Sequence
atgc intronic sequence ATGC exonic sequencegtatgctgtatttcttaatgatatgtttacgttggccttttatttatgaagcacaatagtaaacaatcctctgggtacacatatttcattataattttctggcttttgtcttttcaataaataatatttatttttgttgatgagtcttatttggttaatgctagatgatgccttgcttttctgcagGAATTCAGTGCCAAGAACAAGTTGCTGATCACTGGTACTCCATTACAGAACAGTGTTGAAGAGCTTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G010342_T01 (Zea mays), 3'ss of exon 12
gtatgctgtatttcttaatgatatgtttacgttggccttttatttatgaagcacaatagtaaacaatcctctgggtacacatatttcattataattttctggcttttgtcttttcaataaataatatttatttttgttgatgagtcttatttggttaatgctagatgatgccttgcttttctgcagGAATTCAGTGCCAAGAACAAGTTGCTGATCACTGGTACTCCATTACAGAACAGTGTTGAAGAGCTTTG
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-----------------------------------------------------------------------------------gtatgaaacaattttttagcttctggatc------acacaacttttattgggattaatgact------------agact-gattttgtattgctt--ctacagGAATTCAGCACTAAGAATAAGCTGCTTATCACTGGAACACCTTTGCAGAACAGTGTGGAAGAGCTTTG
upper sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G141258_T01 (Zea mays), 3'ss of exon 13
gtatgctgtatttcttaatgatatgtttacgttggccttttatttatgaagcacaatagtaaacaatcctctgggtacacatatttcattataattttctggcttttgtcttttcaataaataatatttatttttgttgatgagtcttatttggttaatgctagatgatgccttgcttttctgcagGAATTCAGTGCCAAGAACAAGTTGCTGATCACTGGTACTCCATTACAGAACAGTGTTGAAGAGCTTTG
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-----------------------------------------------------------------------------------gtatgaaacaatttcttagtttctg------catcatgtaacttttactgg-gataatga------ttagactaattttgtattgc-ctctactgctctacagGAATTCAGCACTAAGAACAAGCTGCTTATCACGGGAACACCTTTGCAGAACAGTGTGGAAGAGCTTTG
upper sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 13
gtatgctgtatttcttaatgatatgtttacgttggccttttatttatgaagcacaatagtaaacaatcctctgggtacacatatttcattataattttctggcttttgtcttttcaataaataatatttatttttgttgatgagtcttatttggttaatgctagatgatgccttgcttttctgcagGAATTCAGTGCCAAGAACAAGTTGCTGATCACTGGTACTCCATTACAGAACAGTGTTGAAGAGCTTTG
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----------------------------------------------------------------------------------------------gtatgtaacatttgtcttaatt-tatttctctgtgattgtttatgatagagtttaatattttatggtttgtttttgtgctaatctttt--agGAATTTAGCACCAAGAACAAGTTGCTTATCACCGGTACTCCTCTACAGAACAGTGTGGAAGAACTATG
upper sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 13
gtatgctgtatttcttaatgatatgtttacgttggccttttatttatgaagcacaatagtaaacaatcctctgggtacacatatttcattataattttctggcttttgtcttttcaataaataatattta-tttttgttgatgagtcttatttggttaatgctagatgatgccttgcttttctgc-agGAATTCAGTGCCAAGAACAAGTTGCTGATCACTGGTACTCCATTACAGAACAGTGTTGAAGAGCTTTG
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----------------------------------------------------------------------------------------------gtatgtaacattt--ctcttaatttatttttgtgcaattgtttatgatagagtttattt--tttatggtt--tgtttttttgctaatcttttagGAATTTAGCACCAAGAACAAATTGCTTATCACTGGCACTCCTCTACAGAACAGTGTGGAAGAACTATG
upper sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 14
gtatgctgtatttcttaatgatatgtttacgttggccttttatttatgaagcacaatagtaaacaatcctctgggtacacatatttcattataattttctggcttttgtcttttcaataaataatatttatttttgttgatgagtcttatttggttaatgctagatg--atgccttgcttttctgcagGAATTCAGTGCCAAGAACAAGTTGCTGATCACTGGTACTCCATTACAGAACAGTGTTGAAGAGCTTTG
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----------------------------------------------------------------------------------------------------gtatgtgacttttttaagaacttttatctattttcatggttctttttttggttgttcataatgggtggcatatcttatctgttt-tagGAATTTAGCACGAAGAACAAATTGCTTATTACTGGTACTCCACTACAGAATAGTGTCGAAGAGCTTTG
upper sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: PP1S317_10V6.1 (Physcomitrella patens), 3'ss of exon 14
gtatgctgtatttcttaatgatatgtttacgttggccttttatttatgaagcacaatagtaaacaatcctctgggtacacatatttc-attataatttt--ctggcttttgtcttttcaataaataatatttatttttgttgatgagtcttatttggttaatgctagatgatgccttgcttttctgcagGAATTCAGTGCCAAGAACAAGTTGCTGATCACTGGTACTCCATTACAGAACAGTGTTGAAGAGCTTTG
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---------------------------------------------------------------------------tatttatatttccaaaaggatattaaccatattttgtagttttgaca--------ttgcaaatgctaagttgccttatccatttta----aaatcatcactt--tacccaacagGAATTCAGCACCAAAAACAAGGTGCTGGTTACAGGAACTCCGTTGCAGAACAGTGTTGAAGAACTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgttgatgagtcttatttggttaatgctagatgatgccttgcttttctgcagGAATTCAGTGCCAAGAACAAGTTGCTGATCACTGGTACTCCATTACAGAACAGTGTTGAAGAGCTTTG
ggttaat putative branch site (score: 4)
tgccttgcttttct putative PPT
tcttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctgtatttcttaatgatatgtttacgttggccttttatttatgaagcacaatagtaaacaatcctctgggtacacatatttcattataattttctggcttttgtcttttcaataaataatatttatttttgttgatgagtcttatttggttaatgctagatgatgccttgcttttctgcagGAATTCAGTGCCAAGAACAAGTTGCTGATCACTGGTACTCCATTACAGAACAGTGTTGAAGAGCTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT