Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaaaatccttcttttaacccacgttgtatttttttatggcaataacttcgtattcagaattggtggattgtgccacttaatgcatctacatatccataatttaaaatcatgcagatttgacattttcttattatatttccaggcagGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAACCAAAGATGAAAACACACGTTTCTCCCCGACAAATCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G470438_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g06900.1 (Oryza sativa), 3'ss of exon 11
gtaaaaaaatccttcttttaacccacgttgtatttttttatggcaataacttcgtattcagaattggtggattgtgccacttaatgcatctacatatccataatttaaaatcatgcagatttgacattttcttattatatttccaggcagGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAACCAAAGATGAAAACACACGTTTCTCCCCGACAAATCT
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------------tcttgtcaatctgcaacataatattttcttgtggcaatatcatatgta----tattgagttgtgccactaaa---------atatt--tgactga-------------ttgactcctttc------gcttccagGCAGGAATTGGCACTGATGCAACGATGCATGATCACATAAAAAAGTTACTTGACCGTTGTTATGCAACCAAAGATGCAAATACACGGTTCTCCCCAACAA----
upper sequence: GRMZM2G470438_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0044g01570.t01 (Vitis vinifera), 3'ss of exon 5
gtaa--aaaaatccttcttttaacccacgttgtatttttttatggcaataacttcgtattcagaattggtggattgtgccacttaatgcatctacatatccataatttaaaatcatgcagatttgacattttcttattatatttcc-aggcagGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAACCAAAGATGAAAACACACGTTTCTCCCCGACAAATCT
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gtaatgaagattaagtatctgtttttagcttaaggttggttattgaattgtctttttat---ggtctataattttgaattact--agtcatttactttttcagacattgaaagtgaact-attccttttcttttacttgtctttcttagGCTGGCATTGGTACAGATGCAACAATGCATGATCACATAAAAAAGCTGCTGGATCGGTTTTATGCAACTAAGGACTCAAATACTCGTTTCTCACCAACAA----
upper sequence: GRMZM2G470438_T04 (Zea mays), 3'ss of exon 4
lower sequence: EFJ13984 (Selaginella moellendorffii), 3'ss of exon 12
gtaaaaaaatccttcttttaacccacgttgtatttttttatggcaataacttcgtattcagaattggtggattgtgccacttaatgcatctacatatccataatttaaa-atcatgcagatttgacattttcttattatatttccaggcagGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAACCAAAGATGAAAACACACGTTTCTCCCCGACAAATCT
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-------------------------------------------------------------------------------------------gtggtttcttagttccagcattttcaagacctga-attctct----gtgcggccagGAGGGAATTGGAACGGATGCTACTATGCATGATCACATAAAAAAGCTGCTGGACCGGCGCTACGCTACCAAAGATGCGCAGACACGCTTTTGTCCCACAA----
upper sequence: GRMZM2G470438_T04 (Zea mays), 3'ss of exon 4
lower sequence: EFJ28114 (Selaginella moellendorffii), 3'ss of exon 12
gtaaaaaaatccttcttttaacccacgttgtatttttttatggcaataacttcgtattcagaattggtggattgtgccacttaatgcatctacatatccataatttaaa-atcatgcagatttgacattttcttattatatttccaggcagGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAACCAAAGATGAAAACACACGTTTCTCCCCGACAAATCT
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-------------------------------------------------------------------------------------------gtggtttcttagttccagcattttcaagacctga-attctct----gtgtggccagGAGGGAATTGGAACGGATGCTACTATGCATGATCACATAAAAAAGCTGCTGGACCGGCGCTACGCTACCAAAGATGCGCAGACACGCTTTTGTCCCACAA----Mapped 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|211354447|gb|FK991824.1|FK991824EST: GGCCACCGCCTCTTCTGGCTGAAGCCGACCTTCTTAGCTGTATGGATAAA GCAGGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTT
genomic: GGCCACCGCCTCTTCTGGCTGAAGCCGACCTTCTTAGCTGTATGGATAAAgtaaaaaaat ... ttccaggcagG-A--A-TTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTT
EST:
gi|149060846|gb|EE157300.2|EE157300EST: GGCCACCGCCTCTTCTGGCTGAAGCCGACCTTCTTAGCTGTATGGATAAA GCAGGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTT
genomic: GGCCACCGCCTCTTCTGGCTGAAGCCGACCTTCTTAGCTGTATGGATAAAgtaaaaaaat ... ttccaggcagG-A--A-TTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTT
EST:
gi|71327908|gb|DR800590.1|DR800590EST: GGCCACCGCCTCTTCTGGCTGAAGCCGACCTTCTTAGCTGTATGGATAAA GAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACC
genomic: GGCCACCGCCTCTTCTGGCTGAAGCCGACCTTCTTAGCTGTATGGATAAAgtaaaaaaat ... ttccaggcagGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atccataatttaaaatcatgcagatttgacattttcttattatatttccaggcagGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAACCAAAGATGAAAACACACGTTTCTCCCCGACAAATCT
atttgac putative branch site (score: 4)
tatttcc putative PPT
atttgacattttctta 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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gtaaaaaaatccttcttttaacccacgttgtatttttttatggcaataacttcgtattcagaattggtggattgtgccacttaatgcatctacatatccataatttaaaatcatgcagatttgacattttcttattatatttccaggcagGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAACCAAAGATGAAAACACACGTTTCTCCCCGACAAATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG