Sequence
atgc intronic sequence ATGC exonic sequencegtatgcaaaccttccggaaccgacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagctggttgtttttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G069102_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
---------gtatgcaaaccttccggaaccg-acatgctt-gtcttaagttcatggctcaatg---ttcatgc---tctatctg-atatggtctctaagaaagctggttgtt-tttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
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gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaa--aagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
upper sequence: GRMZM2G069102_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
gtatgcaaaccttccggaaccgacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagctggttgtttttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
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---------------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatt-tagtcttgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
upper sequence: GRMZM2G069102_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT4G10610.2 (Arabidopsis thaliana), 3'ss of exon 5
gtatgcaaaccttccggaaccgacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagctggttgtttttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
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-----------gtaaggttttttcttgtgtttcatcacattctgactgcaaagttatggttttttagactcaagaggtttgatt-ttagtcctgtctttgttctt---agACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAG
upper sequence: GRMZM2G069102_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
gtatgcaaaccttccggaaccgacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagctggttgtttttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
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acatgttggtgcta-gaaatgggtatagc--ttagaaacgtgccgatcaaacattgtttactatttcttgtgcttgttaattaaa-------tgttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
upper sequence: GRMZM2G069102_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S62_224V6.1 (Physcomitrella patens), 3'ss of exon 5
gtatgcaaaccttccggaaccgacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagctggttgtttttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
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----ggaattgtttcatacttgcaacgattg--ttagtgatatgccatagttcttgaatacggctcgg-atgaattctggct---ctaacttagttactctccattacagTCTGAAGATGAGCGTGAAATGTGTGCACGGACCATCTACTGTACAAATATTGACAAGAAG
upper sequence: GRMZM2G069102_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S196_50V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatgcaaaccttccggaaccgacatgcttgtcttaagttcatg-gctcaatgttcatgctctatctgatatggtctctaagaaagctggttgtttttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
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----aagaattttgataaatttttag---tgacgtagttgtatgtgaacaatcctggaaattgcttcaataaggtggttgttctaac--acaacttctctatgttt--cagTCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAGMapped 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|94472396|gb|EB701354.1|EB701354EST: TGCCGTCAAAAACTGCCATTGCACCAGTCAACGAAACATTCCTACCCAGG TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATT
genomic: TGCCGTCAAAAACTGCCATTGCACCAGTCAACGAAACATTCCTACCCAGGgtatgcaaac ... tgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgctctatctgatatggtctctaagaaagctggttgtttttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
atctgat putative branch site (score: 4)
tttttctgtgctct putative PPT
ttgttttt 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
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gtatgcaaaccttccggaaccgacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagctggttgtttttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG