Sequence
atgc intronic sequence ATGC exonic sequence...gaccatggaccgtccggcctcagggccggactgtccgccagctcaaaatggcgctcaacaactgctatatgttattgacaatatggtgtacttgttgcggGATGCACAGGACTATGCAGAGAAGAACAAAATGTTTTTCATTGAGACGTCAGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G863105_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 6
gaccatggaccgtccggcctcagggccggactgtccgccagctcaaaatggcgctcaaca-actgctatatgttattgacaatatggtgtacttgttgcggGATGCACAGGACTATGCAGAGAAGAACAAAATGTTTTTCATTGAGACGTCAGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG
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-----------gtcagatcttgtg--tgaagttgtagtaaacatagtat----cacaatatgctgcaaaattgttttgacgatatggtgcacattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCAGCAAAGACAGCTGATAATATAAACCAAGTATTTGAG
upper sequence: GRMZM5G863105_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 6
gaccatggaccgtccggcctcagggccggactgtccgccagctcaaaatggcgctcaacaactgctatatgttattgacaatatggtgtacttgttgcggGATGCACAGGACTATGCAGAGAAGAACAAAATGTTTTTCATTGAGACGTCAGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG
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--------gtagtgcaacactatg--taatatagttgtcatataaacaaaataatcatttttttct-catatagt--atgctttactgtttccatgaaggatggcactg-actatgcagAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG
upper sequence: GRMZM5G863105_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 6
gaccatggaccgtccggc-ctcagggccggactgtccgccagctcaaaatggcgctcaacaactgctatatgttattgacaatatggtgtacttgttgcggGATGCACAGGACTATGCAGAGAAGAACAAAATGTTTTTCATTGAGACGTCAGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG
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--------gtagtgcaacactctgtaatatagttgtcatataaacaaaataattgtttgtttttctcata---tatatatgctttactgtttccatgaagGATGGCACTG-ACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG
upper sequence: GRMZM5G863105_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G54840.1 (Arabidopsis thaliana), 3'ss of exon 6
--gaccatggaccgtccggcctcagggccggactgtccgccagctcaaaatggcgctcaacaactgctatatgttattgacaatatggtgt--acttgttg-cggGATGCACAGGACTATGCAGAGAAGAACAAAATGTTTTTCATTGAGACGTCAGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG
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gtgagtttgcgt-aaacgtcttcatctagattccgtagcgcattttgttgtcactttcattgtccttgcttcttcagtggtatcacattttcaatttcttaacagGATGGAATGGAGCTTGCAGAGAAGAACGGCATGTTCTTCATTGAGACGTCAGCCAAGACAGCCGATAACATAAATCAACTGTTTGAG
upper sequence: GRMZM5G863105_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 6
gaccatggaccgtccggcctcagggccggactgtccgccagctcaaaatggcgctcaacaactgctatatgttattgacaatatg---gtgtacttgttgcggGATGCACAGGACTATGCAGAGAAGAACAAAATGTTTTTCATTGAGACGTCAGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG
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------------gtgagtgtcata--ctatttgtctgaatgcttcagcttttcctatgtattcacaaaatgtgctttaacacgtgtttattttattcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatggcgctcaacaactgctatatgttattgacaatatggtgtacttgttgcggGATGCACAGGACTATGCAGAGAAGAACAAAATGTTTTTCATTGAGACGTCAGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG
tattgac putative branch site (score: 2)
tatatgttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaccatggaccgtccggcctcagggccggactgtccgccagctcaaaatggcgctcaacaactgctatatgttattgacaatatggtgtacttgttgcggGATGCACAGGACTATGCAGAGAAGAACAAAATGTTTTTCATTGAGACGTCAGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- -catggac
- - - - - - - - - - - - - - - - - -cgccagc
- - - - - - - - - - - - - - - - - - - - - - - - tggcgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - caactgc