Sequence
atgc intronic sequence ATGC exonic sequence...tagttgcaaggctttatcttatttaaataagtttgctaatctgcatgagtttcatatttccagctgatactatctaatgcttaaattcttgaacttctagGTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGGTCCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g61590.1 (Oryza sativa), 3'ss of exon 1
--tagttgcaaggctt-tatcttatttaaataagtttgctaatctgca--tgagtttcatatttccagctgatact-atctaatgcttaaattcttgaacttctagGTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGGTCCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
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tggactcacagtgcttgtacaacagttgatcgttgttctttgtatacagacaaaactcctagttccatccagtccttatgtgattgttatgttctt------ttagGTGAGAAGTTTTCTGAAATTGTGGGAAGCCCATATTACATGGCTCCAGAGGTATTGAAGAGAAACTATGGTCCGGAAATAGATATTTGGAGTGCAGGAGT
upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os05g39090.1 (Oryza sativa), 3'ss of exon 1
tagttgcaagg--ctttatcttatttaaata-agtttgctaatctgcatgagtttcatatttccagctgatactatctaatgcttaaattcttgaacttctagGTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGGTCCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
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-ttttgtaagacacctcttcacatttccctgtgaaatgcctgtatgctatatatttaaatatataaaatgtttaatctgatccacta--tcttgattgttcagGTGAAAAATTTTCTGAAATTGTGGGAAGTCCATATTACATGGCTCCTGAAGTGCTGAAGAGAAACTATGGACCTGAAATAGACATATGGAGTGCTGGTGT
upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G030673_T01 (Zea mays), 3'ss of exon 1
-tagttgcaaggctttatcttatttaaataagtttgctaatctgcatgagtttc--atatttccagctgatactatctaatgcttaaattcttgaacttctagGTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGGTCCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
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gcaaaggcttgcctcggttcccttcttcagaccccactcatgtggccgtcttcccactttatttatttgaaactcataaaagcattgttttct---tttctagGTGAAAAGTTTTCGGAAATTGTGGGAAGTCCATACTACATGGCTCCTGAAGTCTTGAAGAGGAACTATGGACCTGAAATAGACATATGGAGCGCTGGTGT
upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G311220_T03 (Zea mays), 3'ss of exon 1
----tagttgcaaggctttatcttatttaaataagtttgc-taatctgcatgagtttcatatttccagctgatactatctaatgcttaaattcttgaacttctagGTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGGTCCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
||||| || | | | | || || | || | | || || | ||| | ||| || ||| | || |||| ||||||| | ||| || |||||||| ||||| || |||||||||||||| || || | ||| | || ||||| ||||||||||| ||||||||||| |||||
tagaacgttgctgattgcaatacttgcaggacaggcatgtgtactacacaagtaaaccctagttttatctggccttttctcatcctt----tgttctactt-tagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAGTATTGAAGAGAAACTATGGGCCAGAAATAGACATATGGAGTGCGGGAGT
upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G088361_T01 (Zea mays), 3'ss of exon 1
tagttgcaaggct-ttatcttatttaaataagttt--gctaatctgcatgagtttcatatttccagctgatactatctaatgcttaaatt-cttgaacttctagGTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGGTCCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
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---ctgcaatgcaactatttttttgcaattgctataaattgtggtccacatatagc-cacaaccaacaattgctgtaaaatgaaagcattgttttcctttccagGCGAAAAGTTTTCGGAAATTGTGGGAAGCCCATACTACATGGCTCCTGAAGTCTTGAAGAGGAACTATGGACCTGAAATAGACATATGGAGCGCTGGTGT
upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G43160.1 (Glycine max), 3'ss of exon 3
-------tagttgcaaggctttatcttatttaaataagtttgctaatctgcatgagtttcatatttccagctgatactatctaatgcttaaattcttgaacttctagGTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGGTCCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
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tgctgtctactcatgtttcgacattatatttcaatctttttcattgcttaca-gtatctgacattttttccatgtgttgtgggtaatataaa------aatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCAGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 1
tagttgcaaggcttt----atcttatttaaataagtttgctaatctgcatgagtttcatatttccagctgatactatctaatgcttaaattcttgaacttctagGTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGGTCCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
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ctcatgtttcactttcaaaattatatttcaatctttttcattgcttaca-gtatctgacatattttcc--ataatgtgttgtgggtaa-tataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 1
tagttgcaaggctt---tatcttatttaa---ataagtttgcta-atctgcatgagtttcatatttccagctgatactatctaatgcttaaattcttgaacttctagGTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGGTCCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
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--attgtaggatttatgtttcttgattgatacatacctttgatgtattttgaccagttt---atttggtgttgatgctgttt--ttgtaatgcttacatatgaccagGTGAGAAATTCTCTGAGATTGTTGGGAGTCCATATTACATGGCACCTGAGGTGCTTAAGCGGAATTATGGACCCGAAATAGATATTTGGAGTGCTGGAGTMapped 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|110702917|gb|EE079305.1|EE079305EST: TTCGCCTTTGAAAGCCATTGATTTCGGCTTGTCTATATTCTTCAAGCCAG GTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGG
genomic: TTCGCCTTTGAAAGCCATTGATTTCGGCTTGTCTATATTCTTCAAGCCAGgtgaagaatc ... gaacttctagGTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGG
EST:
gi|33405399|gb|CF211026.1|CF211026EST: TTCGCCTTTGAAAGCCATTGATTTCGGCTTGTCTATATTCTTCAAGCCAG GTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGG
genomic: TTCGCCTTTGAAAGCCATTGATTTCGGCTTGTCTATATTCTTCAAGCCAGgtgaagaatc ... gaacttctagGTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagtttcatatttccagctgatactatctaatgcttaaattcttgaacttctagGTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGGTCCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
atctaat putative branch site (score: 3)
cttct putative PPT
ttaaattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagttgcaaggctttatcttatttaaataagtttgctaatctgcatgagtttcatatttccagctgatactatctaatgcttaaattcttgaacttctagGTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGGTCCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
- - - - - - - - - - - - aaataag
- - - - - - - - - - - - - - - - - - - - - -catgagt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaatgc