Sequence
atgc intronic sequence ATGC exonic sequence...aatggtcatgaacccaactaatctattctctcttgtagcctttctcatttagtctaaactctatacatagtggctaattatgtccactcttctttatcagGGTATTCGTCGACCTTGGAAAGGAGTTCTTATGTTTGGTCCACCAGGCACGGGAAAGACTCTTTTGGCAAAGGCAGTGGCTACAGAATGTGGAACAACAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 3
aatggtcatgaacccaactaatctattctctcttgtagcctttctcatttagtctaaactc-tatacatagtgg--ctaattatgtccactcttcttt--atcagGGTATTCGTCGACCTTGGAAAGGAGTTCTTATGTTTGGTCCACCAGGCACGGGAAAGACTCTTTTGGCAAAGGCAGTGGCTACAGAATGTGGAACAACAT
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----cgtattcatttcagtcttttcttcttgcatgtgaccttgtt-attcagtttaaatttgttttgatcctcatcctatccatgctcactctatttctgaccagGGTATTCGCCGACCTTGGAAAGGGGTTCTAATGTTTGGTCCACCTGGTACTGGAAAGACTCTTTTAGCGAAGGCAGTAGCTACAGAATGTGGCACAACAT
upper sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G80350.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------------------------aatggtcatg------aacccaactaatctattctctcttgtagcctttctcatttagtctaaactctatacatagtggctaatt--atgtccactcttctttatcagGGTATTCGTCGACCTTGGAAAGGAGTTCTTATGTTTGGTCCACCAGGCACGGGAAAGACTCTTTTGGCAAAGGCAGTGGCTACAGAATGTGGAACAACAT
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gtactttgattctgctccatacgctgtgaaatttggattctatattactattattagacatggagcaatcatacagaataacagtttcaattcatcatttcc-gtagactttat-atttgatcttccaggtatagaggatacttaatttgattgtttttgtttcccttcagGGTATTCGAAGACCATGGAAAGGAGTTCTCATGTTTGGTCCTCCTGGGACAGGTAAAACCCTGTTGGCAAAAGCTGTTGCAACTGAGTGTGGTACCACCT
upper sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 3
aatggtcatgaacccaactaatctattctctcttgtagcctttctcattta-gtctaaactctatacatagtggctaattatgtccactcttc-tttatcagGGTATTCGTCGACCTTGGAAAGGAGTTCTTATGTTTGGTCCACCAGGCACGGGAAAGACTCTTTTGGCAAAGGCAGTGGCTACAGAATGTGGAACAACAT
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gcttatc-tcactattattaaattaagaatttaagggacttttgtgttggaagtttgtattttttattcag-gtcaagttttattgtttctttacttaacagGGAATTAGGAGACCATGGAAAGGTGTTCTTATGTTTGGTCCTCCTGGTACTGGCAAGACACTTTTGGCTAAAGCTGTTGCTACTGAGTGTGGTACAACAT
upper sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ06179 (Selaginella moellendorffii), 3'ss of exon 4
aatggtcatgaacccaactaatctattctctcttgtagcctttctcatttagtctaaactctatacatagtggctaattatgtccactcttctttatcagGGTATTCGTCGACCTTGGAAAGGAGTTCTTATGTTTGGTCCACCAGGCACGGGAAAGACTCTTTTGGCAAAGGCAGTGGCTACAGAATGTGGAACAACAT
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------------------------------------------------gtgagcttgactatgtcactacctagaagacttaacga-ttttttctgtcagGGAATTCGTCGTCCATGGAAAGGTGTTCTGATGTTTGGGCCACCAGGTACTGGGAAAACTCTCTTGGCAAAGGCCGTGGCTACTGAATGCGGGACGACGT
upper sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ36428 (Selaginella moellendorffii), 3'ss of exon 4
aatggtcatgaacccaactaatctattctctcttgtagcctttctcatttagtctaaactctatacatagtggctaattatgtccactcttctttatcagGGTATTCGTCGACCTTGGAAAGGAGTTCTTATGTTTGGTCCACCAGGCACGGGAAAGACTCTTTTGGCAAAGGCAGTGGCTACAGAATGTGGAACAACAT
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----------------------------------gtgagcttgactatgtca-cta---cctagaagacttcaaggatttcgacga-ttttttctgtcagGGAATTCGTCGTCCATGGAAAGGTGTTCTGATGTTTGGGCCACCAGGTACTGGGAAAACTCTCTTGGCAAAGGCCGTGGCTACTGAATGCGGGACGACGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catttagtctaaactctatacatagtggctaattatgtccactcttctttatcagGGTATTCGTCGACCTTGGAAAGGAGTTCTTATGTTTGGTCCACCAGGCACGGGAAAGACTCTTTTGGCAAAGGCAGTGGCTACAGAATGTGGAACAACAT
ggctaat putative branch site (score: 3)
tccactcttctttatc putative PPT
taattatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatggtcatgaacccaactaatctattctctcttgtagcctttctcatttagtctaaactctatacatagtggctaattatgtccactcttctttatcagGGTATTCGTCGACCTTGGAAAGGAGTTCTTATGTTTGGTCCACCAGGCACGGGAAAGACTCTTTTGGCAAAGGCAGTGGCTACAGAATGTGGAACAACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG