Sequence
atgc intronic sequence ATGC exonic sequenceaaaattgctttcattcttgagcaggtaacgtgccaacctattatgttaatactttgtatttttacgaaaaggcttattcatgcaaaacttactattattgTTGTCACAGGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCAAGGAAAATCAGTACTAGAGTATTTGACGCAGATCCATCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G013750_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g63430.2 (Oryza sativa), 3'ss of exon 5
aaaattgctttcattcttgagcaggtaacgtgccaacctattatgttaatactttgtatttttacgaaaaggcttattcatgcaaaacttactattattgTTGTCACAGGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCAAGGAAAATCAGTACTAGAGTATTTGACGCAGATCCATCAA---------
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---------------------------gtatgaagaaatacagtaataaagcttgaaattgttac-aaaagcctgggttctg-gaatcttactgtaatcatgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCCAGGAAAATCAGTCCTAGGGTATTTGATGCAGACCCGTCAAAGGAAAAAA
upper sequence: GRMZM2G013750_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 5
aaaattgctttcattcttgagcaggtaacgtgccaacctattat--gttaatactttgtatttttacgaaaaggcttattcatgcaaaacttactattattgT-TGTCACAGGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCAAGGAAAATCAGTACTAGAGTATTTGACGCAGATCCATCAA---------
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--------gtaaggacttgtgtag-ttacgttgcaattaataatttgctggtgttttctttcattgtgataa---ctatc-------aaactattgtggtcaaactttaaagGTTCGCTTGTGCTTGGATCGTCAAGATTTTGTTCGTGCACAAATCTTATCTAGGAAGATCAATCCTAGAGTTTTTGACGCAGATACAAAAAAAGATAAGA
upper sequence: GRMZM2G013750_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------------------------------aaaattgctttcatt-cttgagcaggtaacgtgccaacctattatgttaatactttgtatttttacgaaaaggcttattcatgcaaaacttactattattgTTGTCACAGGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCAAGGAAAATCAGTACTAGAGTATTTGACGCAGATCCATCAA---------
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gtacgtgttatcttctttcattgttcttttaattacttctaccatttattcttttattgttcttttaattacttgtaccatttattcgt-aacttattttatttttgggttcaaagttgataatgctactt-tttatgtaataat-gttgaaattact-tttcagGTCCGGCTGTGTTTAGACCGCCAAGATTATGTTCGTGCACAAATTCTCTCAAGGAAGATCAGCCCGAGGGTTTTCGATGCTGATTCTTCAAAAGAAAAGAMapped 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|32931087|gb|CF035899.1|CF035899EST: GTCGAAACATTTGGCTCCATGGCAAAGACGGAC TTG--AGCAGGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACA
genomic: GTCGAAACATTTGGCTCCATGGCAAAGACGGAGaaaattgctt ... actattattgTTGTCA-CAGGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACA
EST:
gi|32846815|gb|CD986496.1|CD986496EST: GTCGAAACATTTGGCTCCATGGCAAAGACGGAC TTG--AGCAGGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACA
genomic: GTCGAAACATTTGGCTCCATGGCAAAGACGGAGaaaattgctt ... actattattgTTGTCA-CAGGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACA
EST:
gi|32943967|gb|CF048786.1|CF048786EST: GTCGAAACATTTGGCTCCATGGCAAAGACGGAC TTG--AGCAGGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACA
genomic: GTCGAAACATTTGGCTCCATGGCAAAGACGGAGaaaattgctt ... actattattgTTGTCA-CAGGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatactttgtatttttacgaaaaggcttattcatgcaaaacttactattattgTTGTCACAGGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCAAGGAAAATCAGTACTAGAGTATTTGACGCAGATCCATCAA
aacttac putative branch site (score: 2)
aaaacttactattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaattgctttcattcttgagcaggtaacgtgccaacctattatgttaatactttgtatttttacgaaaaggcttattcatgcaaaacttactattattgTTGTCACAGGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCAAGGAAAATCAGTACTAGAGTATTTGACGCAGATCCATCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT