Sequence
atgc intronic sequence ATGC exonic sequencegtaacttcacctagttaaggccatctttacatatatcaatggaagtccatttgaagcagaatctagtttgttttcagaaagcctttcctaagaaatcttgtcaattgtgtcagGTAAGAAGAACGCGGATAAGCGAGCGAATGAGGAAGTTACAAGAGCTTGTTCCTAACATGGACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G42280.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G42280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G12150.1 (Glycine max), 3'ss of exon 4
gtaacttcacctagtta--aggccatctttacatatatcaatggaagtccatttgaagcagaatctagtttgttttcagaaagcctttcctaagaaatcttgtcaattgtgtcagGTAAGAAGAACGCGGATAAGCGAGCGAATGAGGAAGTTACAAGAGCTTGTTCCTAACATGGACAAG
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-------taccaaaacaataaataaattaagaagatattatctagactatgttgaattcatgaagtaatttgt-----aaaagttgattctgagatg-caagtcattttt--cagGTGAGAAGAACTCGGATCAGTGAAAGAATGAGAAAATTACAAGAGCTTGTCCCAAACATGGACAAG
upper sequence: AT2G42280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G32600.2 (Glycine max), 3'ss of exon 3
----------------------------------------------------------------------gtaacttcacctagttaaggccatctttacatata-tcaatgg-------aagtccatttgaagcagaatctagtttgttttcagaaagcctttcctaagaaatcttgtcaattgtgtcagGTAAGAAGAACGCGGATAAGCGAGCGAATGAGGAAGTTACAAGAGCTTGTTCCTAACATGGACAAG
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gcaagtagatatataatacctatatttgtcaaaacttatttttacaaacatttggtacaatgaagctgttaatactaaaatgaaatactactactatagtacatagtccatgcctttgccaaaactatgagaaatggatgattatttctaattcatggactaattttaagagat--tatcgttt---tcagGTGAGAAGAAGTCGGATCAGTGAACGAATAAGAAAATTGCAAGAGCTTGTTCCAAACATGGACAAG
upper sequence: AT2G42280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G29830.1 (Glycine max), 3'ss of exon 4
gtaacttcacctagttaaggccatctttacatatatcaatggaagtccatttgaagcagaatctagtttgttttcagaaagcctttcctaagaaatcttgtcaattgtgtcagGTAAGAAGAACGCGGATAAGCGAGCGAATGAGGAAGTTACAAGAGCTTGTTCCTAACATGGACAAG
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--tcctataccaaaacaa---taaataagaagatattatttagactatgttgaattcatgaagtaatttgt-----aagagatgattctgagatgtaa-gtc--ttttttcagGTGAGAAGAACTCGGATCAGTGAAAGAATGAGGAAATTACAAGAGCTTGTCCCACACATGGATAAG
upper sequence: AT2G42280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0007g07810.t01 (Vitis vinifera), 3'ss of exon 3
gtaacttcacctagttaaggccatctttacatatatcaatggaagtccatttgaagcagaatctagtttgttttcagaaagcctttcctaagaa--atcttgtcaattgtgt------cagGTAAGAAGAACGCGGATAAGCGAGCGAATGAGGAAGTTACAAGAGCTTGTTCCTAACATGGACAAG
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gtaaattagtcatagtcaccttatctttgttccttaggatggtacacaaattttaactcactggaaccagtgacctcaaatcaaatgttggagatgatctttaggggtgtgttattttcagGTAAGGAGAACCCGGATCAGCGAAAGAATGAGGAAACTACAAGAGCTTGTCCCAAACATGGACAAGMapped 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|19743192|gb|AU228545.1|AU228545EST: TCAGACCCAAACGTGGTTTCGCTACACATCCTCGAAGCATCGCTGAACGG GTAAGAAGAAGCGCGGATAAGCGAGCGAATGAGGAAGTTACAAGAGCTTGT
genomic: TCAGAGCCAAACGTGGTTGCGCTACACATCCTCGAAGCATCGCTGAACGGgtaacttcac ... attgtgtcagGTAAGAAGAA-CGCGGATAAGCGAGCGAATGAGGAAGTTACAAGAGCTTGT
EST:
gi|124957740|gb|EL032541.1|EL032541EST: ATCCTCGAAGCATCGCTGAACGG GTAAGAAGAACGCGGATAAGCGAGCGAATGAGGAAGTTACAAGAGCTTGTT
genomic: ATCCTCGAAGCATCGCTGAACGGgtaacttcac ... attgtgtcagGTAAGAAGAACGCGGATAAGCGAGCGAATGAGGAAGTTACAAGAGCTTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatctagtttgttttcagaaagcctttcctaagaaatcttgtcaattgtgtcagGTAAGAAGAACGCGGATAAGCGAGCGAATGAGGAAGTTACAAGAGCTTGTTCCTAACATGGACAAG
tttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacttcacctagttaaggccatctttacatatatcaatggaagtccatttgaagcagaatctagtttgttttcagaaagcctttcctaagaaatcttgtcaattgtgtcagGTAAGAAGAACGCGGATAAGCGAGCGAATGAGGAAGTTACAAGAGCTTGTTCCTAACATGGACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA