggtaagaagtatgctctattttaactcttaactttgtggt--gcagATGAAGACTGGATGTGTAGCTCTAGTATTATGTTTAAACATTAGTGTCGATCCTCCAGATGTAATAAAGATATCCCCTTGTGCCAGAATGGAGTGCTGGA
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 1
tctcgtcggaagctaaatcaggtgttcattggatctgatagctagggga--gttcttgcaagtctcatattctttgttaacttttcttcttcttctt--tgcagATGAAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGATCCGCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGA
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----cctgtaatccgatctggtcaatcattgtgcttgatgcttacaaattcattattgtacgtatttaggtctgctttggtttaactcccgagttttaatgcagATGAAGACAGGATGTGTAGCTCTTGTTTTATGTTTAAACATTAGTGTTGATCCACCTGATGTAATTAAGATATCTCCTTGTGCCAGAATGGAGTGCTGGAMapped 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|116460308|gb|EG502900.1|EG502900EST: TGGGGACTTCTGAGATCGTATTGGTCCCCAAATGGCGGCTTAAAGAACGA ATGAAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGAT
genomic: TGGGGACTTCTGAGATCGTATTGGTCCCCAAATGGCGGCTTAAAGAACGAgtaagttttc ... ttctttgcagATGAAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGAT
EST:
gi|116454212|gb|EG496804.1|EG496804EST: TGGGGACTTCTGAGATCGTATTGGTCCCCAAATGGCGGCTTAAAGAACGA ATGAAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGAT
genomic: TGGGGACTTCTGAGATCGTATTGGTCCCCAAATGGCGGCTTAAAGAACGAgtaagttttc ... ttctttgcagATGAAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggagttcttgcaagtctcatattctttgttaacttttcttcttcttctttgcagATGAAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGATCCGCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGA
tgttaac putative branch site (score: 2)
tctcatattctttgtt CT-rich tract
atattctttgttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctcgtcggaagctaaatcaggtgttcattggatctgatagctaggggagttcttgcaagtctcatattctttgttaacttttcttcttcttctttgcagATGAAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGATCCGCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - ctaaatc