Sequence
atgc intronic sequence ATGC exonic sequencegcaagtacattaaatctttgcatttcacttgtcctcgttaatacagcaaaaaaagtaatattccttcctttagGTACTTGACTGTGCAGTTCGTTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G017086_T03 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 11
gcaagtacattaaatctttgc---atttcact-tgtcctcgttaatacagcaa---aaaaagtaatattccttcctttagGTACTTGACTGTGCAGTTCGTTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA
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gcaagaac-ctaaatattttcttgattatattatctcttattttattcagaaattataagtatgccaattctgtgttcagGTACTTGACTGTGCAGTTTGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAGAAGGCAAAGATTTTACGG
upper sequence: GRMZM2G017086_T03 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA07G01480.1 (Glycine max), 3'ss of exon 11
----------------gcaagtacattaaatctttgc-atttcacttgt-cctcgttaat-acagcaaaaaaagtaatattccttccttt--------agGTACTTGACTGTGCAGTTCGTTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA
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ttgtaattgttgagatgaagattggttgtttctttgttgtgttatttcttccttggtaattgctatgagtgatgtgattttcaaccttttcctgttcaagGTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCAGAAGGCTAAGATTTTGCGG
upper sequence: GRMZM2G017086_T03 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA08G20900.1 (Glycine max), 3'ss of exon 11
----------------gcaagtacattaaatctttgc-atttcacttgt-cctcgttaat-acagcaaaaaaagtaatattc-----cttccttt---agGTACTTGACTGTGCAGTTCGTTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA
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ttgtaattgttcagatgaagtttggttgtttctttgttgtgttatttcttccttggtaattgctatgagtgatatgattttcaaccttttccttttcaagGTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCAAAAGGCTAAGATTTTGCGG
upper sequence: GRMZM2G017086_T03 (Zea mays), 3'ss of exon 11
lower sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 11
-------------------gcaagtacattaaatctttgcatttcact-tgtcctcgttaatacagcaaaaaaagt------aata-ttccttcctttagGTACTTGACTGTGCAGTTCGTTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA
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tgtggagtctactggcacccttctttttctatctccttgcttttgtttgtatatttctgggtgaagaaagagaattcttacaaataattttttcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG
upper sequence: GRMZM2G017086_T03 (Zea mays), 3'ss of exon 11
lower sequence: EFJ09332 (Selaginella moellendorffii), 3'ss of exon 10
gcaagtacattaaatctttgcatttcacttgtcctcgttaatacagcaaaaaaagtaatattccttcctttagGTACTTGACTGTGCAGTTCGTTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA
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------------------------gtgggttttatgatttatcaattgctctaatgtgcactgttttgttcagatacTTGACTGTGCAGTTTGTTCGTTTCTTCTGGAAACGGGAAACGAAACAGAAAGCAAAGATCTTGAGGMapped 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|32866635|gb|CF006317.1|CF006317EST: GGTCGAACTGCAGTTTATACTAGAGAATCAAGAATAAATGAGCTGCCTAG GTACTTGACTGTGCAGTTCGTTCGCTTCTTTTGGAAAAGGGAATCAAACCA
genomic: GGTCGAACTGCAGTTTATACTAGAGAATCAAGAATAAATGAGCTGCCTAGgcaagtacat ... cttcctttagGTACTTGACTGTGCAGTTCGTTCGCTTCTTTTGGAAAAGGGAATCAAACCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcatttcacttgtcctcgttaatacagcaaaaaaagtaatattccttcctttagGTACTTGACTGTGCAGTTCGTTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA
cgttaat putative branch site (score: 4)
tattccttccttt putative PPT
aaaaaaagtaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagtacattaaatctttgcatttcacttgtcctcgttaatacagcaaaaaaagtaatattccttcctttagGTACTTGACTGTGCAGTTCGTTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG