Sequence
atgc intronic sequence ATGC exonic sequenceTGTACCTATGTGGGAGCTTATTTGGTTCTCCATTGTCGCTAATGTCTCTATTGCTGCTATGAACTTCAGTCTCATGCTCAATTCCGTTGGCTTCTACCAAgtaattcatctcgatctcgatcttgagcatatagaatcaaattgctttgatttgagcatatatagactttgattttggtttagtggattcacatttttttgtgttgattag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G42420.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G42420.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G055216_T01 (Zea mays), 5'ss of exon 2
TGTACCTATGTGGGAGCTTATTTGGTTCTCCATTGTCGCTAATGTCTCTATTGCTGCTATGAACTTCAGTCTCATGCTCAATTCCGTTGGCTTCTACCAAgta-attcatctcgatctcgatcttgagcatatagaatcaaattgctttgatttgagcatatatagactttgattttggtttagtggattcacatttttttgtgttgattag---
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CGTCCCGCTCTGGGAGCTCGTCTGGTTCTCTCTCGTCGCCAACACCTCCATCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAGgtacgtacaccctgctct--gctctgacagcgccagcggcagcgcctacg--ccggccattttcggcctggg---ttgcttgtgtgcgcgcgtggctgaagctgggaacctgcag
upper sequence: AT5G42420.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA11G00210.2 (Glycine max), 5'ss of exon 2
TGTACCTATGTGGGAGCTTATTTGGTTCTCCATTGTCGCTAATGTCTCTATTGCTGCTATGAACTTCAGTCTCATGCTCAATTCCGTTGGCTTCTACCAAgta---attcatctcgatctcgat-cttgagcatatagaatcaaattgctttgatttgagcatatatagactttgattttggtttagtggattcacatttttttgtgttgattag
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TGTTCCTATGTGGGAGCTTATTTGGTTCTCACTGGTTGCCAATATGTCTATCACGGGGATGAACTTTAGCCTCATGCTCAACTCCGTTGGATTCTACCAAgtatggttttatatcatgttcatcgcttggacggttaaactttaattttctt--tcttattaagaatttcatccaataatctttt--taaaatccccttgcttc-----------
upper sequence: AT5G42420.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA01G45700.1 (Glycine max), 5'ss of exon 2
TGTACCTATGTGGGAGCTTATTTGGTTCTCCATTGTCGCTAATGTCTCTATTGCTGCTATGAACTTCAGTCTCATGCTCAATTCCGTTGGCTTCTACCAAgtaattcatctcgatctcgatcttgagcatatagaatcaaattgctttgatttgagcatatatagactttgattttggtttagtggattcacatttttttgtgttgattag
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TGTTCCTATGTGGGAGCTTATTTGGTTCTCACTGGTTGCCAATATGTCTATCACGGGGATGAACTTTAGCCTCATGCTCAACTCCGTTGGATTCTACCAAgta---tggttttacttttatatca--catatcatgttca-tcgcttggact-gtttaactttaattttcttttcttgtttag---aatttcatccaatagtctttttaa-
upper sequence: AT5G42420.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S54_317V6.1 (Physcomitrella patens), 5'ss of exon 3
TGTACCTATGTGGGAGCTTATTTGGTTCTCCATTGTCGCTAATGTCTCTATTGCTGCTATGAACTTCAGTCTCATGCTCAATTCCGTTGGCTTCTACCAAgtaattcatctcgatctcgatcttgagcatatagaatcaaattgctttgatttgagcatatatagactttgattttggtttagtggattcacatttttttgtgttgattag
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TTTGCCCTTCAGAGATTTGTTTCTATTCTCCCTAGTGTCAAATACCTCGATTGTTTCCATGAACTTGAGTCTCATGCTCAATTCAGTGGGTTTCTACCAGgtaggt--gtatgatcctgaatagctgtgtgcgataacgaaggttcctaat---actatagagggagttgcaggatgatctaggcgaaccag---tgtgtgtgtatat---Mapped 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|125004539|gb|EL076808.1|EL076808EST: TGAACTTCAGTCTCATGCTCAATTCCGTTGGCTTCTACCAA ATCTCGAAGCTGAGCATGATTCCTGTGGTATGTGTAATGGAATGGATTCTA
genomic: TGAACTTCAGTCTCATGCTCAATTCCGTTGGCTTCTACCAAgtaattcatc ... tgttgattagATCTCGAAGCTGAGCATGATTCCTGTGGTATGTGTAATGGAATGGATTCTA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGTACCTATGTGGGAGCTTATTTGGTTCTCCATTGTCGCTAATGTCTCTATTGCTGCTATGAACTTCAGTCTCATGCTCAATTCCGTTGGCTTCTACCAAgtaattcatctcgatctcgatcttgagcatatagaatcaaattgctttgatttgagcatatatagactttgattttggtttagtggattcacatttttttgtgttgattag
- - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT