Sequence
atgc intronic sequence ATGC exonic sequenceCACGGCCAGCCAAGTGGTGGTACTCCACCTTCCACACCGTCACCGCCATGATTGGCGCGGGAGTCCTCAGCCTTCCTTATGCCATGGCTTACCTTGGCTGgtacggatactctttcgtcaatcatatttacaaattttatggcctatatgtgtgtaaaattaaaacatgcaagtaaatgaaaagtcaaatctatgcagat...
Basic information
species | Arabidopsis thaliana |
transcript | AT1G25530.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G25530.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os04g38860.1 (Oryza sativa), 5'ss of exon 2
CACGGCCAGCCAAGTGGTGGTACTCCACCTTCCACACCGTCACCGCCATGATTGGCGCGGGAGTCCTCAGCCTTCCTTATGCCATGGCTTACCTTGGCTGgtacggatactctttcgt-caatcatat-ttacaaattttatggcctatatgtgtgtaaaattaaaacatgcaagtaaatgaaaagtcaaatctatgcagat
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CTCGCCGGGCGAAATGGTGGTACGCGACGTTCCACAGCGTCACCGCCATGGTCGGCGCCGGCGTGCTCAGCTTGCCGTACGCCATGGCTCACCTAGGATGgtaagtcaattatactgtacgtacgcgcgccatggctagctggagctgtgtgcatgcagcgaatgactgtggtaatcgatcgaacgatcgagcag-------
upper sequence: AT1G25530.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G114523_T01 (Zea mays), 5'ss of exon 1
CACGGCCAGCCAAGTGGTGGTACTCCACCTTCCACACCGTCACCGCCATGATTGGCGCGGGAGTCCTCAGCCTTCCTTATGCCATGGCTTACCTTGGCTGgtacggatactctttcgtcaatcatatttacaaattttatggcctata--tgtgtgtaaaattaaaacatgcaagtaaatgaaaagtcaaatctatgcagat----------
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CTCGCCGCGCCAAGTGGTGGTACGTGACGTTCCACAACGTCACCGCGATGGTCGGCGCCGGCGTGCTCAGCCTGCCGTACGCCATGGCTCACCTGGGATGgtatggtaaccgactggattgactgaccctccactttgacggcatgcaatggctcgctgactcgagcagtgtttctttcttgttgcttggtttcatcgtcatcatcatgcag
upper sequence: AT1G25530.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA02G10870.1 (Glycine max), 5'ss of exon 2
CACGGCCAGCCAAGTGGTGGTACTCCACCTTCCACACCGTCACCGCCATGATTGGCGCGGGAGTCCTCAGCCTTCCTTATGCCATGGCTTACCTTGGCTGgtacgga--tactctttcgtcaatcatatttacaaattttatggcctatatgtgtgtaaaattaaaacatgcaagtaaa-tgaaaagtcaaatctatgcagat
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CTCGCAATGCCAAATGGTGGTACTCAACTTTTCACACTGTGACGGCCATGATTGGTGCAGGTGTTCTCAGCCTTCCCTATGCCATGGCATATCTAGGATGgtaaagtacaactctgacttcgagtct-ttaacatatcaca-aacaggtgacaacttgaacataatatttttttttaaaacatggtaataagattctttagc-
upper sequence: AT1G25530.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA01G21510.1 (Glycine max), 5'ss of exon 2
CACGGCCAGCCAAGTGGTGGTACTCCACCTTCCACACCGTCACCGCCATGATTGGCGCGGGAGTCCTCAGCCTTCCTTATGCCATGGCTTACCTTGGCTGgtacggatactctttcgtcaatcatatttacaaattttatggcctatatgtgtgtaaaattaaaacatgcaagtaaatgaaaagtcaaatctatgcagat---
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CTCGCAATGCCAAATGGTGGTACTCAACTTTTCACGCTGTGACAGCCATGATTGGTGCAGGTGTTCTCAGCCTTCCCTATGCCATGGCATATCTAGGATGgtaaag-tacaactctgcctttaagtctttaacatatcacaaaa-aggtctcaactttaacacaatatttgttttaaccatg-gtaaaagagtctcagactcc
upper sequence: AT1G25530.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv01s0011g03180.t01 (Vitis vinifera), 5'ss of exon 2
CACGGCCAGCCAAGTGGTGGTACTCCACCTTCCACACCGTCACCGCCATGATTGGCGCGGGAGTCCTCAGCCTTCCTTATGCCATGGCTTACCTTGGCTGgtacggatactctttcgtcaatcatatttacaaattttatggcctatatgtgtgtaaaattaaaacatgcaagtaaatgaaaagtcaaatctatgcagat-----
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CTCGGCGGGCCAAATGGTGGTACTCAACTTTTCATACTGTCACAGCCATGATTGGTGCTGGAGTTCTCAGCTTGCCTTATGCCATGGCTTATTTAGGATGgtatatatatact---aaaactcaattctacaagctagactaagtcgtttggtacttaattctagaaagcatttt--ttatttttctagtatttgaaatttttat
upper sequence: AT1G25530.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ10950 (Selaginella moellendorffii), 5'ss of exon 2
CACGGCCAGCCAAGTGGTGGTACTCCACCTTCCACACCGTCACCGCCATGATTGGCGCGGGAGTCCTCAGCCTTCCTTATGCCATGGCTTACCTTGGCTGgtacggatactctttcgtcaatcatatttacaaattttatggcctatatgtgtgtaaaattaaaacatgcaagtaaatgaaaagtcaaatct-atgcagat--
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CCAGGAACGCCAAGTGGTGGTACTCGGCCTTCCATAATGTCACCGCCATGGTTGGAGCTGGAGTTCTTAGCCTCCCCTCGGCGATGGTCTATCTTGGCTGgta--agttcttcgcagctcttcttcgtttcaatcgcta-gcttcaaattcgcttagtttcgatccaaattcttggtcagtcagtgttttctcattcgtgctcMapped 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|19875845|gb|AU236676.1|AU236676EST: ATTGGCGCGGGAGTCCTCAGCCTTCCTTATGCCATGGCTTACCTTGGCTG GGGACCAGGGACCTTTGTGTTGGCAATGACGTGGGGACTGACCCTAAACAC
genomic: ATTGGCGCGGGAGTCCTCAGCCTTCCTTATGCCATGGCTTACCTTGGCTGgtacggatac ... gtgaaaacagGGGACCAGGGACCTTTGTGTTGGCAATGACGTGGGGACTGACCCTAAACAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CACGGCCAGCCAAGTGGTGGTACTCCACCTTCCACACCGTCACCGCCATGATTGGCGCGGGAGTCCTCAGCCTTCCTTATGCCATGGCTTACCTTGGCTGgtacggatactctttcgtcaatcatatttacaaattttatggcctatatgtgtgtaaaattaaaacatgcaagtaaatgaaaagtcaaatctatgcagat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctttcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caagtaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagtcaaa