Sequence
atgc intronic sequence ATGC exonic sequence...gtagttttgtgcttgcgtggggaatagcctgtatttacatctgtttattttgtctgtttttttttttcttcaattgtttctttaaccaactatgtacaagACAAATGTCATGGGGACCTTGAATATGCTTGGACTGGCTAAGAGGGTTGGGGCTCGGTTCTTGTTGACTAGTACCAGTGAAGTGTATGGTGATCCTCTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G347717_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g17230.1 (Oryza sativa), 3'ss of exon 1
gtagttttgtgcttgcg-tggggaatagcctgtatttacatctgtttattttgtctgtttttttttttcttcaa----ttgtttctttaaccaactatgtacaagACAAATGTCATGGGGACCTTGAATATGCTTGGACTGGCTAAGAGGGTTGGGGCTCGGTTCTTGTTGACTAGTACCAGTGAAGTGTATGGTGATCCTCTTG
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-gaatcttgtgcctgcggttgccatttgcctggaagaacctgaaattttgtt-ccagtcctatttttccttataaattttggttccctaactgttatagtacAAGACAAATGTGATGGGGACCTTGAACATGCTGGGATTGGCAAAGAGGGTGGGAGCCCGGTTCTTATTGACCAGTACCAGTGAGGTGTACGGTGATCCTC---
upper sequence: GRMZM2G347717_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 2
gtagttttgtgcttgcgtggggaatagcctgtattt--acatctgtttattttgtctgttttttttttt--cttcaattgtttctttaaccaactatg--tacaagACAAATGTCATGGGGACCTTGAATATGCTTGGACTGGCTAAGAGGGTTGGGGCTCGGTTCTTGTTGACTAGTACCAGTGAAGTGTATGGTGATCCTCTTG
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-----agggtgccaa-atgatgaataatttaggattcaaaaaccaaatgtaaggttagtgattttgtgaaatttggatctcttttatccttgactgtgattacaagACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGGGCAAGGTTTTTGCTCACAAGTACAAGTGAAGTTTATGGTGACCCCCTTG
upper sequence: GRMZM2G347717_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S120_29V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------gtagttttgtgcttgcgtggggaatagcctgtatttacatctgtttattttgtctgtttttttttttcttcaattgtttctttaaccaactatgtacaagACAAATGTCATGGGGACCTTGAATATGCTTGGACTGGCTAAGAGGGTTGGGGCTCGGTTCTTGTTGACTAGTACCAGTGAAGTGTATGGTGATCCTCTTG
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gttcgggatcttgaatttattctgaattattgagtttatgtagtgt-tattttgcatagtccttctagcagagagaatgtatccgtggtcgtgca---gcctccttgacctgcc-tccacaagACCAACGTGGTGGGAACCTTGAACATGCTTGGATTGGCGAAGCGCATCGGAGCACGGTTCTTGCTGACCAGTACTAGTGAGGTTTATGGTGATCCTTTGG
upper sequence: GRMZM2G347717_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S209_52V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------gtagttttgtgcttgcgtggggaatagcctgtatttacatctgtttattttgtctgttttt--ttttttcttca-attgtttctttaaccaactatgtacaagACAAATGTCATGGGGACCTTGAATATGCTTGGACTGGCTAAGAGGGTTGGGGCTCGGTTCTTGTTGACTAGTACCAGTGAAGTGTATGGTGATCCTCTTG
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atatccttttttgtgcgagatcttgtgtgttatgaatctgaaatccccttgcgtttttcctatgaatgtctcacgttttgtttgctgtagagaagatgttttcgattcgtcattcgtgcggcccccttaatcttcc-tacacAAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATTGGAGCACGGTTCTTGTTGACCAGTACGAGTGAGGTTTATGGTGATCCTT--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattttgtctgtttttttttttcttcaattgtttctttaaccaactatgtacaagACAAATGTCATGGGGACCTTGAATATGCTTGGACTGGCTAAGAGGGTTGGGGCTCGGTTCTTGTTGACTAGTACCAGTGAAGTGTATGGTGATCCTCTTG
ttctttaac putative branch site
tttttttttttcttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttttgtgcttgcgtggggaatagcctgtatttacatctgtttattttgtctgtttttttttttcttcaattgtttctttaaccaactatgtacaagACAAATGTCATGGGGACCTTGAATATGCTTGGACTGGCTAAGAGGGTTGGGGCTCGGTTCTTGTTGACTAGTACCAGTGAAGTGTATGGTGATCCTCTTG
- - - - -tgcttgc
- - - - - - - - - - - - - gcctgta
- - - - - - - - - - - - - - - - - - - -tctgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaccaac