Sequence
atgc intronic sequence ATGC exonic sequencegtaagacattgctggctgtttttttgttcatttcttgatttacctatttacttgtgtcacattattgtggtgttgcactcttttagGTATGTGTGGGAATCAAAAGCTGATGGATCATTTGCCATCTCTGAGGATACATGGAATGAGCCCCTTGGCCGTGGAACTGAGATAAGATTGCATCTGCGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 6
-----------------------------gtaagacattgctggctgtttttttgttcatttcttgatttacctatttactt-gtgtcacattattgtggtgttgcactcttttagGTATGTGTGGGAATCAAAAGCTGATGGATCATTTGCCATCTCTGAGGATACATGGAATGAGCCCCTTGGCCGTGGAACTGAGATAAGATTGCATCTGCGA
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gtaagacaccactgaaatacagcggctacatattgtgtttttggttcatcttcttttccttcactggcatgacaacctacttcatgttctgctgttgcactttttc--tctgatagGCATGTCTGGGAGTCCAAAGCTGATGGATCATTCGCTATCTCTGAGGATACATGGAATGAACCCCTGGGCCGTGGAACTGAAATAAGACTGCACCTCCGA
upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 6
-gtaagacattgctggc-tgtttttttgttcatttcttgatttacctatttacttgtgtcacattattgtggtgttgcactcttttagGTATGTGTGGGAATCAAAAGCTGATGGATCATTTGCCATCTCTGAGGATACATGGAATGAGCCCCTTGGCCGTGGAACTGAGATAAGATTGCATCTGCGA
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agtaagtctttttggacctgatatcgtttttgtttgttgacttgta-acccagctatctgacttgaaaattattcggt----tttcaGGTATGTATGGGAATCAAAAGCTGATGGAGCATTTGCAATTTCAGAAGATACATGGAATGAACCTCTAGGGCGTGGAACTGAGATTAGATTACACCT-CAA
upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 6
gtaagacattgctggc-------tgtttttttgttcatttc---ttga---------tttacctatttacttgtgtcacattattgtggtgttgcactc-------ttttagGTATGTGTGGGAATCAAAAGCTGATGGATCATTTGCCATCTCTGAGGATACATGGAATGAGCCCCTTGGCCGTGGAACTGAGATAAGATTGCATCTGCGA
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gtaagtccttttggacctgatgttgtttttgtaatcagttagtattgaaggaaaatttttgtttgttgacttgtaacccagctgcctaacttgaaacttatttggttttcagGTATGTATGGGAATCAAAAGCTGATGGAGCATTCGCTATTTCAGAAGATACATGGAATGAACCACTTGGACGAGGAACTGAGATTAGATTACACCTCAAG
upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaagacattgctggctgtttt-tttgttcatttcttgatttacctatttacttgt-gtcacattattgtggtg-----ttgcactcttttagGTATGTGTGGGAATCAAAAGCTGATGGATCATTTGCCATCTCTGAGGATACATGGAATGAGCCCCTTGGCCGTGGAACTGAGATAAGATTGCATCTGCGA
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gtaagttgatttagagggctttgtttggcaatatacttgtgggcatgtaaaatcattgaaaagcttttctgataacttcttttccgttttcagGTATGTATGGGAATCAAAGGCTAACGGTAAATTTGCTGTTTCCGAGGATACATGGAATGAGCCTCTTGGACGTGGAACCGAGATTAGATTACATCTTAGG
upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 6
----------gtaagacattgctggctgtttttttgttcatttcttgatttacctatttacttgtgtcacatta-------ttgtggtgttgca----ctcttttagGTATGTGTGGGAATCAAAAGCTGATGGATCATTTGCCATCTCTGAGGATACATGGAATGAGCCCCTTGGCCGTGGAACTGAGATAAGATTGCATCTGCGA
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gtgagcctcttgaagattttattttattttatttttattattattttttttttttgtgaaccagaggtttatgaaatggattgatgatcattcaaatttccattcagGTATGTATGGGAGTCTAAAGCTGATGGAGCTTTTGCAATTTCTGAGGATGTATGGAATGAACCACTCGGACGTGGAACTGAGATCAGATTGCATCTCAGAMapped 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|32849330|gb|CD989011.1|CD989011EST: TTGGTTGCTGACTATGTTGAAGTGGTCAGCAAGCACAATGATGATAAACA GTATGTGTGGGAATCAAAAGCTGATGGATCATTTGCCATCTCTGAGGATAC
genomic: TTGGTTGCTGACTATGTTGAAGTGGTCAGCAAGCACAATGATGATAAACAgtaagacatt ... actcttttagGTATGTGTGGGAATCAAAAGCTGATGGATCATTTGCCATCTCTGAGGATAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttgatttacctatttacttgtgtcacattattgtggtgttgcactcttttagGTATGTGTGGGAATCAAAAGCTGATGGATCATTTGCCATCTCTGAGGATACATGGAATGAGCCCCTTGGCCGTGGAACTGAGATAAGATTGCATCTGCGA
tcttgat putative branch site (score: 4)
cactctttt putative PPT
tatttactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagacattgctggctgtttttttgttcatttcttgatttacctatttacttgtgtcacattattgtggtgttgcactcttttagGTATGTGTGGGAATCAAAAGCTGATGGATCATTTGCCATCTCTGAGGATACATGGAATGAGCCCCTTGGCCGTGGAACTGAGATAAGATTGCATCTGCGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA