Sequence
atgc intronic sequence ATGC exonic sequencegtaatctcaaatttcatcccatgattagattctattttctgaagcaatgttccattactggtttctcagatctattggtttgttaacattgttctaattgagatttcatgtttctcccagGATTTTGAGTTCAAAGAGTTGAACGAAGTACTCAAGTACTATCCTCAGGGTTATCACGGTGTGGATAAGGAGGGGAGACCCGTTTATATTGAAAGACTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 4
gtaatctcaaatttcatcccatgattagattctattttctgaagcaatgttccattactggtttctcagatctattggtttgttaacattgttctaattgagatttcatgtttctcccagGATTTTGAGTTCAAAGAGTTGAACGAAGTACTCAAGTACTATCCTCAGGGTTATCACGGTGTGGATAAGGAGGGGAGACCCGTTTATATTGAAAGACTTG
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-----------------------gttag-tgttcttgcttgtgcctataaaacaatttggattt--------tgtttggctataaataatgcc-----tgtaactacatttctctgt-agGATTTTGATTACAATGAGTTAGACGCTGTTCTGCAATATTATCCTCACGGTTATCATGGAGTTGACAAAGACGGGAGACCTGTTTATATTGAAAGGCTTG
upper sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 4
gtaatctcaaatttcatcccatgattagattctattttctgaagcaatgttccattactggtttctcagatctattggtttgttaacattgttctaattgagatttcatgtttctcccagGATTTTGAGTTCAAAGAGTTGAACGAAGTACTCAAGTACTATCCTCAGGGTTATCACGGTGTGGATAAGGAGGGGAGACCCGTTTATATTGAAAGACTTG
||| | | | | ||| ||||| | | | | | | ||| | || || | |||| | ||| | |||| ||||| || |||| || || | || |||||| ||| || | | || |||||||| |||||||| || || || || |||||||||||||||||||||||||| ||||
-----gtcagtgtctgagctttagtcagac---attttttaagtttgtttggcttatatggctcct-----------gtcttaaaacaataatctgaa-atcattttgtgtttttcatagGACTTCGAATACACTGAGTTGGACGCTGTTTTGCAATATTATCCTCATGGTTATCATGGAGTTGACAAAGAGGGGAGACCCGTTTATATTGAAAGGCTTG
upper sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G073571_T03 (Zea mays), 3'ss of exon 3
gtaatctcaaatttcatcccatgattagattctattttctgaagcaatgttccattactggtttctcagatctattggtttgttaacattgttctaattgagatttcatgtttctcccagGATTTTGAGTTCAAAGAGTTGAACGAAGTACTCAAGTACTATCCTCAGGGTTATCACGGTGTGGATAAGGAGGGGAGACCCGTTTATATTGAAAGACTTG
| ||| | | || | | | | | || | | || | || || || | || |||| |||| |||| | | |||| || || | || ||||||| | || | | || |||||||| |||||||| || || || || ||||||||||| ||||| |||||||| ||||
--------------------gttattgg-ctgagcttattcagtt--tttcactttgtttgatttatatggctcctgtcttaaaacaatgaccggaatt---attttatgtgttccatagGACTTCGAATACACTGAGTTGAGCACCGTTTTGCAATATTATCCTCATGGTTATCATGGAGTTGACAAAGAGGGGAGACCTGTTTACATTGAAAGGCTTG
upper sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA14G07850.1 (Glycine max), 3'ss of exon 3
----gtaatctcaaatttcatcccatgattagattctattttctgaagcaatgttccattactggtttctcagatctattgg----tttgttaacattgttctaattgagatttc-atgtttctccc-agGATTTTGAGTTCAAAGAGTTGAACGAAGTACTCAAGTACTATCCTCAGGGTTATCACGGTGTGGATAAGGAGGGGAGACCCGTTTATATTGAAAGACTTG
|| ||| | | || | || || | || | || ||| | | || | | | | | | | ||| ||||| | | | ||| || | || | | |||||| |||||||||| ||| |||||||| ||||| || |||||||||| || |||||||| |||||||||||||| || ||||| ||||||||||| || | |
gtgagttatc-cgatttgaaaaatataatcaacttattttggttgatcctgttttatttgatcaactgtactgtttttttgaaatcgttgttcatgctatactactttggtttcctgtctttctctttagGATTTTGAATTCGGTGAGTTGAATGAAGTCCTGCAGTACTATCCACATGGTTATCATGGTGTGGATAAGGAAGGAAGACCTGTTTATATTGAGAGGTTAG
upper sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G03300.1 (Glycine max), 3'ss of exon 3
----gtaatctcaaatttcatcccatgattagattctattttctgaagcaatgttccattactggtttctcagatctattggtttgttaacattgttctaattgagatttcatgtttctcccagGATTTTGAGTTCAAAGAGTTGAACGAAGTACTCAAGTACTATCCTCAGGGTTATCACGGTGTGGATAAGGAGGGGAGACCCGTTTATATTGAAAGACTTG
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gtgatccatcttatacattaatatatgttta-atttgataatctgaa-cattgatttttttctt-tctttcggaatttggggttcatgtatattac----actgtggtttctactctat---agGATTTTGAATTCAAGGAGTTGAATGAAGTCCTGAAGTACTACCCGCATGGTTATCATGGTGTAGATAGGGAAGGAAGACCTGTTTATATTGAGAGGCTAG
upper sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G03230.1 (Glycine max), 3'ss of exon 2
gtaatctcaaatttcatcccatgattagattctattttctgaagcaatgttccattactggtttctcagatctattggtttgttaacattgttctaattgagatttcatgtttctcccagGATTTTGAGTTCAAAGAGTTGAACGAAGTACTCAAGTACTATCCTCAGGGTTATCACGGTGTGGATAAGGAGGGGAGACCCGTTTATATTGAAAGACTTG
|| ||| || | || | ||| ||| || ||||| || || | ||| ||| || || | | || | | | | ||| | |||| | | | |||||||||| ||||| |||||||| ||||| || |||||||| || || ||| |||| ||||| |||| ||| || || || ||||||||||| || || |
gtgatcc---atctaat---acaatttaatttgataacctgaa-cattgatttattttatttttttcgaatttgg-gtttcatgtatactactctct----ggtttctactctat---agGATTTTGAATTCAAGGAGTTGAATGAAGTCCTAAAGTACTACCCGCATGGTAATCATGGTGTAGATAGGGAAGGAAGGCCTGTTTATATTGAGAGGCTAG
upper sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G37150.1 (Glycine max), 3'ss of exon 3
---------------------gtaatctcaaatttcatcccatgattagattctatttt-ctgaagcaatgttccattactggtttctcagatctattggtttgttaacattgttctaattgagatttcatgtttctccc-agGATTTTGAGTTCAAAGAGTTGAACGAAGTACTCAAGTACTATCCTCAGGGTTATCACGGTGTGGATAAGGAGGGGAGACCCGTTTATATTGAAAGACTTG
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gtgagtcatctgatttgaaaaatatatttcaacttcttattttggtt-gatcctgttttgtttgattaactgtacttttttagttttttgaaatcattgttcatgatatactactttggtt----tcctgtctttctctttagGATTTTGAATTCGGTGAGTTGAATGAAGTCCTGCAGTGCTATCCACATGGCTATCATGGTGTGGATAAGGAAGGAAGACCTATTTATATTGAGAGGTTAGMapped 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|33407754|gb|CF213381.1|CF213381EST: CCGAAATGATTCACTGGAGGAAAAACTTCGGCACCGACACTATCTTGGAG GATTTTGAGTTCAAAGAGTTGAACGAAGTACTCAAGTACTATCCTCAGGGT
genomic: CCGAAATGATTCACTGGAGGAAAAACTTCGGCACCGACACTATCTTGGAGgtaatctcaa ... tttctcccagGATTTTGAGTTCAAAGAGTTGAACGAAGTACTCAAGTACTATCCTCAGGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagatctattggtttgttaacattgttctaattgagatttcatgtttctcccagGATTTTGAGTTCAAAGAGTTGAACGAAGTACTCAAGTACTATCCTCAGGGTTATCACGGTGTGGATAAGGAGGGGAGACCCGTTTATATTGAAAGACTTG
ttctaat putative branch site (score: 2)
tttcatgtttctccc putative PPT
tttgttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatctcaaatttcatcccatgattagattctattttctgaagcaatgttccattactggtttctcagatctattggtttgttaacattgttctaattgagatttcatgtttctcccagGATTTTGAGTTCAAAGAGTTGAACGAAGTACTCAAGTACTATCCTCAGGGTTATCACGGTGTGGATAAGGAGGGGAGACCCGTTTATATTGAAAGACTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG