Sequence
atgc intronic sequence ATGC exonic sequencegtcggtctccacaacttatgttcaatttgctgaagtttgtcaatgaatgatgtttttgcttcactcagtaggtcatttaccaactgatgttttctgtatgtcgcactgtagATCCATTCAAGAAAAATGAACGTAAATCCGGATGTCAACTTCGAAGAATTGGCTCGCTCAACAGATGACTTCAACGGAGCACAGCTGAAGGCAGTCTGTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G100873_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 8
gtcggtctccacaactt---atgttcaatttgctgaagtttgtcaatgaatgatgtttttgcttcactcagtaggtcatttaccaactgatgttttctgtatgtcgcactgtagATCCATTCAAGAAAAATGAACGTAAATCCGGATGTCAACTTCGAAGAATTGGCTCGCTCAACAGATGACTTCAACGGAGCACAGCTGAAGGCAGTCTGTG
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gtaggtttccagaacctgtgatgtctaatcagctaatgtttattcatccatt-tgcttttgt---aatccacaagtcatgctttaactaatat-------gtggttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG
upper sequence: GRMZM2G100873_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 8
gtcggtctccacaacttatgttcaatttgctgaagtttgtcaatgaatgatgtttttgcttcactcagtaggtcatttaccaactgatgttttctgtatgtcgcactgtagATCCATTCAAGAAAAATGAACGTAAATCCGGATGTCAACTTCGAAGAATTGGCTCGCTCAACAGATGACTTCAACGGAGCACAGCTGAAGGCAGTCTGTG
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-------------------gtttggtgtctttaaact--tcatctgctgacttgttt--ttca---aacagaacatttactgactgctctcactttgatatttca-----gATCCATTCGAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTTGCTCGGTCCACAGATGATTTCAATGGAGCTCAACTGAAGGCTGTTTGTG
upper sequence: GRMZM2G100873_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 8
gtcggtctccacaacttatgttcaatttgctgaagtttgtcaatgaatgatgtttttgcttcactcagtaggtcatttaccaactgatgttttctgtatgtcgcactgtagATCCATTCAAGAAAAATGAACGTAAATCCGGATGTCAACTTCGAAGAATTGGCTCGCTCAACAGATGACTTCAACGGAGCACAGCTGAAGGCAGTCTGTG
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-------------------gtttggtatcttcaaatt--ttatttgctgacattttttctc----tgacagaacttttgc----ttatgtttttcacat-taatatcatagATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTAGCTCGGTCCACAGATGATTTCAATGCAGCACAACTTAAAGCTGTCTGTG
upper sequence: GRMZM2G100873_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 8
gtcggtctccacaacttatgttcaatttgctgaagtttgtcaatgaatgatgtttttgcttcactcagtaggtcatttaccaactgatgttttctgtatgtcgcactgtagATCCATTCAAGAAAAATGAACGTAAATCCGGATGTCAACTTCGAAGAATTGGCTCGCTCAACAGATGACTTCAACGGAGCACAGCTGAAGGCAGTCTGTG
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-----------------gtttgttgtcttccaaactttacctgc---tgacacatt--gttcaatcaaaa---catttactgacta-----ccctcactttgatattttagATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTTGCCCGGTCCACAGATGATTTCAATGGCGCACAACTGAAGGCTGTCTGTG
upper sequence: GRMZM2G100873_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 8
gtcggtctccacaacttatgttcaatttgctgaagtttgtcaatgaatgatgtttttgcttcactcagtaggtcatttaccaactgatgttttctgtatgtcgcactgtagATCCATTCAAGAAAAATGAACGTAAATCCGGATGTCAACTTCGAAGAATTGGCTCGCTCAACAGATGACTTCAACGGAGCACAGCTGAAGGCAGTCTGTG
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-------------gtatgtcttcaatgaa-tattttcttctagatcattacacattgatcactctttgcagagctcttattgactctttcacattgtat------ttgtagATCCACTCGAGAAAGATGACTGTTCATCCGGATGTCAATTTTGAAGAACTGGCTCGATCCACAGATGATTTCAATGGGGCACAACTGAAAGCTGTTTGTG
upper sequence: GRMZM2G100873_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 9
gtcggtctccacaacttatgttcaatttgctgaagtttgtcaatgaatgatgtttttgcttcactcagtaggtcatttaccaactgatgttttctgtatgtcgcactgtagATCCATTCAAGAAAAATGAACGTAAATCCGGATGTCAACTTCGAAGAATTGGCTCGCTCAACAGATGACTTCAACGGAGCACAGCTGAAGGCAGTCTGTG
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gtgagactgtactggcagtagtcctttgtcagaaattttt---tgcatt-tatatttaccactctt-gtaaatctttt-----tggatgttttcc------tgta-tgcagATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTCGCTCGTTCAACTGATGATTTCAATGGAGCACAGCTGAAAGCCGTTTGTG
upper sequence: GRMZM2G100873_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------------------------gtcggtctccacaacttatgttcaatttgctgaagttt--gtca-atgaatgatgtttttgcttcactcagtaggtcatttaccaactgatgttttctgtatgtcgcactgtagATCCATTCAAGAAAAATGAACGTAAATCCGGATGTCAACTTCGAAGAATTGGCTCGCTCAACAGATGACTTCAACGGAGCACAGCTGAAGGCAGTCTGTG
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gtatgaatacttgacacgggcatgcacatgcaaagtgattatgaactgggtaaagcctcttgtttgcaatgacgtgcttgttcagtcatatgatttacgtagaggctt-actacttagttttcattttcaataat-tttcttggactttctaccgcagATTCATTCGAGGAAAATGAATTTAAGGCCTGATGTCAACTTTGAGGAGTTGGCTCGCTCAACAGATGACTTTAACGGAGCTCAATTGAAGGCTGTGTGTAMapped 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|14242818|gb|BG840607.2|BG840607EST: AGATTGAGTTCCCTCACCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA ATCCATTCAAGAAAAATGAACGTAAATCCGGATGTCAACTTCTAAGAATTG
genomic: AGATTGAGTTCCCTCACCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtcggtctcc ... cgcactgtagATCCATTCAAGAAAAATGAACGTAAATCCGGATGTCAACTTCGAAGAATTG
EST:
gi|14243285|gb|BG840998.2|BG840998EST: AGATTGAGTTCCCTCACCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA ATCCATTCAAGAAAAATGAACGTAAATCCGGATGTCAACTTCGAAGAATTG
genomic: AGATTGAGTTCCCTCACCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtcggtctcc ... cgcactgtagATCCATTCAAGAAAAATGAACGTAAATCCGGATGTCAACTTCGAAGAATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttcactcagtaggtcatttaccaactgatgttttctgtatgtcgcactgtagATCCATTCAAGAAAAATGAACGTAAATCCGGATGTCAACTTCGAAGAATTGGCTCGCTCAACAGATGACTTCAACGGAGCACAGCTGAAGGCAGTCTGTG
aactgat putative branch site (score: 3)
tcattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcggtctccacaacttatgttcaatttgctgaagtttgtcaatgaatgatgtttttgcttcactcagtaggtcatttaccaactgatgttttctgtatgtcgcactgtagATCCATTCAAGAAAAATGAACGTAAATCCGGATGTCAACTTCGAAGAATTGGCTCGCTCAACAGATGACTTCAACGGAGCACAGCTGAAGGCAGTCTGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG