Sequence
atgc intronic sequence ATGC exonic sequencegtatgccttatgtttttagacatccatacatgtaaatgcacatgcatgttcaatttgtacataaatcatgtaaattttctttggccattgaccaccttgtcagGCTAGTGAGAGGTTGCATGAGAAGATGACCAACTTCATATCAAAAAATAAAGCTGCACAAATCCAACATGGTTCAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os04g18030.3 (Oryza sativa), 3'ss of exon 12
gtatgccttatgtttttagacatccatacatgtaaatgcacatgcatgttcaatttgtacataaatcatgtaaat-tttctttggc----cattga-ccaccttgtcagGCTAGTGAGAGGTTGCATGAGAAGATGACCAACTTCATATCAAAAAATAAAGCTGCACAAATCCAACATGGTTCAAG
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---------------------gtacatata-gccaatgtgagactgtcaccattgtctccaaacattatctatatgcttcattaatgcatcatggagtcaatattgcagGCTAGTGAAAGATTGCATGAGAAGATGACCAATTTTGTATCAAAAAACAAAGCTGCTCAACTACATCAAG---CAAG
upper sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 11
gtatgccttatgtttttagacatccatacatgtaaatgcacatgcatgttcaatttgtacataaatcatgtaaat-tttctttggccattgaccaccttgtcagGCTAGTGAGAGGTTGCATGAGAAGATGACCAACTTCATATCAAAAAATAAAGCTGCACAAATCCAACATGGTTCAAG
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-----------------------gtaagattattccttaatctaccttcctacttggcacatgtattcaacaattgcttgtttaaccat-gactatca---cagGCAAGTGAGAGGCTACATGATAAGATGACCAACTTCATTTCAAAGAACAAAGCTGCACAATTGCATCA-AGCACG--
upper sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 12
----gtatgccttatgtttttagacat---ccatacatgtaaatgcacatgcatgttcaatttgtacataaatcatgtaaatt--ttctttggccattgaccaccttgt------cagGCTAGTGAGAGGTTGCATGAGAAGATGACCAACTTCATATCAAAAAATAAAGCTGCACAAATCCAACATGGTTCAAG
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gtatgtccttcttttactatttggtgtaggctctatagtttactatttagggttatctcttccatttacaacttaagcaacatgatcctttgggtattgatggccttgccaatgccagGCTAGTGAACGGCTGCATGAGAAGATGACCAACTTCATTTCAAAGAATAAAGCTGCACAAATCCAACATGGTTCAAG
upper sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA17G14450.1 (Glycine max), 3'ss of exon 11
-------------gta-tgccttatgtttttaga--catccatacatgtaaatgcacatgcatgttcaatttgtacataaatcatgtaaattt--tctttggccattgaccaccttgtca------gGCTAGTGAGAGGTTGCATGAGAAGATGACCAACTTCATATCAAAAAATAAAGCTGCACAAATCCAACATGGTTCAAG
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gtatgtcctgtttttactatttgatgtttatagtgtagactctatagtttactatttagggttatctcttctatttacaacttaagcaacatgaacctttggatattgatggccttgccaatgccagGCTAGTGAACGGCTGCACGAGAAGATGACCAACTTCATTTCAAAGAATAAAGCTGCACAAATCCAACATGGTTCAAG
upper sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA01G42140.1 (Glycine max), 3'ss of exon 7
gtatgccttatgtttttagacatccatacatgtaaatgc-acatgcatgttcaatttgtacataaatcatgtaaattttctttggccattgaccaccttgtcagGCTAGTGAGAGGTTGCATGAGAAGATGACCAACTTCATATCAAAAAATAAAGCTGCACAAATCCAACATGGTTCAAG
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-------------------------------gtacgtcctgcttttatgcctttactagatctaagcaacatgaataccttttgat-attgatgaccattccagGCTAGTGAACGGCTCCATGAGAAGATGACCAACTTTATTTCAAAGAACAAAGCTGCACAAATACAACATGGTTCAAA
upper sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA11G03230.1 (Glycine max), 3'ss of exon 11
gtatgccttatgtttttagacatccatacatgtaaatgcacatgcatgttcaatt-tgtacataaatcatgtaaattttctttggccattgaccaccttgtcagGCTAGTGAGAGGTTGCATGAGAAGATGACCAACTTCATATCAAAAAATAAAGCTGCACAAATCCAACATGGTTCAAG
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-------------------------gtacatcctgcttt-tatgcctttactataataggtctaagcaacatgaataccttttgat-attgatgaccattccagGCTAGTGAACAGCTGCATGAGAAGATGACCAACTTCATTTCGAAGAACAAAGCTGCACAAATACAACATGGTTCAAA
upper sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatgccttatgtttttagacatccatacatgtaaatgcacatgcatgttcaatttgtacataaatcatgtaaattttctttggccattgaccaccttgtcagGCTAGTGAGAGGTTGCATGAGAAGATGACCAACTTCATATCAAAAAATAAAGCTGCACAAATCCAACATGGTTCAAG
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------------------gtgagtctgatgcctaggtatttatttctctttggtaacggaaaaaaaaaagttaaacttctt-gac--ttgtgtttttcatcagGCTAGTGAAAGATTGCATGACAAGATGACCAATTTCTTATCGAAAAACAAAGCTGCTCAGCTTCAG---GGTAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaatttgtacataaatcatgtaaattttctttggccattgaccaccttgtcagGCTAGTGAGAGGTTGCATGAGAAGATGACCAACTTCATATCAAAAAATAAAGCTGCACAAATCCAACATGGTTCAAG
cattgac putative branch site (score: 3)
ccacctt CT-rich tract
ataaatcatgtaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgccttatgtttttagacatccatacatgtaaatgcacatgcatgttcaatttgtacataaatcatgtaaattttctttggccattgaccaccttgtcagGCTAGTGAGAGGTTGCATGAGAAGATGACCAACTTCATATCAAAAAATAAAGCTGCACAAATCCAACATGGTTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC