Sequence
atgc intronic sequence ATGC exonic sequence...ggatacttttcattttttcctgtatcaatcaatagttgatacaaattttagcatttactttcaagaaattatctgatcctgatatggctgtgatatgcagGGCATAGAGATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGCCGAAGTCTTGAAGTGTTTACAAGGTTTCCAGCTGGAAATGGGGGAACAATTGAAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G109987_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g01890.1 (Oryza sativa), 3'ss of exon 6
-ggatacttttcattttttcctgtatcaatcaatagttga--tacaaattttagcatttactttcaagaaattatctgatcctgatatggctgtgatatgcagGGCATAGAGATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGCCGAAGTCTTGAAGTGTTTACAAGGTTTCCAGCTGGAAATGGGGGAACAATTGAAC
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actgttatcatcaaatttaatcgtgaagataagcagatatcttgctttttttgttactt-tattcaggagattttgtg--tctcatagaactttgttacgtagGTGGTAGAGATATTGAAAGATCGTCCATCTTGGTTCCGTGATTGTCGAAACCTGGAAGTCTTTACAATGATTCCAGCAGGAAATGGAGGAACGGTTGAAC
upper sequence: GRMZM2G109987_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 5
-------------------ggatacttttcattttttcctgtatcaatcaatagttgatacaaattttagcatttactttcaagaaattatctgatcctgatatggctgtgatatgc-agGGCATAGAGATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGCCGAAGTCTTGAAGTGTTTACAAGGTTTCCAGCTGGAAATGGGGGAACAATTGAAC
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gtaaattcaccaagtaaaagtatggtttggattttttttgtcatatcttggtatgccagttaatgtctggaatctgttt----ggaatt-tgaatttctga-atgcctgattttcaccagATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAAC
upper sequence: GRMZM2G109987_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G20520.1 (Glycine max), 3'ss of exon 5
----------------ggatacttttcattttttcctgtatcaatcaatagttgatacaaattttagcatttactttcaagaaattatctgatcctgatatggctg-tgatatgcagGGCATAGAGATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGCCGAAGTCTTGAAGTGTTTACAAGGTTTCCAGCTGGAAATGGGGGAACAATTGAAC
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gtaaattgacttagaagtatggtttggattttttttt-catttcttggtatgcca-gtgaatgtctgtaa--gctgtttggaatttgaat--ttctga-atgcctgattttcaacagATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAAC
upper sequence: GRMZM2G109987_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------ggatacttttcattttttcctgtatcaatcaatagttgatacaaattttagcatttactttcaagaaattatctgatcctgata-----------tggctgtgatatgcagGGCATAGAGATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGCCGAAGTCTTGAAGTGTTTACAAGGTTTCCAGCTGGAAATGGGGGAACAATTGAAC
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gtaagcttcagccaattatgtggtcaggtcatttatgaaaatttgaacatttttcttgatattttattgtaggacctttattttttcatgt--tataataatattagcatgctttgaaaagtaatatttttgtttgcgactgacagATTGCAGAGATCCTCAAAGATCGTCCATCTTGGTTCCGGGACTGTCGGAGCCTTGAAGTTTTCACCATGTTTCCAGCTGGAAATGGAGGAACTGTTGAACMapped 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|28873580|gb|CB329550.1|CB329550EST: GTGGCGTTGCTGCCCGCGCCTGTGGTTTGGTGAATCTAGAACCAACAAAA GGCATAGAGATCTTGAAAGATCG
genomic: GTGGCGTTGCTGCCCGCGCCTGTGGTTTGGTGAATCTAGAACCAACAAAAgtaagttttt ... tgatatgcagGGCATAGAGATCTTGAAAGATCG
EST:
gi|21809883|gb|BQ668201.1|BQ668201EST: GTGGCGTTGCTGCCCGCGCCTGTGGTTTGGTGAATCTAGAACCAACAAAA GGCATAGAGATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGCCGAAGT
genomic: GTGGCGTTGCTGCCCGCGCCTGTGGTTTGGTGAATCTAGAACCAACAAAAgtaagttttt ... tgatatgcagGGCATAGAGATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGCCGAAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttagcatttactttcaagaaattatctgatcctgatatggctgtgatatgcagGGCATAGAGATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGCCGAAGTCTTGAAGTGTTTACAAGGTTTCCAGCTGGAAATGGGGGAACAATTGAAC
tcctgat putative branch site (score: 3)
tttcaagaaattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggatacttttcattttttcctgtatcaatcaatagttgatacaaattttagcatttactttcaagaaattatctgatcctgatatggctgtgatatgcagGGCATAGAGATCTTGAAAGATCGTCCCTCTTGGTTCCGTGATTGCCGAAGTCTTGAAGTGTTTACAAGGTTTCCAGCTGGAAATGGGGGAACAATTGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA