Sequence
atgc intronic sequence ATGC exonic sequence...agagacagttgaatgtttgactactgctgctattttactgtgattgtttttacttatctaatattctttggggatcggttctggtgaatattgtgtacagGCTGATGGTTGGATTGTGGAGCTTATTAGTTTACTGGCAAACCCTAACCAAGTGCGGCCAAAGAGATTTTGGGGTGTCTACACAAAGCTAAAAATATTTA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os04g43700.1 (Oryza sativa), 3'ss of exon 1
-------agagacagttgaatgtttgactactgctgctattttactgtgattgtttttacttatctaatattctttggggatcggttctggtgaatattgtgtacagGCTGATGGTTGGATTGTGGAGCTTATTAGTTTACTGGCAAACCCTAACCAAGTGCGGCCAAAGAGATTTTGGGGTGTCTACACAAAGCTAAAAATATTTA
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gcatgcagtaaacatcaggatgtgcgatgacta--gctacatcctcagatttttttttactagtctaat-cagttagttaatctggcctt----acactaatttcagGCAGATGGTTGGATTGTGAGTCATATAACGTTACTGGCCAATCCTAATCAAGTGAGGCCAAAGAGATTTTGGGGCGTCTACACCAAGCTTAAGATATTCA
upper sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G43630.1 (Glycine max), 3'ss of exon 1
--------------------------------------------------agagacagttgaatgtttgacta----ctgctgctattttactgtgattgtttttacttatctaatattctttggggatcggttctggtgaatattgtgtacagGCTGATGGTTGGATTGTGGAGCTTATTAGTTTACTGGCAAACCCTAACCAAGTGCGGCCAAAGAGATTTTGGGGTGTCTACACAAAGCTAAAAATATTTA
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gtaataatcatcttctctttaatgggtcttcgtcaaaatttgaaattttgaactttaactttctgtttgacatgaatctgttgacacctgagttttgtgtagtttgtaattttaactctatatttgg-tggatttttgttcgaattttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTGGCTAATCCTAATCGAGTGCGTCCAAAGAGATTTTGGGGTGTCTACACAAAGCTCAAAATATTTA
upper sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G40980.1 (Glycine max), 3'ss of exon 1
------------------------------------------agagacagttgaatgtttgact----actgctgctattttactgtgattgtttttacttatctaatattctttggggatcggttctggtgaatattgtgtacagGCTGATGGTTGGATTGTGGAGCTTATTAGTTTACTGGCAAACCCTAACCAAGTGCGGCCAAAGAGATTTTGGGGTGTCTACACAAAGCTAAAAATATTTA
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gtattcatcatcttctttttaatgggtcttcctcaaatttgaaatttgaactctatgtttgacatgaatctgttgacacctgagttttgtgtagtttgtgattttaactctttatttgg-tggatttgtgtttgaattttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTTGCTAATCCTAATCGAGTGCGTCCAAAGAGGTTTTGGGGTGTCTACACAAAGCTCAAAATATTTA
upper sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G37000.1 (Glycine max), 3'ss of exon 1
----------------------------------------------------------------------------------------------agagacagttgaatgtttgactactgctgctattttactgtgattgtttttact-tatctaatattctttggggatcggttctggtgaata--ttgtgtacagGCTGATGGTTGGATTGTGGAGCTTATTAGTTTACTGGCAAACCCTAACCAAGTGCGGCCAAAGAGATTTTGGGGTGTCTACACAAAGCTAAAAATATTTA
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gtactcttttcctttgccaattgtattattgcggaacgagaaatgaaaaatttctgatcactttatattaaatttgatattaatgtttcatttgacatgaatcctaaattttgttagttataacttattttaagtgatattgttgattatagacctcgtgggtagggtaaagggttttatgattgctttttgtgtagGCTGATGGGTGGATAGTTGAGAAGATTAGTTTACTGGCAAATCCTAATCAAGTACGTCCAAAGAGATTTTGGGGTGTCTATACAAAGCTCAAAATATTTA
upper sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G30700.1 (Glycine max), 3'ss of exon 1
---------------------------------------------------------------------------------------agagacagttgaatgtttgac--tactgctgctattttactgt-gattgtttttacttatc-taatattctttg----gggatcggttctggtgaata--ttgtgtacagGCTGATGGTTGGATTGTGGAGCTTATTAGTTTACTGGCAAACCCTAACCAAGTGCGGCCAAAGAGATTTTGGGGTGTCTACACAAAGCTAAAAATATTTA
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gtactcttttcctttgcgaaatgtattaacgcggaaccagaaatgaaattttgtgatcactttatattaaatttaatatcagtgtttcattttatatgaatcctagattttgttagttataacttattattaagtgatactgttgattatagaactcgtggatagggtaaagggttttatgattggtttttttgtagGCTGATGGGTGGATAGTTGAGAAGATTAGTTTATTGGCGAATCCTAATCAAGTACGTCCAAAGAGATTTTGGGGT------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttttacttatctaatattctttggggatcggttctggtgaatattgtgtacagGCTGATGGTTGGATTGTGGAGCTTATTAGTTTACTGGCAAACCCTAACCAAGTGCGGCCAAAGAGATTTTGGGGTGTCTACACAAAGCTAAAAATATTTA
atctaat putative branch site (score: 3)
ttatctaatattcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agagacagttgaatgtttgactactgctgctattttactgtgattgtttttacttatctaatattctttggggatcggttctggtgaatattgtgtacagGCTGATGGTTGGATTGTGGAGCTTATTAGTTTACTGGCAAACCCTAACCAAGTGCGGCCAAAGAGATTTTGGGGTGTCTACACAAAGCTAAAAATATTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
agagaca
- - - - - - - - - - - actgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctggtga