Sequence
atgc intronic sequence ATGC exonic sequencegtagtgaacatctgtatattatctgtctgttaatatctctttaatagtttattcaattataagcatatatccatgctaaatctacttttatcccttatttttacagCAACTATATTTGCATATGGGCAAACCAGCAGTGGGAAGACTTACACAATGAGAGGAATAACAGAGAAAGCTGTTAATGATATCTATAAGCATATAATAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g03290.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g33040.1 (Oryza sativa), 3'ss of exon 3
gtagtgaacatctgtatattatctgtctgttaatatctctttaatagtttattcaattataagcatatatccatgctaaatctacttttatcccttatttttacagCAACTATATTTGCATATGGGCAAACCAGCAGTGGGAAGACTTACACAATGAGAGGAATAACAGAGAAAGCTGTTAATGATATCTATAAGCATATAATAAA
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-------------gtaaattaattctcactcagtagtttgaataaagttga-------atgatcctttatctactctttattctttaccttcctttgtttt-gcagCCACCATTTTTGCCTATGGTCAAACCAGCAGTGGTAAGACATTCACCATGAGAGGCGTCACAGAGAGTGCTGTAAATGATATATACAGGCACATAGAAAA
upper sequence: Vv17s0000g03290.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G136838_T02 (Zea mays), 3'ss of exon 3
gtagtgaacatctgtat-attatctgtctgttaatatctctttaatagtttattcaattataagcatatatccatgctaaatctacttttatcccttatttttacagCAACTATATTTGCATATGGGCAAACCAGCAGTGGGAAGACTTACACAATGAGAGGAATAACAGAGAAAGCTGTTAATGATATCTATAAGCATATAATAAA
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-------------gtattgttaatgctcagtttgtatattcgtggtagtggagt-gatcatctgcatgtgaccccttc---cttaccttg---tgtttgttttgcagCCACCATTTTTGCATATGGGCAAACCAGCAGTGGTAAAACATTCACGATGAGGGGCGTTACAGAGAGTGCTGTTAGTGATATTTATAGACACATAGATAG
upper sequence: Vv17s0000g03290.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G10790.1 (Glycine max), 3'ss of exon 2
gtagtgaacatctgtatattatctgtctgttaatatctctttaatagtttattcaattataagcatatatccatgctaaatctacttttatcccttattt-ttacagCAACTATATTTGCATATGGGCAAACCAGCAGTGGGAAGACTTACACAATGAGAGGAATAACAGAGAAAGCTGTTAATGATATCTATAAGCATATAATAAA
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gtactg--tttcagatatttgtatctttgttttaaccttccttatgatttgtgacactgttaaggaccatttgcattacataaccattgcatgcttattcattgcagCTACAGTTTTTGCTTATGGACAAACTAGCAGTGGAAAGACATACACAATGAGAGGAATAACAGAGAAGGCTGTCAATGATATCTACGAGCATATTATGAA
upper sequence: Vv17s0000g03290.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G31270.1 (Glycine max), 3'ss of exon 2
-----gtagtgaacatctgtatattatctgtctgttaatatctctttaatagtttattcaattataagcatatatccatgctaaatctacttttatcccttattt-ttacagCAACTATATTTGCATATGGGCAAACCAGCAGTGGGAAGACTTACACAATGAGAGGAATAACAGAGAAAGCTGTTAATGATATCTATAAGCATATAATAAA
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gtactgcttcagatatttgtgtatc-tttgtct--taacctcccat--atgatttgtggccctgttagggactctctgcattacataacccttgcatacttatttattgcagCTACAGTTTTTGCTTATGGACAAACTAGCAGTGGAAAGACATACACAATGAGAGGAATAACAGAGAAGGCTGTCTATGATATCTACAAGCATATTATGAA
upper sequence: Vv17s0000g03290.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G18370.1 (Arabidopsis thaliana), 3'ss of exon 3
gtagtgaacatctgtatattatctgtctgttaatatctctttaatagtttattcaattataagcatatatccatgctaaat--ctacttttatcccttatttttacagCAACTATATTTGCATATGGGCAAACCAGCAGTGGGAAGACTTACACAATGAGAGGAATAACAGAGAAAGCTGTTAATGATATCTATAAGCATATAATAAA
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----------------------------gtacttgtctttttaatgattc-ttctgtcttttactcggatttatcatagatgactaacttccctttttaatgattcagCAACAATATTTGCATATGGACAAACAAGCAGTGGAAAGACATATACCATGAGAGGAGTAACGGAGAAAGCTGTCAATGATATTTACAATCACATAATTAA
upper sequence: Vv17s0000g03290.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S343_28V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------gtagtgaacatctgtatattatctgtctgttaatatctctttaatagtttattcaattataagcatatatccatgctaaatctacttttatcccttatttttacagCAACTATATTTGCATATGGGCAAACCAGCAGTGGGAAGACTTACACAATGAGAGGAATAACAGAGAAAGCTGTTAATGATATCTATAAGCATATAATAAA
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gtaagcatgtcctcgaccaaatcctctgataatttcttgcacttaccttctgaaggcagtagaagctgcaagattttgtaacctgaaacttcttgagctcccatgcgtgggtgtcaaatttgttctgaacttggatcgtcgcagCTACGATCTTCGCATATGGGCAGACCAGCAGCGGGAAGACTTTCACAATGAGGGGTGTCACCGATAGTGCTATTGCAGACATTTTTGACTACATTCAACG
upper sequence: Vv17s0000g03290.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S255_53V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------gtagtgaacatctgtatattatctg-tctgttaatatctctttaat--agtttattcaattataagcatatatccatgctaaatc-tacttttatccc---ttattttta--cagCAACTATATTTGCATATGGGCAAACCAGCAGTGGGAAGACTTACACAATGAGAGGAATAACAGAGAAAGCTGTTAATGATATCTATAAGCATATAATAAA
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gtgagtcgagctctcaccacttgctcagagttgcgtgtccacgaataccacaagccgatctgatcctgttgtttctcttggttccaattccctcgtgtctcctc-cgtattcttaatgggtgataattctgacctggtttggctctattcagCCACTATTTTTGCATATGGCCAAACCAGCAGTGGGAAAACGTATACAATGAGGGGAGTCACTGAAAGCGCCATTGCAGACATTTTTGAGTACATCGAACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaattataagcatatatccatgctaaatctacttttatcccttatttttacagCAACTATATTTGCATATGGGCAAACCAGCAGTGGGAAGACTTACACAATGAGAGGAATAACAGAGAAAGCTGTTAATGATATCTATAAGCATATAATAAA
tgctaaa putative branch site (score: 2)
tctacttttatccctt CT-rich tract
taaatctacttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtgaacatctgtatattatctgtctgttaatatctctttaatagtttattcaattataagcatatatccatgctaaatctacttttatcccttatttttacagCAACTATATTTGCATATGGGCAAACCAGCAGTGGGAAGACTTACACAATGAGAGGAATAACAGAGAAAGCTGTTAATGATATCTATAAGCATATAATAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT