Sequence
atgc intronic sequence ATGC exonic sequencegtaggtttgaaaaggttccatccggattcaattgtatttttgtttagctaccaataacaagtgcatccagaagaaacatgatacgagatcgctaaaataattgtcccttggacttctagACTTTACTCGCGAAAGCAGTAGCAACTGAATGCTCATTGAACTTTCTTAGCGTCAAAGGTCCAGAACTGATAAACATGTATGTTGGAGAATCAGAGAAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G445617_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g52690.3 (Oryza sativa), 3'ss of exon 9
-------------------------------gtaggtttgaaaaggttccatccggattcaattgtatttttgtttagctaccaataacaagtgcatccagaagaaacatgatacgagatcgctaaaataattgtcccttggacttctagACTTTACTCGCGAAAGCAGTAGCAACTGAATGCTCATTGAACTTTCTTAGCGTCAAAGGTCCAGAACTGATAAACATGTATGTTGGAGAATCAGAGAAAA
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gttggtttacggtgtttttctattttatactttgtttttagttaagctttacct---tttcgtt-tcttcccatctgtccaaagaggataagcacatagaaaagcactgt-atacgtgctcattattattatgtttc----aatttgcagACATTATTGGCAAAAGCTGTAGCAACAGAGTGCTCTTTAAACTTTCTTAGTGTAAAAGGTCCAGAATTGATTAACATGTATGTTGGAGAATCGGAGAAGA
upper sequence: GRMZM2G445617_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA03G36930.1 (Glycine max), 3'ss of exon 14
gtaggtttgaaaaggttccatccggattcaattgtatttttgtttagctaccaataacaagtgcatccagaagaaacatgatacgagatcgctaaaataattgtcccttggacttctagACTTTACTCGCGAAA--GCAGTAGCAACTGAATGCTCATTGAACTTTCTTAGCGTCAAAGGTCCAGAACTGATAAACATGTATGTTGGAGAATCAGAGAAAA-----------------------
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gt-gatctggtgttcttttgtacctgta-aatgacaatgct-ctacctcatttctgttacttttatcttaaaaagatttaaaac---accattttctcactcttttatttaa--tacagacattattagcaaaaaagctgttgctacatagtgttccttaaattttcttagCGTGAAAGGTCCTGAACTGATCAACATGTACATTGGAGAGTCTGAAAAGAATGTTCGAGACATTTTCCAGAAG
upper sequence: GRMZM2G445617_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv07s0104g01610.t01 (Vitis vinifera), 3'ss of exon 9
gtaggtttgaaaaggttccatccggattcaattgtatttttgtttagctaccaataacaagtgcatccagaagaaacatgatacgagatcgctaaaataattgtcccttggacttctagACTTTACTCGCGAAAGCAGTAGCAACTGAATGCTCATTGAACTTTCTTAGCGTCAAAGGTCCAGAACTGATAAACATGTATGTTGGAGAATCAGAGAAAA
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gtaagtttttgtttgtt--agccacttatggtgatatctcaatacgttatttcttgtttatttttttaaccaggaacctggttcattgctttcttggttactcctattgcaaatctcagACTTTATTGGCAAAAGCTGTTGCAACAGAGTGCTCCCTCAATTTTCTGAGTGTAAAAGGGCCTGAACTGATCAACATGTATATAGGAGAATCAGAGAAAA
upper sequence: GRMZM2G445617_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S68_6V6.1 (Physcomitrella patens), 3'ss of exon 10
-------gtaggtttgaaaaggttc--catccggatt-caattgtattttt-----------gtttagctaccaataacaagtgcatc--cagaagaaacatgatacgag---atcgctaaaataatt--gtcccttggacttc------tagACTTTACTCGCGAAAGCAGTAGCAACTGAATGCTCATTGAACTTTCTTAGCGTCAAAGGTCCAGAACTGATAAACATGTATGTTGGAGAATCAGAGAAAA
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gtataagataatttcgagctcattagacatgctgactgcggttgtgctttttatgatagaaagtcttgttctgaacattaggcaaattatcaacactaccaaagtttggttgcatgactgaatcgattatgtaccgtgatgtttgtgttgcagACATTGCTCGCCAAGGCTGTTGCCACTGAGTGCGCGTTGAACTTTCTGAGTGTCAAAGGTCCTGAGCTCATCAACATGTACATTGGAGAGTCAGAGAAGAMapped 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|32848459|gb|CD988140.1|CD988140EST: TGCGCAAGCGATCAGGTGTCCTGCTATATGGACCTCCAGGAACAGGGAAG ACTTTACTCGCGAAAGCAGTAGCAACAGAATGCTCATTGAACTTTCTTAGC
genomic: TGCGCAAGCGATCAGGTGTCCTGCTATATGGACCTCCAGGAACAGGGAAGgtaggtttga ... ggacttctagACTTTACTCGCGAAAGCAGTAGCAACTGAATGCTCATTGAACTTTCTTAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atccagaagaaacatgatacgagatcgctaaaataattgtcccttggacttctagACTTTACTCGCGAAAGCAGTAGCAACTGAATGCTCATTGAACTTTCTTAGCGTCAAAGGTCCAGAACTGATAAACATGTATGTTGGAGAATCAGAGAAAA
cgctaaa putative branch site (score: 3)
tcccttg putative PPT
taaaataattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggtttgaaaaggttccatccggattcaattgtatttttgtttagctaccaataacaagtgcatccagaagaaacatgatacgagatcgctaaaataattgtcccttggacttctagACTTTACTCGCGAAAGCAGTAGCAACTGAATGCTCATTGAACTTTCTTAGCGTCAAAGGTCCAGAACTGATAAACATGTATGTTGGAGAATCAGAGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA