Sequence
atgc intronic sequence ATGC exonic sequence...aatatctttttattttgccatgccttttggtttacaagacagcaagataatttcactcttttgactcagattttatctttgttctgctttatcatgcaagGTTATGGAAGTACTTATGTCATTGCAAGGATCTCAAATGGAGACAGATGACCCAACAACAAGCTACATGCTACAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g49420.2 (Oryza sativa), 3'ss of exon 4
--------------------------------------------------------------aatatctttttattttgccatgccttttggtttacaagacagcaagataatttcact-cttttgactcag---attttatctttgttctgc---tttatcatgcaagGTTATGGAAGTACTTATGTCATTGCAAGGATCTCAAATGGAGACAGATGACCCAACAACAAGCTACATGCTACAA
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gtaataatttgctagttgctctgatacattgtaatacgtttgaagaaaatgtcaaagcacactgtataaatgttatttatgacttgttctgattgtattgctgatgggcttatttgaatgctgtttgctgaattcgttgtttctttggctaacatatttctcttgctagGTGATGGAAGTTTTGATGACATTGCAAGGATCTCAGATGGAGGCTGATGACCCTATAACAAGTTACATGCTGCAA
upper sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os07g38760.1 (Oryza sativa), 3'ss of exon 5
aatatctttttattttgccatgccttttggtttacaagacagcaagataatttcactcttttgactcagattttatctttgttctgctttatcatgcaagGTTATGGAAGTACTTATGTCATTGCAAGGATCTCAAATGGAGACAGATGACCCAACAACAAGCTACATGCTACAA
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--------gtaattgtgtcttctccactgtaattttgttctgtatgctatgttctatgcatgcacttt--tctaatctacacattgattgat------agGTCATGGAAGTACTTATGAGTTTGCAAGGAACTACAATGGAAAATGATGATCCAATAACAAGCTACATGCTTCAG
upper sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 4
----------------------------------------------------------------------------aatatctttttattttgccatgccttttggtttacaagaca----------gcaagataat-----ttcactcttttgactcagattttatctttgttc-tgctttatcatgcaagGTTATGGAAGTACTTATGTCATTGCAAGGATCTCAAATGGAGACAGATGACCCAACAACAAGCTACATGCTACAA
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gtaatggtttgctagttccccttatattacagtatacagtcgagtccataactctttccgtctataaaagtgttaaaacattattttttgtggcctttgtactcaataaacgaaatcaaattgggttgtaggatgttatatgctatctgttctgtatctgttaatgctattgataattcattttggtgttagGTGATGGAGGTCCTTATGACACTGCAAGGATCTCAGATGGAGGCTGATGACCCTATAACAAGCTACATGCTGCAA
upper sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM5G887631_T01 (Zea mays), 3'ss of exon 5
---aatatctttttattttgccatgccttttggtttacaagacagcaagataatttcactcttttgactcagattttat--ctttgttctgctttatcatgcaagGTTATGGAAGTACTTATGTCATTGCAAGGATCTCAAATGGAGACAGATGACCCAACAACAAGCTACATGCTACAA
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tggcagttccacccacttgctctttatgtgttctttcctcgccggctg--tgatttttttattgtggc---aattttattattctaatcatctgccctctgctagGTTATGGAAGTACTTATGGCTTTGCAAGGAGCTCCAATGGAAACTGATGATCCAATTACCAGCTACATGTTGCAG
upper sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G28950.2 (Glycine max), 3'ss of exon 7
aatatctttttattttgccatgc---cttttggtttacaagacagcaagataatt-tcactcttttgactcagattttatctttgttctgctttatcatgcaagGTTATGGAAGTACTTATGTCATTGCAAGGATCTCAAATGGAGACAGATGACCCAACAACAAGCTACATGCTACAA
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--tgccctgcatctctgttaagcacttctttctctctctctctctctggttagctatgtctcttatgattttaatattctatgtgtgctggttcttca--ctagGTTATGGAAGTTCTTATGTCCCTTCAAGTATCTCAAATGGAGACAGATGATCCAACAACAAGTTACATGCTACAG
upper sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G12120.1 (Glycine max), 3'ss of exon 5
aatatctttttattttgccatgccttttggtttacaagacagcaagata-atttcactcttttgactcagattttatctttgttctgctttatcatgcaagGTTATGGAAGTACTTATGTCATTGCAAGGATCTCAAATGGAGACAGATGACCCAACAACAAGCTACATGCTACAA
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---gtaggtgtttcttgtttatttttatactttgtcaaacaagaatgcatgtctgtctcgtatgattttaatattctatgtgtgttggttcttcaat--agGTTATGGAAGTTCTTATGTCCCTTCAAGTATCTCAAATGGAGACAGATGATCCAACAACAAGTTACATGCTACAG
upper sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 5
aatatctttttattttgccatgccttttggtttacaagacagcaagataatttcactcttttgactcagattttatctttgttctgctttatcatgcaagGTTATGGAAGTACTTATGTCATTGCAAGGATCTCAAATGGAGACAGATGACCCAACAACAAGCTACATGCTACAA
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-gtatgcttatat---gcgaggg--tcaaatcatgatgctatctatatccagtagttctattca-tcatcgcatgaaaatatttcacatatccatgccagGTCATGGAAGTGCTAATGTCATTGCAAGGTTCTCAGATGGAGGCAGACGATCCAATAACAAGTTACATGTTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gataatttcactcttttgactcagattttatctttgttctgctttatcatgcaagGTTATGGAAGTACTTATGTCATTGCAAGGATCTCAAATGGAGACAGATGACCCAACAACAAGCTACATGCTACAA
ttttgac putative branch site (score: 3)
ctttatc putative PPT
attttatctttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatatctttttattttgccatgccttttggtttacaagacagcaagataatttcactcttttgactcagattttatctttgttctgctttatcatgcaagGTTATGGAAGTACTTATGTCATTGCAAGGATCTCAAATGGAGACAGATGACCCAACAACAAGCTACATGCTACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - -ccatgcc
- - - - - - - - - - - - - - - - -acaagac
- - - - - - - - - - - - - - - - - - - - - -aagataa