Sequence
atgc intronic sequence ATGC exonic sequenceGCTCAGCGGCTTATGGAAATAGTGATTTTCAACAATACCAAGGGCTTCAGCCTGAATTGTTCTTCAAGATGTCTCATGAAATCTACAATTATGGAGAAGGgtctgtgaggataatttttcagcaaaaattaaatgatatttacacaaagaaatataaccttttttctatttatatttttgtatatagtactttctctctt...
Basic information
species | Arabidopsis thaliana |
transcript | AT1G60060.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G60060.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os02g50900.1 (Oryza sativa), 5'ss of exon 3
GCTCAGCGGCTTATGGAAATAGTGATTTTCAACAATACCAAGGGCTTC-AGCCTGAATTGTTCTTCAAGATGTCTCATGAAATCTACAATTATGGAGAAGGgtctgtgaggataatttttcagcaaaaattaaa--tgatatttacacaaagaaatataaccttttttctatttatatttttgtatatagtactttctctctt--------------------------------------------------------------------------
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-CCGGGTACACTGACTATGCAGCAGCTGGGCATGAGGTGAAGGGCCTCCAGCCTGAGCTCTTCTTCAAGATGTCCCATGACATCTACAACTATGGGGAAGGgtatgtggtagtactaattaattagcagtttggcttgaaacatcattaattaattagtgtcatagtattggccgtctttcttaat-tagtaatctatgttctttgggaaaacctacgctaatcactttagtcagcacgtgaagcacgatctcatgatgcgatgatccatcttgaag
upper sequence: AT1G60060.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G136831_T01 (Zea mays), 5'ss of exon 2
GCTCAGCGGCTTATGG-AAATAGTGATTTTCAACAATACCAAGGGCTTCAGCCTGAATTGTTCTTCAAGATGTCTCATGAAATCTACAATTATGGAGAAGGgtctgtgaggataatttttcagcaaaaattaaatgatatttacacaaagaaatataaccttttttctatttatatttttgta--tatagtactttctctctt-------------------------------
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-CTGTGCAGGATGCGGTGAAGCACCAGCACCAGCAGGCGCAGGGCCTGCAGCCTGAGCTGTTCTTCAAGATGTCCCATGACATCTACAACTACGGCGAAGGgtaggtg--gctgactagtccgcatgcacaccacgattagcgagccggttaaccttcctctcctgttaatgatggcgccggggccctcctcctcctcctcctgttcttggtgcggtttcctttcgtgctgcag
upper sequence: AT1G60060.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA02G03740.1 (Glycine max), 5'ss of exon 3
GCTCAGCGGCTTATGGAAATAGTGATTTTCAACAATACCAAGGGCTTCAGCCTGAATTGTTCTTCAAGATGTCTCATGAAATCTACAATTATGGAGAAGGgtctgtgaggataatttttcagcaaaaattaaatgatatttacacaaagaaatataaccttttttctatttatatttttgtatatagtactttctctctt---------------------
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CCCCACCTGCTTATGGGAACTGTGAATTTCAGCCCTACCAAGGGCTTCAACCGGAGCTCTTCTTCAAGATGTCACATGAGATCTATAACTATGGAGAAGGgtatgcaatattaatcaacattcatttacttatttgtgtcacatttctcttgttttgctcttgaaagatgttcatcaaagcaaagaggttataggctaattaatcatgtctaatggagcag
upper sequence: AT1G60060.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA01G03940.1 (Glycine max), 5'ss of exon 3
GCTCAGCGGCTTATGGAAATAGTGATTTTCAACAATACCAAGGGCTTCAGCCTGAATTGTTCTTCAAGATGTCTCATGAAATCTACAATTATGGAGAAGGgtctgtgaggataatttttcagcaaaaattaaatgatatttacacaaagaaatataacctt-ttttctatttatatttttgtatatagtactttctctctt--------------------
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CCCCACCTGTTTATGGGAACTGTGAATTTCAGCCCTACCAAGGGCTGCAACCGGAGCTCTTCTTCAAGATGTCACATGAGATCTATAACTATGGAGAAGGgtatatgcaat--attaatcaacattaatttacctatttgtgt-cacatttctcttactttgttcttgaaagatgttcaaagctaagaggttgatttaattaattatgtttaatggagcag
upper sequence: AT1G60060.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv01s0026g00350.t01 (Vitis vinifera), 5'ss of exon 3
GCTCAGCGGCTTATGGAAATAGTGATTTTCAACAATACCAAGGGCTTCAGCCTGAATTGTTCTTCAAGATGTCTCATGAAATCTACAATTATGGAGAAGGgtctgtgaggataatttttcagcaaaaattaaatgatatttacacaaagaaatataaccttttttctatttatatttttgtatatagtactttctctctt--------
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GCTCATCAGTCTATGGCAACTGTGAATTTCAACACTTTCAAGGACTCCAACCAGAGCTCTTCTTCAAGATGTCCCATGAAATCTACAACTATGGGGAAGGgtaataaagaatcgccacttcatttttcttctct-atagatgttgattgatcattcgccctgctagtgatttcacaagtaatcgaagaagattcaatcctgtcaacagMapped 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|164155631|gb|ES063379.1|ES063379EST: CCTGAATTGTTCTTCAAGATGTCTCATGAAATCTACAATTATGGAGAAGG GTTGATAGGAA
genomic: CCTGAATTGTTCTTCAAGATGTCTCATGAAATCTACAATTATGGAGAAGGgtctgtgagg ... ttttgtgcagGTTGATAGGAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCTCAGCGGCTTATGGAAATAGTGATTTTCAACAATACCAAGGGCTTCAGCCTGAATTGTTCTTCAAGATGTCTCATGAAATCTACAATTATGGAGAAGGgtctgtgaggataatttttcagcaaaaattaaatgatatttacacaaagaaatataaccttttttctatttatatttttgtatatagtactttctctctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaggataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagcaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttctct