Sequence
atgc intronic sequence ATGC exonic sequence...tggatttttttcatattttgcctatcaatcaataattgatacaaattttagcatttactttcaagaaattatttgatcctgatatagctgtgtcatgcagGTCATAGAAATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGTCGAAGTCTGGAAGTGTTTACAATGTTTCCAGCTGGAAATGGGGGAACAATTGAAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G042250_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g01890.1 (Oryza sativa), 3'ss of exon 6
tggatttttttcatattttgcc-tatcaatcaataattga--tacaaattttagcatttactttcaagaaattatttgatcctgatatagctgtgtcatgcagGTCATAGAAATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGTCGAAGTCTGGAAGTGTTTACAATGTTTCCAGCTGGAAATGGGGGAACAATTGAAC
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actgttatcatcaaatttaatcgtgaagataagcagatatcttgctttttttgttactt-tattcaggagattttgtg--tctcatagaactttgttacgtagGTGGTAGAGATATTGAAAGATCGTCCATCTTGGTTCCGTGATTGTCGAAACCTGGAAGTCTTTACAATGATTCCAGCAGGAAATGGAGGAACGGTTGAAC
upper sequence: GRMZM2G042250_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 5
----------------tggatttttttcatattttgcctatcaatcaataattgatacaaattttagcatttactttcaagaaattatttgatcctgatatagctgtgtcatgc-agGTCATAGAAATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGTCGAAGTCTGGAAGTGTTTACAATGTTTCCAGCTGGAAATGGGGGAACAATTGAAC
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gtaaattcaccaagtaaaagtatggtttggattttttttgtcatatcttggt--atgccagttaatgtctggaatctgtttggaatttgaatttctga-atgcctgattttcaccagATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAAC
upper sequence: GRMZM2G042250_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G20520.1 (Glycine max), 3'ss of exon 5
-tggatttttttcatattttgcct---atcaatcaataattgatacaaattttagcatttactttcaagaaatt----atttga--tcctgatatagctg-tgtcatgcagGTCATAGAAATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGTCGAAGTCTGGAAGTGTTTACAATGTTTCCAGCTGGAAATGGGGGAACAATTGAAC
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gtaaattgacttagaagtatggtttggatttttttttcatttcttggtatgccagtgaatgtctgtaagctgtttggaatttgaatttctga-atgcctgattttcaacagATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAAC
upper sequence: GRMZM2G042250_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------------------tggatttttttc---atattttgcctatcaatcaataattgatacaaattttagcatttactttcaagaaattatttgatcctgatatagctgtgtcatgcagGTCATAGAAATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGTCGAAGTCTGGAAGTGTTTACAATGTTTCCAGCTGGAAATGGGGGAACAATTGAAC
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gtaagcttcagccaattatgtggtcaggtcatttatgaaaatttgaacatttttcttgatattttat-tgtaggacctttattttttcatgttataataat-attagcatgctttgaaaagtaatatttttgtttgcgactgacagATTGCAGAGATCCTCAAAGATCGTCCATCTTGGTTCCGGGACTGTCGGAGCCTTGAAGTTTTCACCATGTTTCCAGCTGGAAATGGAGGAACTGTTGAACMapped 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|29167992|gb|CB411252.1|CB411252EST: GTGGCGTTGCTGCCCGCGCCTGTGGTTTGGTGAATCTAGAACCAACAAAA GTCATAGAAATCT
genomic: GTGGCGTTGCTGCCCGCGCCTGTGGTTTGGTGAATCTAGAACCAACAAAAgtaagtattt ... tgtcatgcagGTCATAGAAATCT
EST:
gi|211282791|gb|FL192982.1|FL192982EST: GTGGCGTTGCTGCCCGCGCCTGTGGTTTGGTGAATCTAGAACCAACAAAA GTCATAGAAATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGTCGAAGT
genomic: GTGGCGTTGCTGCCCGCGCCTGTGGTTTGGTGAATCTAGAACCAACAAAAgtaagtattt ... tgtcatgcagGTCATAGAAATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGTCGAAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttagcatttactttcaagaaattatttgatcctgatatagctgtgtcatgcagGTCATAGAAATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGTCGAAGTCTGGAAGTGTTTACAATGTTTCCAGCTGGAAATGGGGGAACAATTGAAC
tcctgat putative branch site (score: 3)
atttactttcaagaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggatttttttcatattttgcctatcaatcaataattgatacaaattttagcatttactttcaagaaattatttgatcctgatatagctgtgtcatgcagGTCATAGAAATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGTCGAAGTCTGGAAGTGTTTACAATGTTTCCAGCTGGAAATGGGGGAACAATTGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA