Sequence
atgc intronic sequence ATGC exonic sequence...gaagcaagtgtttcctctactaaagataaatattctttttgttgttcctttaatctaggcattctttgacaatttgtctcattttttcccctatgctcagTGTTGGTGCTGGATGTTCTCAACTACTTTCAGACATGCAGGCTTTCAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0090g00690.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os07g32670.1 (Oryza sativa), 3'ss of exon 7
gaagcaagtgtttcctctac-taaagataaatattctttttgttgttcctttaatctaggc-attctttgacaatt--tgtctcattttttcccctatgctcagTGTTGGTGCTGGATGTTCTCAACTACTTTCAGACATGCAGGCTTTCAAG
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---gcatcacagtcatataccttaatatcaatccactatt-attttttttttgatttaagtgatagagcaatggttgtgatgctgtttgtatttatactctcagTGTTGGTGCTGGGTGTTCTCAACTTCTATCAGATATGCAAGCCTTCAAG
upper sequence: Vv19s0090g00690.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G076387_T01 (Zea mays), 3'ss of exon 7
gaagcaagtgtttcctctactaaagataaatattctttttgttgttcctttaatctaggcattctttgacaatttgtctcattttttcccctatg----ctcagTGTTGGTGCTGGATGTTCTCAACTACTTTCAGACATGCAGGCTTTCAAG
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tgtgtgatgatgtcctatatctac----atttctgtcaatgcaattcttatacttgctaagtaataaaacagtttttgtgatgcttttttttattatttctcagTCTTGGTGCTGGATGCTCTCAACTTCTATCAGATATGCAGGCTTTCAAG
upper sequence: Vv19s0090g00690.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA18G10700.1 (Glycine max), 3'ss of exon 2
---gaagcaagtgtttcctctactaaa--gataaatattctttttgttgttcctttaatctaggcattctttgacaatttgtctcattttttcccctatgctcagTGTTGGTGCTGGATGTTCTCAACTACTTTCAGACATGCAGGCTTTCAAG
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atttcactgcatatctgcatttatgatctaataggttctagacttatagttactatagggtaggcatttcataatagttttctttactttgt-----atgctcagTGTTGGTGCTGGATGCTCTCAACTCCTCTCTGATATGCAGGCTTTCAAG
upper sequence: Vv19s0090g00690.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G43140.1 (Glycine max), 3'ss of exon 7
---gaagcaagtgtttcc-tctactaaa-gataaatattctttttgttgttcctttaatctaggcattctttgacaatttgtctcattttttcccctatgctcagTGTTGGTGCTGGATGTTCTCAACTACTTTCAGACATGCAGGCTTTCAAG
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atttcactgcttatctgcatctacgatctaataggttctagacttatagttactattgggtaggcatttcatgatagttttctttaccttgt-----atgaccagTGTTGGTGCTGGATGCTCTCAACTCCTCTCTGATATGCAGGCTTTCAAG
upper sequence: Vv19s0090g00690.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA02G46190.1 (Glycine max), 3'ss of exon 8
gaagcaagtgtttcctctactaaagataaatattctttttgttgttcctttaatctaggcattctttgacaatttgtc----tcattttttcccctatgctcagTGTTGGTGCTGGATGTTCTCAACTACTTTCAGACATGCAGGCTTTCAAG
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---gctagc-tttatttaattgcagatgtgcatcaatcatgtaatagcttatagttagcattagttaggcattttcttcttactatgttacattttatggtcagTGTTGGTGCTGGGTGCTCTCAACTGCTCTCAGATATGCAAGCTTTCAAG
upper sequence: Vv19s0090g00690.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA14G02550.1 (Glycine max), 3'ss of exon 8
gaagcaagtgtttcctctactaaagataaatattctttttgttgttcctttaatctaggcattctttgacaatttgtctcatt------ttttcccctatgctcagTGTTGGTGCTGGATGTTCTCAACTACTTTCAGACATGCAGGCTTTCAAG
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---gctagc-tttctttaattgcagatgtgcatcaattatgtaatagcttatagttag-catcatttaggaattt-tcttattactgagttaccttttatggtcagTGTTGGTGCTGGGTGCTCTCAATTGCTCTCAGATATGCAGGCTTTCAAG
upper sequence: Vv19s0090g00690.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G55060.2 (Arabidopsis thaliana), 3'ss of exon 7
gaagcaagtgtttcctctactaaagataaatattctttttgttgttcctttaatctaggcattctttgacaatttgtctcattttttcccctatg-ctcagTGTTGGTGCTGGATGTTCTCAACTACTTTCAGACATGCAGGCTTTCAAG
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aatagacgtattatctggctgaataatatataattccgtt-tcgttattcagacatccaattatcttgatagattggattattgtctttcttatggttcagCATGGGGGCTGGATGTTCTCAACTCTTGTCTGACATGCAGGCTTTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctttaatctaggcattctttgacaatttgtctcattttttcccctatgctcagTGTTGGTGCTGGATGTTCTCAACTACTTTCAGACATGCAGGCTTTCAAG
ctttgac putative branch site (score: 4)
tttgtctcattttttc putative PPT
tcatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaagcaagtgtttcctctactaaagataaatattctttttgttgttcctttaatctaggcattctttgacaatttgtctcattttttcccctatgctcagTGTTGGTGCTGGATGTTCTCAACTACTTTCAGACATGCAGGCTTTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
gaagcaa
- - - - - - -cctctac
- - - - - - - - - - - aagataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcattct