Sequence
atgc intronic sequence ATGC exonic sequence...tcaactacatggaagattgaaagttttgctaagataatgcaagtgcccttcttatctggatcaacttttccccacacaaaccattttactgcattctcagGCTGAGAAGATGGGACTTGACTACATGGATGTTGAGGCCCTCAAGAAAATGAACAGGAACAAGAAGCTTGTTAAGAAGCTTGTCAAGAAGTACCATGCTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G862017_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os08g44450.1 (Oryza sativa), 3'ss of exon 2
tcaactacatggaagattgaaagttttgctaagataatgcaagtgcccttcttatctggatcaacttttc--cccacacaaaccattttactgcattctcagGCTGAGAAGATGGGACTTGACTACATGGATGTTGAGGCCCTCAAGAAAATGAACAGGAACAAGAAGCTTGTTAAGAAGCTTGTCAAGAAGTACCATGCTT
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ctgaaattaagaatgttcacacgttgtttgtggatcaatttatt--ctgtctaatgagaatttatttatctgccaacttgctgcggattggctcgtgtgcagGCTGAGAAGATTGGGCTTGACTACATGGATGTTGAGGCTCTTAAGAAAATGAACAAGAACAAGAAGCTGGTTAAGAAGCTTGCCAAGAAGTACCATGCTT
upper sequence: GRMZM5G862017_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os08g44380.2 (Oryza sativa), 3'ss of exon 3
----tcaactacatggaagattgaaagttttgctaagataatgcaagtgcccttcttatctggatcaacttttccccacacaaaccattttactgcattctcagGCTGAGAAGATGGGACTTGACTACATGGATGTTGAGGCCCTCAAGAAAATGAACAGGAACAAGAAGCTTGTTAAGAAGCTTGTCAAGAAGTACCATGCTT
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ggatttttctctctgtaatatctgtctttattctgtc-taatg---gtactgtttctccctaattttcttcctactaacatgctgcaccatggcatttaaacagGCTGAGAAGATTGGGCTCGACTACATGGATGTTGAGGCCCTTAAGAAGATGAACAAGAACAAGAAGCTTGTGAAGAAGCTTGCCAAGAAGTACCATGCTT
upper sequence: GRMZM5G862017_T01 (Zea mays), 3'ss of exon 9
lower sequence: PP1S18_121V6.1 (Physcomitrella patens), 3'ss of exon 2
-----tcaactacatggaagattgaaagttttgctaaga----taatgcaagtgcccttc-ttatctggatcaacttttccccacacaa--accattttactgcattctcagGCTGAGAAGATGGGACTTGACTACATGGATGTTGAGGCCCTCAAGAAAATGAACAGGAACAAGAAGCTTGTTAAGAAGCTTGTCAAGAAGTACCATGCTT
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gtatttcctctaactcaactaatgccacccatgttgagaagcattttgtcagcatgccacattacgcaggttgattacctcttatttattcgccccattattgcgtaa-cagGCCAACAAGATGGGCATGGAATACATGGACGTCGAGAGCTTGAAGAAAATGAACAAGAACAAGAAGCTCGTGAAGAAACTGGCGAAGAAGTACCACGCTT
upper sequence: GRMZM5G862017_T01 (Zea mays), 3'ss of exon 9
lower sequence: PP1S427_1V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------------------tcaactacatggaagattgaaagttttgctaagataatgcaagtgcccttcttatctggatcaacttttccccacacaaaccattttactgcat------tctcagGCTGAGAAGATGGGACTTGACTACATGGATGTTGAGGCCCTCAAGAAAATGAACAGGAACAAGAAGCTTGTTAAGAAGCTTGTCAAGAAGTACCATGCTT
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gtatgcttattctcaaattttgattctttctatttgttgatggtgccagaaattgaataaaacattgtagaattttctgctctgggtctcatct-cactggcctttgtatattaaaactagaaattatcaccctttacttgataatggataattgctgatgtcgtgagtttcttttggtcgtaactcgtcacagGCGACCAAGAATGGTATCGAGTGCATGGATGTCGAGAGCTTGAAGAAGATGAACAAGAACAAGAAACTTGTGAAGAAGCTGGCTAAGAAGTACCACGCTT
upper sequence: GRMZM5G862017_T01 (Zea mays), 3'ss of exon 9
lower sequence: PP1S40_297V6.1 (Physcomitrella patens), 3'ss of exon 2
-tcaactacatggaagattgaaagttttgctaagataatgcaagtgcccttc--ttatctggatcaacttttccccacacaaaccattttactgcattctcagGCTGAGAAGATGGGACTTGACTACATGGATGTTGAGGCCCTCAAGAAAATGAACAGGAACAAGAAGCTTGTTAAGAAGCTTGTCAAGAAGTACCATGCTT
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gtcatattcgcacattggaataatttttgccttcatatttgtttcatttttagattatcttgattaatgtctcatttcttaaccaacgttcatctgacaatagGCAAACAAAATCGGTATGGAATACATGGATGTTGAGAGCTTGAAGAAGATGAACAAGAATAAGAAGCTCGTCAAGAAGCTGGCTAAGAAGTACCATGCTT
upper sequence: GRMZM5G862017_T01 (Zea mays), 3'ss of exon 9
lower sequence: EFJ34353 (Selaginella moellendorffii), 3'ss of exon 2
tcaactacatggaagattgaaagttttgctaagataatgcaagtgcccttcttatctggatcaacttttccccacacaaaccattttactgcattctcagGCTGAGAAGATGGGACTTGACTACATGGATGTTGAGGCCCTCAAGAAAATGAACAGGAACAAGAAGCTTGTTAAGAAGCTTGTCAAGAAGTACCATGCTT
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----------------------------gtaagattgagcgccctgtctccttttgttgccggattgaatcac---tggtccgttgctttttttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
upper sequence: GRMZM5G862017_T01 (Zea mays), 3'ss of exon 9
lower sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
tcaactacatggaagattgaaagttttgctaagataatgcaagtgcccttcttatctggatcaacttttccccacacaaaccattttactgcattctcagGCTGAGAAGATGGGACTTGACTACATGGATGTTGAGGCCCTCAAGAAAATGAACAGGAACAAGAAGCTTGTTAAGAAGCTTGTCAAGAAGTACCATGCTT
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----------------------------gtaagat----tgagcgccctctctcctttagttgccggattgaatcactggtccattgcttttttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccttcttatctggatcaacttttccccacacaaaccattttactgcattctcagGCTGAGAAGATGGGACTTGACTACATGGATGTTGAGGCCCTCAAGAAAATGAACAGGAACAAGAAGCTTGTTAAGAAGCTTGTCAAGAAGTACCATGCTT
cattctc CT-rich tract
attttact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaactacatggaagattgaaagttttgctaagataatgcaagtgcccttcttatctggatcaacttttccccacacaaaccattttactgcattctcagGCTGAGAAGATGGGACTTGACTACATGGATGTTGAGGCCCTCAAGAAAATGAACAGGAACAAGAAGCTTGTTAAGAAGCTTGTCAAGAAGTACCATGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - ctacatg
- - - - - - - - - - - -ttttgct
- - - - - - - - - - - - - - - - - - atgcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaacca