Sequence
atgc intronic sequence ATGC exonic sequence...agatcaccttatttttcaattttcactccctttctaacgcattattgtttagaaacatacatatgtagtttgaattgatagtctttttgttgaaccttagGTTTGGGTGAAAGACCCTGGAAAACATCCGATGCTAGACTTGTTCTTGAAGATGGCTCAGTCTGGAAGGCAAAGTCATTTGGTGCTTCAGGAACTCAAGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0044g00550.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g47850.3 (Oryza sativa), 3'ss of exon 2
--------------------------------agatcaccttatttttcaattttcactcc-----------------ctttctaacgcattattgtttagaaacataca-tatgtagtttgaa------ttgatagtcttt-----ttgttgaaccttagGTTTGGGTGAAAGACCCTGGAAAACATCCGATGCTAGACTTGTTCTTGAAGATGGCTCAGTCTGGAAGGCAAAGTCATTTGGTGCTTCAGGAACTCAAGT------
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gtgagtcaggttgccttttcgctagctgattcgaatcgctctagttttgcagtcgcagcgcggaatacgtgctcagggttctgctacggatttgcgattaggcaattgtgctccacagttaagaagatgatgaatactgtttcaccatttttggattcttcgtgcagTGCAAAGACCATGGAAGCTCAGCGATGCTCGGCTCGTTCTTGAGGATGGTTCAGTTTGGAAGGCCAAGTCTTTTGGTGCTTCAGGAACACAAGTTGGTGA
upper sequence: Vv04s0044g00550.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G029573_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------------------agatcaccttatttttcaattttcactccctttctaacgcattat-tgtttagaaacatacatatgtagtttgaattgatagtctttttgttgaaccttagGTTTGGGTGAAAGACCCTGGAAAACATCCGATGCTAGACTTGTTCTTGAAGATGGCTCAGTCTGGAAGGCAAAGTCATTTGGTGCTTCAGGAACTCAAGT------
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gtgggttgtctttactagctgttcagatatcaagttttgtattcggcagtcggcacgtggagtatgcgcttgggattttgtagcacgattcatcaattatgtaccttacaatttaagagctctattatttctggtttcactatttttgaaatctccatgcagCGGAAAGGCCGTGGAAGCTCAGTGATGCTCGTCTTGTCCTGGAAGATGGATCAGTGTGGACGGCCAAGTCTTTTGGTGCTTCAGGAACACAAGTTGGTGA
upper sequence: Vv04s0044g00550.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G32190.1 (Glycine max), 3'ss of exon 1
-------agatcaccttatttttcaattttcactccctttctaacgcattattgttta----gaaacatacatatgtagtttgaattgatagtctttttgttgaaccttagGTTTGGGTGAAAGACCCTGGAAAACATCCGATGCTAGACTTGTTCTTGAAGATGGCTCAGTCTGGAAGGCAAAGTCATTTGGTGCTTCAGGAACTCAAGT
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gtaactcgtaacccctgcttcttcccttttcttaaagtgaaacacactctgtactttttcatggagcttgaagaaattgatgcatttttttttttttgtattgaaatatagGCAATGGAGAAAGGCCTTGGAAAACTTCAGGCGCTAGACTTATGTTAGAAGATGGATCAATCTGGAAAGCAAAGTCATTTGGTGCTTCAGGAACCCAAGT
upper sequence: Vv04s0044g00550.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA06G15510.4 (Glycine max), 3'ss of exon 1
agatcaccttattt-ttcaattttcactccctttctaacgcatt-attgtttagaaacatacatatgtagtt-tgaattgat--agtctttttgt-tgaaccttagGTTTGGGTGAAAGACCCTGGAAAACATCCGATGCTAGACTTGTTCTTGAAGATGGCTCAGTCTGGAAGGCAAAGTCATTTGGTGCTTCAGGAACTCAAGT
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------ctttgcccctttgatgtgaatgtcgtatttttcgcttttattgttggagggtattttgttaaaattgttaactgacgcagttctgttgcatgtgacatagGTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAGATGGTTCAATTTGGAAAGCAAAATCGTTTGGTGCTTCGGGGACTCAAGT
upper sequence: Vv04s0044g00550.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA04G39390.1 (Glycine max), 3'ss of exon 1
-------------------------------------------------------------------------------------agatcaccttatttttcaattttcactccctttctaacgcattatt--gtttagaaacatacatatgtagtttgaattgatagtct------ttttgttgaacct----tagGTTTGGGTGAAAGACCCTGGAAAACATCCGATGCTAGACTTGTTCTTGAAGATGGCTCAGTCTGGAAGGCAAAGTCATTTGGTGCTTCAGGAACTCAAGT
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gtactctctctctcggtttttttttttttcgcaatacctttaaaaaagttttattttttcatgtacccatttgttcactgcatgaaaatttgtttttttttccgcccatttggtgtgaatgtcgtatttttcgcttttaatgttggagggtattgttaaaattgttaattgatgcagttctgttgcatgtgacatagGTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAGATGGTTCAATTTGGAGAGCAAAATCGTTTGGTGCTTCAGGGACCCAAGTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|37187345|gb|CF606698.1|CF606698EST: TAGGATTTTCACCATCAGATGCTCCTCAGGTGCCGCTGCCACCGCCGTCG GTTTGGGTGAAAGACCCTGGAAAACATCCGATGCTAGACTTGTTCTTGAAG
genomic: TAGGATTTTCACCATCAGATGCTCCTCAGGTGCCGCTGCCACCGCCGTCGgtaccactct ... tgaaccttagGTTTGGGTGAAAGACCCTGGAAAACATCCGATGCTAGACTTGTTCTTGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttagaaacatacatatgtagtttgaattgatagtctttttgttgaaccttagGTTTGGGTGAAAGACCCTGGAAAACATCCGATGCTAGACTTGTTCTTGAAGATGGCTCAGTCTGGAAGGCAAAGTCATTTGGTGCTTCAGGAACTCAAGT
aattgat putative branch site (score: 4)
tctttttgtt putative PPT
atacatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agatcaccttatttttcaattttcactccctttctaacgcattattgtttagaaacatacatatgtagtttgaattgatagtctttttgttgaaccttagGTTTGGGTGAAAGACCCTGGAAAACATCCGATGCTAGACTTGTTCTTGAAGATGGCTCAGTCTGGAAGGCAAAGTCATTTGGTGCTTCAGGAACTCAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - cacctta
- - - - - - - - - - - -cactccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - acataca