Sequence
atgc intronic sequence ATGC exonic sequence...tttttcctcttttttttttttttaaataagttttgttgtaagaatcactcagtgcataacttgtgggatgagtgttacttacatcgttttattgttgcagTACGGATAACCAAAGTGTTGACCGTGCTTACCGAATTGGCCAAACAAAGGACGTCATTGTGTACAGGTTAATGACATGTGGCACCATTGAAGAAAAGATA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0044g01680.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os04g59624.3 (Oryza sativa), 3'ss of exon 12
----tttttcctcttttttttttttttaaataagttttgttgtaagaatcactcagtgcataacttgtgggatgagtgttacttacatcgttttattgttgcagTACGGATAACCAAAGTGTTGACCGTGCTTACCGAATTGGCCAAACAAAGGACGTCATTGTGTACAGGTTAATGACATGTGGCACCATTGAAGAAAAGATA
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gtacctgaacaacgccgtttccttactgagtttattgcctttttatt-ttactgaatgtttgtctct--gtatgtttactaatgctcctgtttcccatcttcagTACGGACAATCAAAGTGTTGATCGTGCTTATCGAATTGGGCAGATGAAAGATGTCATCGTATACCGCCTTATGACATCTGGAACCATCGAAGAAAAGATA
upper sequence: Vv04s0044g01680.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os04g59620.1 (Oryza sativa), 3'ss of exon 11
tttttcctcttttttttttttttaaataagttttgttgtaagaatcactcagtgcataacttgtgggatgagtgttacttacatcgttttattgttgcagTACGGATAACCAAAGTGTTGACCGTGCTTACCGAATTGGCCAAACAAAGGACGTCATTGTGTACAGGTTAATGACATGTGGCACCATTGAAGAAAAGATA
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------------------gtacccagcaattctaaat-tgtgaatgctttacatca-actttcttcaattaat----catatatgttttttactttatagCATAGATAACCAAAGTGTCGACCGTGCTTATCGAATTGGGCAGACTAAAGATGTGATTGTATATCGTTTGGTAACTTGTGGGACCATTGAGGAGAAGATT
upper sequence: Vv04s0044g01680.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G138125_T02 (Zea mays), 3'ss of exon 13
---tttttcctcttttttttttttttaaataagttttgttgtaagaatcactcagtgcataacttgtgggatgagtgttacttacatcgttttattgttgcagTACGGATAACCAAAGTGTTGACCGTGCTTACCGAATTGGCCAAACAAAGGACGTCATTGTGTACAGGTTAATGACATGTGGCACCATTGAAGAAAAGATA
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gtatctgagctatgatacgtatctgtatgtctgtatcgattgaagttttcttgaatgaa--gttt------tcaatcttacacccttgtttttctatttacagTACAGACAATCAAAGTGTTGATCGTGCTTACCGAATTGGACAGACTAAAAATGTGATTGTATACCGCTTGATGACATCTGCGACCATTGAAGAAAAGATA
upper sequence: Vv04s0044g01680.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA05G32740.1 (Glycine max), 3'ss of exon 13
--tttttcctcttttttttttttttaaat--aagt--tttgttgtaagaatcactcagtgcataacttgtgggatgagtgttacttacatcgttttattgttgcagTACGGATAACCAAAGTGTTGACCGTGCTTACCGAATTGGCCAAACAAAGGACGTCATTGTGTACAGGTTAATGACATGTGGCACCATTGAAGAAAAGATA
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tattgtgtttctttcttataatttgcaatttgagtcattcattgagggaggta-tctgcttatg-tttacttgttaagcactac----aattttttgttctaccagTACGGATAATCAAAGTGTTGACCGGGCATATCGAATTGGTCAAAAGAAAGATGTTCTGGTATATAGACTGATGACATGCGGAACTGTTGAAGAAAAGATC
upper sequence: Vv04s0044g01680.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA08G00400.1 (Glycine max), 3'ss of exon 15
----tttttcctcttttttttttttttaaataagt--tttgttgtaagaatcactcagtgcataacttgtgggatgagtgttacttacatcgttttattgttgcagTACGGATAACCAAAGTGTTGACCGTGCTTACCGAATTGGCCAAACAAAGGACGTCATTGTGTACAGGTTAATGACATGTGGCACCATTGAAGAAAAGATA
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tgctgtatttctttcttataatttgcaatttgagtccttcattgagggaggtatt---ttcttatgttacttgttaagcacta-taatattttgtttctac--cagTACGGATAATCAAAGTGTTGACCGGGCATATCGAATTGGTCAAAAGAAAGATGTTCTGGTATATAGACTGATGACATGCGGAACTGTTGAAGAAAAGATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cactcagtgcataacttgtgggatgagtgttacttacatcgttttattgttgcagTACGGATAACCAAAGTGTTGACCGTGCTTACCGAATTGGCCAAACAAAGGACGTCATTGTGTACAGGTTAATGACATGTGGCACCATTGAAGAAAAGATA
tacttac putative branch site (score: 1)
ttttatt putative PPT
ttttattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttcctcttttttttttttttaaataagttttgttgtaagaatcactcagtgcataacttgtgggatgagtgttacttacatcgttttattgttgcagTACGGATAACCAAAGTGTTGACCGTGCTTACCGAATTGGCCAAACAAAGGACGTCATTGTGTACAGGTTAATGACATGTGGCACCATTGAAGAAAAGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- -ttcctct
- - - - - - - - - - - -aaataag
- - - - - - - - - - - - - - - - - - - - - - tcactca
- - - - - - - - - - - - - - - - - - - - - - - - - -gtgcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgagtgt