Sequence
atgc intronic sequence ATGC exonic sequence...ttgcatttaacagtaacatattttttatgtcaaggatgtacacagtatttcctggtcctgataccttttattttgtgtgcacttctgtataatataaaagGTTTCAAACCTGCAAAACACATGGTATTTTCTGGTCTTTATCCGGCTGATGGCTCTGACTTTGAAGCACTTAACCATGCAATAGAAAGGCTGACATGCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0108g00130.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g05250.3 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------------ttgcatttaac--agtaacatattttttatgtcaaggatgtacacagtatttcctggtcctgataccttttattttgtgt-gcacttctgtataatataaa-----agGTTTCAAACCTGCAAAACACATGGTATTTTCTGGTCTTTATCCGGCTGATGGCTCTGACTTTGAAGCACTTAACCATGCAATAGAAAGGCTGACATGCAA
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gtatggcatctcctaccctcctgaaatagttttgtcattctattagttttaactagtctgattcagcctgataaaacactgcagttggtacataaaaaaagtctaatgctttgttgctttagttttttttttatgttgtcactatatagagaatatcctttcagGTTTCAAGCCTGCTAGACACATGGTCTTCTCTGGTCTATACCCAGCTGATGGCTCTGACTTTGACGCTCTTAGCCATGCAATTGAAAAACTAACATGTAA
upper sequence: Vv14s0108g00130.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G028928_T02 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------ttgcatttaacagta-acatattttttatgtcaaggatgtac----acagtatttcctggt-cctgataccttttattttgtgtgcacttctgtataatataaaa----------gGTTTCAAACCTGCAAAACACATGGTATTTTCTGGTCTTTATCCGGCTGATGGCTCTGACTTTGAAGCACTTAACCATGCAATAGAAAGGCTGACATGCAA
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gtatggcatcccattctcggaacatttttatggtcttgtctgtatttttttccttcttttattttgtatgatttagactgaaaagaacacacatgatctattgcagtcccatactcctatagcattatttcgtatcccctttctttagtttttggttgcatgcggcatcatacagaatagtctttcagGTTTCAAGCCTGTAAAACACATGGTCTTCTCTGGTCTCTATCCTGCCGATGGTTCCGACTTTGAAGCTCTTAGCCATGCGATTGAGAAACTAACATGTAA
upper sequence: Vv14s0108g00130.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G39400.1 (Glycine max), 3'ss of exon 3
ttgcatttaacagtaacatattttttatgtcaaggatgtacaca-gtatttcctggtcctgataccttttattttgtgtgcacttctg-tataatataaaagGTTTCAAACCTGCAAAACACATGGTATTTTCTGGTCTTTATCCGGCTGATGGCTCTGACTTTGAAGCACTTAACCATGCAATAGAAAGGCTGACATGCAA
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--gggtccatttctttcctcttctttttttggtgaatatatgggtacatttcttggtcctaaatgttttgtttttgaatcattttataactttaaactgtagGCTTCAAGCCAGCAAAACATATGGTGTTCTCTGGCCTTTATCCAGCTGATGGATCTGATTTTGAAGCTCTAAATCATGCAATAGAGAGGCTGACATGCAA
upper sequence: Vv14s0108g00130.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G46900.1 (Glycine max), 3'ss of exon 2
ttgcatttaacagtaacatattttttatgtcaaggatgtacacagtatttcctggtcctgataccttttattttgtgtgcacttctgtataatataaaagGTTTCAAACCTGCAAAACACATGGTATTTTCTGGTCTTTATCCGGCTGATGGCTCTGACTTTGAAGCACTTAACCATGCAATAGAAAGGCTGACATGCAA---------------------------------------------
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---------------------------------------gcccgagattgaccatgcacaagattgaccagccaacttctgatcctg-attgcgctaaag--cccaa---ttgaaatcatatggtgttctctggtctttatccagCTGATGGATCTGATTTTGAAGCTCTAAATCATGCAATAGAGAGGCTGACATGCAATGATGCCAGTGTCTCTATTACTAAAGAAACTAGCACTGCTCTAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttcctggtcctgataccttttattttgtgtgcacttctgtataatataaaagGTTTCAAACCTGCAAAACACATGGTATTTTCTGGTCTTTATCCGGCTGATGGCTCTGACTTTGAAGCACTTAACCATGCAATAGAAAGGCTGACATGCAA
tcctgat putative branch site (score: 3)
ttctgtataatataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgcatttaacagtaacatattttttatgtcaaggatgtacacagtatttcctggtcctgataccttttattttgtgtgcacttctgtataatataaaagGTTTCAAACCTGCAAAACACATGGTATTTTCTGGTCTTTATCCGGCTGATGGCTCTGACTTTGAAGCACTTAACCATGCAATAGAAAGGCTGACATGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - -agtaaca
- - - - - - - - - - - - - - - - - - -gtacaca
- - - - - - - - - - - - - - - - - - - - - - - - ttcctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttctgt