Sequence
atgc intronic sequence ATGC exonic sequencegtacttggtggtatcattgggtttcagaacttcaaccatagctgagaagtagcttgatccttgtttggcctattaatcagATGAGGATGTGGTGTTTATTGTAGATGATAAATGAGAAGCCACAGGTGATTCAGGAGTATGAATCAGGCAAGGCAATCCCCAACCAGCAGATCATTAGCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G800112_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g27850.2 (Oryza sativa), 3'ss of exon 3
gtacttggtggtatcattgggtttcagaacttc--aaccata-gctgagaagtagcttgatccttgtttggcctattaatca--gATGAGGATGTGGTGTTTATTGTA----GATGATAAATGAGAAGCCACAGGTGATTCAGGAGTATGAATCAGGCAAGGCAATCCCCAACCAGCAGATCATTAGCA------------------------
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gtgccctgtccaaccatacaattttagaatttcctagcgttacattaacttttaccacagccactcgcacatacactaaccttcaactaaaatatggtgtgttttgcaaacagATGATCAATGAGAAGCCCCAGGTGATCCAGGAGTACGAGTCAGGTAAAGCTATTCCGAACCAGCAGATCATCGGGAAGCTTGAAAGGGCTCTTGGAACAA
upper sequence: GRMZM5G800112_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G42890.1 (Glycine max), 3'ss of exon 3
gtacttggtggtatcattgggtttcagaacttcaaccatagctgagaagtagcttgatccttgtttggcctattaatcagATGAGGATGTGGTGTTTATTGTAGATGATAAATGAGAAGCCACAGGTGATTCAGGAGTATGAATCAGGCAAGGCAATCCCCAACCAGCAGATCATTAGCA------------------------
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-------------gtattgctcgtc-gtatattatcggtctcttt--attttccttattagtatttaggc-atta-tca-atgatg-tgcattgttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTATGAGTCAGGGAAGGCCATTCCAAACCAGCAGATAATTAGCAAGTTGGAAAGAGCTCTTGGAGCTA
upper sequence: GRMZM5G800112_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G15420.1 (Glycine max), 3'ss of exon 3
-------gtacttggtggtatcattgggtttcagaacttcaaccatagctgagaagtagcttgatccttgtttggcctattaatcagATGAGGATGTGG--TGTTTATTGTAGATGATAAATGAGAAGCCACAGGTGATTCAGGAGTATGAATCAGGCAAGGCAATCCCCAACCAGCAGATCATTAGCA------------------------
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gtattgctttcttctctgtag-attttttttgaatatattattcattattggtctct--tttttttcctactagtatttaggcatgatcaatgatgtgcattgttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGGAAGGCCATTCCAAACCAGCAGATAATTGGGAAGTTGGAAAGGGCTCTTGGAGCAA
upper sequence: GRMZM5G800112_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G42900.1 (Glycine max), 3'ss of exon 3
gtacttggtggtatcattgggtttcagaacttcaaccatagctgagaagtagcttgatccttgtt-tggcctattaatca--gATGAGGATGTGG--TGTTTATTGTAGATGATAAATGAGAAGCCACAGGTGATTCAGGAGTATGAATCAGGCAAGGCAATCCCCAACCAGCAGATCATTAGCA------------------------
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gta-ttact--ctcccttcagtagaattatttttaatatatc--atcgatctctttatttttcttattagcaattaggcattatcaatgacgtgcattgttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCCATTCCAAACCAGCAGATAATTGGCAAGTTGGAAAGAGCCCTTGGAGCTA
upper sequence: GRMZM5G800112_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT2G42680.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacttggtggtatcattgggtttcagaacttcaaccatagctgagaagtagcttgatccttgtttggcctattaatcagATGAGGATGTGGTGTTTATTGTAGATGATAAATGAGAAGCCACAGGTGATTCAGGAGTATGAATCAGGCAAGGCAATCCCCAACCAGCAGATCATTAGCA------------------------
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----------gtat-attatccttct---ctctatatgtcccttattattaccctattttgtaactcggttcatgacaaagtgtt--tgtttctttttgtgtagATCATCAATGAGAAGCCACAAGTGATTCAAGAGTATGAGTCTGGCAAAGCTATACCCAACCAGCAAATCCTTTCTAAGCTGGAGAGAGCGCTTGGAGCTA
upper sequence: GRMZM5G800112_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ33541 (Selaginella moellendorffii), 3'ss of exon 3
gtacttggtggtatcattgggtttcagaacttcaaccatagctgagaagtagcttgatccttgtttggcctattaatcagATGAGGATGTGGTGTTTATTGTAGATGATAAATGAGAAGCCACAGGTGATTCAGGAGTATGAATCAGGCAAGGCAATCCCCAACCAGCAGATCATTAGCA------------------------
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-----------------------------gtttgg--atgattgattctttggttttttctt-tttggctgatttgttttccttgttggtt-tgcttggtccagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCGGGAAAAGCCATCCCCAACCAGCAGATCATCTCCAAGCTCGAGCGCGCGCTGGGAGCCA
upper sequence: GRMZM5G800112_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ36890 (Selaginella moellendorffii), 3'ss of exon 3
gtacttggtggtatcattgggtttcagaacttcaaccatagctgagaagtagcttgatccttgtttggcctattaatcagATGAGGATGTGGTGTTTATTGTAGATGATAAATGAGAAGCCACAGGTGATTCAGGAGTATGAATCAGGCAAGGCAATCCCCAACCAGCAGATCATTAGCA------------------------
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-----------------------------gtttgg--atgattgattctttggttgtgtctt-tttggctgatttgttttccttgttggtt-tgcttggtccagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCCATCCCCAACCAGCAGATAATCTCCAAGCTCGAGCGCGCGCTGGGAGCCAMapped 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|101399867|gb|EB821780.1|EB821780EST: TCATGCAAGCAAGGCTCGATAAGAAGCTGACACAGGCACAACTTGCTCAG ATGAGGATGTGGTGTTTATTGTAGATGATAAATGAGAAGCCACAGGTGATT
genomic: TCATGCAAGCAAGGCTCGATAAGAAGCTGACACAGGCACAACTTGCTCAGgtacttggtg ... tattaatcagATGAGGATGTGGTGTTTATTGTAGATGATAAATGAGAAGCCACAGGTGATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaacttcaaccatagctgagaagtagcttgatccttgtttggcctattaatcagATGAGGATGTGGTGTTTATTGTAGATGATAAATGAGAAGCCACAGGTGATTCAGGAGTATGAATCAGGCAAGGCAATCCCCAACCAGCAGATCATTAGCA
gcttgat putative branch site (score: 5)
tattaatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttggtggtatcattgggtttcagaacttcaaccatagctgagaagtagcttgatccttgtttggcctattaatcagATGAGGATGTGGTGTTTATTGTAGATGATAAATGAGAAGCCACAGGTGATTCAGGAGTATGAATCAGGCAAGGCAATCCCCAACCAGCAGATCATTAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA