Sequence
atgc intronic sequence ATGC exonic sequence...ggaaagactagagatcaaatactatgatgtaaaacctgagtgttgaacatgctactaatatttctcataactacttattaactgtttatgaaatttatagGGGGAAACCAGTCCTCCAGATTATCTTAGTGAAAGTGAGCTGATATCCCTAATGGAGAAGAATGGGATAGGCACAGATGCATCCATTCCTGTGCATATTA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0062g00860.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os09g32450.1 (Oryza sativa), 3'ss of exon 11
ggaaagactagagatcaaatactatgatgtaaaacctgagtgttgaacatgctactaatatttctcataactacttattaactgtttatgaaatttatagGGGGAAACCAGTCCTCCAGATTATCTTAGTGAAAGTGAGCTGATATCCCTAATGGAGAAGAATGGGATAGGCACAGATGCATCCATTCCTGTGCATATTA
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gtatggcttgtgaatttattcacatcacatgag-ctcaccttttttttttgggtctgaaaatgttcataattatc-----attcttcattaa-------gGGTAGCACCACACCTCCTGACTACCTTAGTGAGAGTGAATTGATCTCTCTCATGGAGAAGAATGGCATAGGTACAGATGCATCAATTCCTGTGCATGTAA
upper sequence: Vv05s0062g00860.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G102181_T01 (Zea mays), 3'ss of exon 6
ggaaagactagagatcaaatactatgatgtaa-aacctgagtgttgaacatgctactaatatttctcataactacttattaactgtttatgaaa-tttatagGGGGAAACCAGT---CCTCCAGATTATCTTAGTGAAAGTGAGCTGATATCCCTAATGGAGAAGAATGGGATAGGCACAGATGCATCCATTCCTGTGCATATTA
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---------------------gtaaggtctatcagtttgctcaaaccacatgcacttaacttttatcaggatatgatgttgatcaatcataattctttgttgaagGGAAGCACTACACCACCTGATTACCTCACTGAAAGTGAATTGATTTCCCTCATGGAGAAGAATGGCATAGGTACAGATGCATCAATTCCTGTACATATAA
upper sequence: Vv05s0062g00860.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA11G36800.1 (Glycine max), 3'ss of exon 11
ggaaagactagagatcaaatactatgatgtaaaacctgagtg--ttgaacatgctactaatatttctcata-actacttattaactgt-ttatgaaatttatagGGGGAAACCAGTCCTCCAGATTATCTTAGTGAAAGTGAGCTGATATCCCTAATGGAGAAGAATGGGATAGGCACAGATGCATCCATTCCTGTGCATATTA
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----atacatataaccatttctggggagaagaaaaaaggttgaaattcatttcccattggagttctgtgtgtattacacatagctaacaccacaaattctgcagGGGAGCACCAGTCCTCCAGATTTCCTTACTGAAAGTGAGCTGATATCCCTGATGGAGAAGAATGGAATAGGAACAGATGCATCGATTCCTGTTCATATTA
upper sequence: Vv05s0062g00860.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G32000.1 (Arabidopsis thaliana), 3'ss of exon 11
------------------------ggaaagactagagatcaaatactatgatgtaaaacctgagtgttgaacatgctactaatatttctcataactacttattaactgtttatgaaatttatagGGGGAAACCAGTCCTCCAGATTATCTTAGTGAAAGTGAGCTGATATCCCTAATGGAGAAGAATGGGATAGGCACAGATGCATCCATTCCTGTGCATATTA
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gtcacattcttctccagtttttgttactgctctctttgctttgtactaggacacaaattacta-taatgtttccacttttagtttattttttctgtttgtatttgaatgttgtaaaatctacagGGGAACACTGCGCCTCCGGACTACCTTACTGAGAGTGAGCTGATATCTCTCATGGAGAAGCATGGCATAGGCACAGATGCATCAATAGCTGTACATATAA
upper sequence: Vv05s0062g00860.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S474_3V6.1 (Physcomitrella patens), 3'ss of exon 11
--ggaaagactagagatcaaatactatgatgtaaaacctgagtgttgaa----catgctactaatatttctcataactacttattaactgtttatgaaatttatagGGGGAAACCAGTCCTCCAGATTATCTTAGTGAAAGTGAGCTGATATCCCTAATGGAGAAGAATGGGATAGGCACAGATGCATCCATTCCTGTGCATATTA
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ttgtatgcaccataaatgttcttctgccctgcatgtcttaaatacctggtcctcatgcagcattggtttgttgaaagcattggt---ctattt---ggatgtgcagGGGCGAACTTCAGCTCCAGATTATTTAACTGAAAGTGAACTCATAACTCTAATGGAAAAGCATGGCATAGGCACTGATGCGTCCATTTCAGTGCACATCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacatgctactaatatttctcataactacttattaactgtttatgaaatttatagGGGGAAACCAGTCCTCCAGATTATCTTAGTGAAAGTGAGCTGATATCCCTAATGGAGAAGAATGGGATAGGCACAGATGCATCCATTCCTGTGCATATTA
tattaac putative branch site (score: 1)
tacttattaactgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggaaagactagagatcaaatactatgatgtaaaacctgagtgttgaacatgctactaatatttctcataactacttattaactgtttatgaaatttatagGGGGAAACCAGTCCTCCAGATTATCTTAGTGAAAGTGAGCTGATATCCCTAATGGAGAAGAATGGGATAGGCACAGATGCATCCATTCCTGTGCATATTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
ggaaaga
- - - - - - - -caaatac
- - - - - - - - - - - - - - gtaaaac
- - - - - - - - - - - - - - - - - - tgagtgt
- - - - - - - - - - - - - - - - - - - - - - - acatgct