Sequence
atgc intronic sequence ATGC exonic sequence...agttcattctcgatactgctgttgcatctgagagatgttgttgccccatgcatatatgatatcatacagtctctgtcatggattgccattgagtttgcagATCGGTATAACACCGCCCTCGTTTGCCACAGATGGCATTACCTGGCATGTCACCCACGTCTATGGCTGCGAGTAGATCGGTCTGTGAAAGATTCATCTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0139g00260.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os07g46555.1 (Oryza sativa), 3'ss of exon 1
agttcattctcgatactgctgttgcat-ctgagagatgttgttgccccatgcatatatgatatcatacagtctctgtcatggattgccattgagtttgcagATCGGTATAACACCGCCCTCGTTTGCCACAGATGGCATTACCTGGCATGTCACCCACGTCTATGGCTGCGAGTAGATCGGTCTGTGAAAGATTCATCTGA
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tgcttgattttgtccctgctaccatttattgcctgataatgtgacgctgtttatgtactttaa-atgagctttttttagcatttcatttttgaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCCATCCTCGACTGTGGTTGCGTGTTGAGAGGCCAATCAGAAATACAATAGA
upper sequence: Vv13s0139g00260.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G009021_T01 (Zea mays), 3'ss of exon 1
agttcattctcgatactgctgttgcatctgagagatgttgttgccccatgcatatatgatatcatacagtctctgtcatggattgc--cattgagtttgcagATCGGTATAACACCGCCCTCGTTTGCCACAGATGGCATTACCTGGCATGTCACCCACGTCTATGGCTGCGAGTAGATCGGTCTGTGAAAGATTCATCTGA-------------------------------
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---------------------------ttaacatatactgctgacgtggtttaaaatga------actgttttttttatcaatttcattgttgaacctgcagataggtataacaccgccctcgtttgccacagATGGCGCTTCCTTGCATGCCACCCTCGGCTATGGCTGCGTGTCGAGAGGCCAATCAGAGATGCGATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCT
upper sequence: Vv13s0139g00260.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G009021_T02 (Zea mays), 3'ss of exon 1
-agttcattctcgatactgctgttgcat---ctgagagatgttgttgccccatgcatatatgatatcatacagtctctgtcatggattgc--cattgagtttgcagATCGGTATAACACCGCCCTCGTTTGCCACAGATGGCATTACCTGGCATGTCACCCACGTCTATGGCTGCGAGTAGATCGGTCTGTGAAAGATTCATCTGA
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ctggatgtcacatgttttttgatagcatgccttaacatatactgctgacgtggtttaaaatga------actgttttttttatcaatttcattgttgaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCCACCCTCGGCTATGGCTGCGTGTCGAGAGGCCAATCAGAGATGCGATGGA
upper sequence: Vv13s0139g00260.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G21550.1 (Glycine max), 3'ss of exon 1
agttcattctcgatactgctgttgcatctgagagatgttgttgccccatgcatatatgatatcatacag--------tctctgtcatgga-ttgccattgagtttgcagATCGGTATAACACCGCCCTCGTTTGCCACAGATGGCATTACCTGGCATGTCACCCACGTCTATGGCTGCGAGTAGATCGGTCTGTGAAAGATTCATCTGA
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-------cttaggcgctaatcctctcttaaaataattttctt--tgaaaaaataattaatagcatacagcagagcattttctatcacaaagctgctattgagtttgcagATCGCTTTAATACCGCCCTCGTTTGCCACAGATGGAATTACTTGGCATGTCATCCTCGCTTGTGGCTTCGGGTTGATCGATCAGTTAAAGAGTTATCTGA
upper sequence: Vv13s0139g00260.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G54480.2 (Arabidopsis thaliana), 3'ss of exon 1
--agttcattctcgatactgctgttgcatctgagagatgttgttgccccatgcatatatgatatcatacagt-ctctgtcatggattgccattgagtttgcagATCGGTATAACACCGCCCTCGTTTGCCACAGATGGCATTACCTGGCATGTCACCCACGTCTATGGCTGCGAGTAGATCGGTCTGTGAAAGATTCATCTGA
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tttgaaaatttcgtattttgtttgtatgattgacttgggcatttgttgcgtac---tacagtctgtttcaatgctgttttgtgtatctcttgtgagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGCGTGTCACCCTCGCTTGTGGCTCCGTGTTGACCGTTTTGTCAAGGATTTATCTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatgcatatatgatatcatacagtctctgtcatggattgccattgagtttgcagATCGGTATAACACCGCCCTCGTTTGCCACAGATGGCATTACCTGGCATGTCACCCACGTCTATGGCTGCGAGTAGATCGGTCTGTGAAAGATTCATCTGA
atatatgatatcata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agttcattctcgatactgctgttgcatctgagagatgttgttgccccatgcatatatgatatcatacagtctctgtcatggattgccattgagtttgcagATCGGTATAACACCGCCCTCGTTTGCCACAGATGGCATTACCTGGCATGTCACCCACGTCTATGGCTGCGAGTAGATCGGTCTGTGAAAGATTCATCTGA
- - cattctc
- - - - - - - actgctg
- - - - - - - - - - - -gcatctg
- - - - - - - - - - - - - - - - - - - tgttgcc
- - - - - - - - - - - - - - - - - - - - - - -ccatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gattgcc