Sequence
atgc intronic sequence ATGC exonic sequencegtatgctagatctctgctgcatgagaggtggtatattttcatagtttttcctgatattggtgtttgtgattgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 5
------------------------gtatgctagatctctgctgcatgagaggtggtatattttcatagtttttcctgatattggtgtttgtg-attgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG
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gtacagtctctattatatatataactctgttaagtc-caactattcaaatacaaatct-tgttcatgtcctgttctgatatttaaatggatgtataatcatgtacagACCATCAAGACAAACGTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAG
upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 5
-------------gtatgctagatctctgctgcatgagaggtggtatattttcatagtttttcctgatattg------gtgtttgtgat-tgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG
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atattaattctacttctgtcatgtgt-tattgcttgaaagttc-tgtttttcagctgatccttgagacactatctaatatgttaggaaaataatttttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAACGAGTTGGGGCAAG
upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 6
gtatgctagatctctgctgcatgagaggtggtatattttcatagttt-----ttcctga-----tattggt---gtttgtgattgtctg------taacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG
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-tgtctacctcctgtcatgcatcattgatcgaaagttctctctgcttatctgtccttgaaagactatatatctaatttgtaatggagtaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAG
upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 5
-----gtatgctagatctctgctgcatgagaggtggtatatt----ttcatagtttttcct---gatattg------gtgtttgtgattgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG
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tatatttattctacttctgtcatgtgtcatatcttgaaagttctgtttttcagcttatccttgagacactatctaatatgttgggaaataatttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG
upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 3'ss of exon 5
gtatgctagatctctgctgcatgagaggtggtatattttc--------atagttt-----ttcctgatattggtgtttgtgatt------gtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG
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-tcttctaatttcttaatgagtaatcaattatatgtttttccctgagtatgctttggacattaatgatggttttccttgtaaatcatgcaatacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAG
upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 11
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------gtatgctagatc-tctgctgcatgagaggtggtatat-tttca----tagtttttcctgatattggtgtttgtgattgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG
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tatatatatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttcagattggtttgaaatttg-gtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtggtatattttcatagtttttcctgatattggtgtttgtgattgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG
tcctgat putative branch site (score: 3)
atattttcatagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctagatctctgctgcatgagaggtggtatattttcatagtttttcctgatattggtgtttgtgattgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT