Sequence
atgc intronic sequence ATGC exonic sequence...actatttaagtgccactttttcatttggacttcggccctgtcatgtgcccaatataatgggcacaatttagactcacttttatttctgctccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G147446_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g05830.1 (Oryza sativa), 3'ss of exon 4
------actatttaagtgccactt---tttcatttggacttcggccctgtcatgtgcccaatataatgggcacaatttagactcacttttatttctgctccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT
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tttgtcatttcttaagttatagccaaatagcaccttaatttcttttcc-ttacctggacg-catagacaatacaattttaactc--ttctatttt-----cctttgcagTATGTTCATTTTCTCCAACGAAAGTACTCTCTGAACTCATTCAACCTCCTGGGTCACACTGCTCCAGCCCAAGCAGGATCCCTTCTGCTAGTGGGGCCCT
upper sequence: GRMZM2G147446_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g05780.3 (Oryza sativa), 3'ss of exon 4
actatttaagtgccactttttcatttggacttcggccctgtcatgtgcccaat---ataatgggcacaatttagactcacttttatttctgctccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT
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--tgaataattggcactccctaaatcatttgtttgtt-tgtcacttctttaattatagacaaattactcattagtttcctttccttttctattttccttgcagTATGTTCATTTTCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTGGGCCACACTGCTCCAGCCCAAGCGGGATCTCTTCTGCTAGTTGGGCCCT
upper sequence: GRMZM2G147446_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 4
actatttaagtgccactttttcatttggacttcggccctgtca-tgtgcccaatataatgggcacaatttagactcacttttatttctgctccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT
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-----gtaagtgttctgtgctcttacggagtaacatatcgtttctttgtttaagataatactaata--ttggtgtggttttta--------catgatgcagTATGTACATTACCTTCAGCGCAAGTACTCGCTTAACTCATTCAACCTATTGGGACATACCGCTCCAGCCCAAGCCGCAACATTACTGGTAGTTGGCCCGT
upper sequence: GRMZM2G147446_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
actatttaagtgccactttttcatttggacttcggccctgtca--tgtgcccaatataatgggcacaatttagactcacttttatttctgctccttc--tgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT
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------------------------------gtaagttctttgagctacggtttacacaaagattaagattaagatttacacaaagtttctctcttttgttgcagTATGTACATTATCTACAGCGAAAGTACTCGCTTAGCTCATTCAACCTACTGGGTCATACTGCTCCAGCTCAGGCTGCAACGTTATTGATAGTCGGTCCATMapped 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|78115997|gb|DV534385.1|DV534385EST: GTCTAATTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTGCAACAATAC TATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTG
genomic: GTCTAATTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTGCAACAATACgtgagtttta ... ccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcccaatataatgggcacaatttagactcacttttatttctgctccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT
gactcac putative branch site (score: 2)
ctcacttttatttctg CT-rich tract
acttttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actatttaagtgccactttttcatttggacttcggccctgtcatgtgcccaatataatgggcacaatttagactcacttttatttctgctccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT