Sequence
atgc intronic sequence ATGC exonic sequencegtatgccatcattcttctgattcttatccctcatttattttctgtcattcatcgtctactcccttggtgcagGTTGTTGAGATAACGAAAGGAAGTAAAGTTAAGTATGAGCTTGACAAGAAAACTGGGCTGATTAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g59040.3 (Oryza sativa), 3'ss of exon 3
-----------------------gtatgccatcattcttctgattcttatccctcatttattttctgtcattcatcgtctac-----tcccttggtgcagGTTGTTGAGATAACGAAAGGAAGTAAAGTTAAGTATGAGCTTGACAAGAAAACTGGGCTGATTAAG
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attgttctgtttaacgattctagaagctttatctacagtcggttcctgacagtgcatgcaacctacatggttaatggcttccatttatatcacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 3
------------------gtatgcc-atcattcttctgattcttatccctc-atttattttctgt--cattcatcgtctac---tcccttggtgcagGTTGTTGAGATAACGAAAGGAAGTAAAGTTAAGTATGAGCTTGACAAGAAAACTGGGCTGATTAAG
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gtaagcatcgtgttcataatatatttgtcatcaaattgaagcaaacactgcgatttatttcaggatgcatctggacctgacatgtttttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G061928_T04 (Zea mays), 3'ss of exon 3
----------------------------gtatgccatcattcttctgattcttatccctcatttattttctgtcatt-catcgtctactcccttggtgcagGTTGTTGAGATAACGAAAGGAAGTAAAGTTAAGTATGAGCTTGACAAGAAAACTGGGCTGATTAAG
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atttgcttgtcgagcaaaaaagtgcattttttatcataatgtttaacaaatctactagttcgcttcatacagtgactgcattatttacatcttta-tgcagGTTGTTGAGATCACAAAGGGAAGCAAAGTTAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G104918_T03 (Zea mays), 3'ss of exon 3
-------------------gtatgccatcattct---tctgattcttatcc--ctcatttattttctgtcattcatcgtctact----cccttggtgcagGTTGTTGAGATAACGAAAGGAAGTAAAGTTAAGTATGAGCTTGACAAGAAAACTGGGCTGATTAAG
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ttgttgaggaaaaataagtgcatggtttttttttaattacgatatttaacaaatctagttagctccaaacaatgaccgcgttatataattttttattcagGTTGTTGAGATCACAAAGGGAAGCAAAGTCAAATACGAGCTTGACAAGAAAACTGGACTGATTAAG
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G015418_T01 (Zea mays), 3'ss of exon 3
-----------gtatgccatcattcttctgattcttatccctcat-------------ttattttctgtcattca----tcgtctactcccttggt-gcagGTTGTTGAGATAACGAAAGGAAGTAAAGTTAAGTATGAGCTTGACAAGAAAACTGGGCTGATTAAG
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gtacgcatcatgtgtcttgttgttcatcctggctatagtgaaagtagagagggagacattagtctcagacctccagaagccaacaccttccatgcttgcagGTTGTTGAGATCACAAAGGGCAGTAAAGTGAAATATGAGCTAGACAAGAAGACCGGAATGATCAAG
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 2
---------------------gtatgccatcattcttctgattcttatccctcattta-ttttctgtcat-------tcatcgtctactcccttggtgcagGTTGTTGAGATAACGAAAGGAAGTAAAGTTAAGTATGAGCTTGACAAGAAAACTGGGCTGATTAAG
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tatagcaattgcatgatgacaccacacctatataattcc-attcttgatttgcatttagttttctagtaaaagggtgtttctgcttgttcaatggctgcagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAGTATGAACTTGACAAGAAGACTGGATTGATTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattcttatccctcatttattttctgtcattcatcgtctactcccttggtgcagGTTGTTGAGATAACGAAAGGAAGTAAAGTTAAGTATGAGCTTGACAAGAAAACTGGGCTGATTAAG
ttctgat putative branch site (score: 3)
tcgtctactccctt putative PPT
tcatttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgccatcattcttctgattcttatccctcatttattttctgtcattcatcgtctactcccttggtgcagGTTGTTGAGATAACGAAAGGAAGTAAAGTTAAGTATGAGCTTGACAAGAAAACTGGGCTGATTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT