Sequence
atgc intronic sequence ATGC exonic sequence...aggtactaaaccagtttctttaacactttttgcccttttcatttgtagttgtgttaatgttcgattaaataattctttttttccttgtgatgtactgaagGTGCCCAAAAACTTGCTCACATCCGCGAGAATAGTAATTTCTTCAGGTCAGAGCTCAAGAAGATGGTTTTTGAGGTTCTTGGTGACAATGACTCTCCTGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G137556_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 9
aggtactaaaccagttt----ctttaacactttttgcccttttcatttgtagttgtgttaatgttcgattaaataattcttt-ttttccttgtgatgtactgaagGTGCCCAAAAACTTGCTCACATCCGCGAGAATAGTAATTTCTTCAGGTCAGAGCTCAAGAAGATGGTTTTTGAGGTTCTTGGTGACAATGACTCTCCTGT
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--gtactagccttttcttctgcttcgaccctttcaatgcgctgcaggc-tatccatgtaagttttactttcaattcttatttattttggttttgatgtcttgcagGTGCCCAGAAACTTGCACGCATCCGTGAGAACAGCAATTTCTTTAGGTCAGAGCTCAAGAAGATGGGTTTTGAGGTTCTCGGAGACAATGACTCTCCAGT
upper sequence: GRMZM2G137556_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 9
-------aggtactaaaccagtttctttaacactttttgcccttttcatttgtagttgtgttaatgttcgattaaataattctttttttccttgtg----atgtactgaag-
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gtttggctggcactagttctgctctttgctttgcatttgtattgtttgatgattttt-tatgtgcatcaatccaaataatattcgtctactttgtttaccgtgcattgaagtaagttttttctatatagGTGCCCAGAAACTTGCACAAATTCGAGAGAATAGCAACTTTTTTAGGTCAGAACTGCAGAAGATGGGATTTGAGGTTCTTGGGGATAATGATTCTCCAGT
upper sequence: GRMZM2G137556_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 9
-------aggtactaaaccagtttctt---taacactt---tttgcc--cttttcatttgtagttgtgt---taatgttcgattaaataattctttttttcct----tgtgatgtactga---agGTGCCCAAAAACTTGCTCACATCCGCGAGAATAGTAATTTCTTCAGGTCAGAGCTCAAGAAGATGGTTTTTGAGGTTCTTGGTGACAATGACTCTCCTGT
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gtttggctggcactagttctgctctttgctttgcatttgtatttgatggttttttacgtgcatcaatccaaataatattcatctactttgtttaccttgcattgaagtaagttgtttctatatagGTGCCCAGAAACTTGCACAAATTCGAGAAAATAGCAACTTTTTCAGGTCAGAATTGCAGAAGATGGGATTTGAGGTTCTTGGGGATAATGATTCTCCAGT
upper sequence: GRMZM2G137556_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 9
-----------aggtactaaacca-gttt--ctttaacac---tttttgcccttttcatttgtagttgtgttaatgttcgattaaataattctttttttccttgtgatgtactgaagGTGCCCAAAAACTTGCTCACATCCGCGAGAATAGTAATTTCTTCAGGTCAGAGCTCAAGAAGATGGTTTTTGAGGTTCTTGGTGACAATGACTCTCCTGT
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gtaggataaataaatcttctgtcatgcttggttttaacttctattcttgaatctttaggtttcagactctccattgctttaattgtttttgattttagtgctcttgtgtccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT
upper sequence: GRMZM2G137556_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 10
------------aggtactaaaccagtttctttaacactttttgcccttttcatttgtagttgtgttaatgttcgattaaataattctttttttccttgtgatgtactgaagGTGCCCAAAAACTTGCTCACATCCGCGAGAATAGTAATTTCTTCAGGTCAGAGCTCAAGAAGATGGTTTTTGAGGTTCTTGGTGACAATGACTCTCCTGT
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gttcaccctcttctatatttcaccatttatggtggctcatgcagctctgcaaacctagatct-tgagcttatttgcttat-tgtttgatctgcttttgtttaaatatt--agGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagttgtgttaatgttcgattaaataattctttttttccttgtgatgtactgaagGTGCCCAAAAACTTGCTCACATCCGCGAGAATAGTAATTTCTTCAGGTCAGAGCTCAAGAAGATGGTTTTTGAGGTTCTTGGTGACAATGACTCTCCTGT
tgttaat putative branch site (score: 3)
ttaatgttcgattaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aggtactaaaccagtttctttaacactttttgcccttttcatttgtagttgtgttaatgttcgattaaataattctttttttccttgtgatgtactgaagGTGCCCAAAAACTTGCTCACATCCGCGAGAATAGTAATTTCTTCAGGTCAGAGCTCAAGAAGATGGTTTTTGAGGTTCTTGGTGACAATGACTCTCCTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - tgccctt
- - - - - - - - - - - - - - - - - - -ttcattt
- - - - - - - - - - - - - - - - - - - - - - - - ttgtgtt