Sequence
atgc intronic sequence ATGC exonic sequence...cattcaggttccatagaaatttgggctagacataatggatagcactatgacatttcctgtagtcctctgattatgttctaacaagctgcttgttgtttagGTGAGTCACCACCCAATGATTGTTGCTTGCCACTGTGAGGGGAGAGGCTGGAAGTTCTGGGCAGACTCTAATCTCAAAGGGAAGTTCTGGGGCCGTTCCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os12g18770.1 (Oryza sativa), 3'ss of exon 5
--------------------cattcagg----ttccatagaaatttgggctagacataatggatagcactatgacatttcctgtagtcctct----gattatgttctaacaagctgct----tgttgtttagGTGAGTCACCACCCAATGATTGTTGCTTGCCACTGTGAGGGGAGAGGCTGGAAGTTCTGGGCAGACTCTAATCTCAAAGGGAAGTTCTGGGGCCGTTCCA
||| || |||| || || || | || || || | | | | | |||| | | | | ||||||| | || | ||| || |||| ||||| ||||||||| ||||||| || |||||||| || ||||| |||||||| |||| || || ||||| ||||||||||||||||| || || |
gttgtgtagttatttgagagcatggagaattattccttactaaattatttccta-attctgaatgcttttctta-gtgttgtgtaatttttttgagaaacatgttcttattgtgtgttaacgtgtctttcagGTCAGTCATCACCCAATGGTTGTTGCATGTCACTGTGAAGGAAGAGGTTGGAAGTTTTGGGGGGATTCAAATCTGAAAGGGAAGTTCTGGGGTCGATCAA
upper sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G156608_T04 (Zea mays), 3'ss of exon 2
-----cattcaggttccatagaaatttgggctagacataatggatagcactatgacatttcctgtagtcctctgattatgttctaacaagctgcttgttgttt-agGTGAGTCACCACCCAATGATTGTTGCTTGCCACTGTGAGGGGAGAGGCTGGAAGTTCTGGGCAGACTCTAATCTCAAAGGGAAGTTCTGGGGCCGTTCCA
| | || ||| ||| || | || | | || |||| ||| | || || || || || || ||| | || ||| |||| ||||| ||||||||| ||||||| ||||||||||| || ||||| |||| ||||||| || || ||||| ||||||||||||||||| || ||||
agtaacctatagtgctcattgaactt---atttgattaagaaggtattcacatga-attgattaaagaaacatggttgtgac--aaaaaactgatatttatttcagGTCAGTCATCACCCAATGGTTGTTGCATGCCACTGTGACGGCAGAGGTTGGAGATTCTGGGGTGATTCCAATCTGAAAGGGAAGTTCTGGGGTCGATCCA
upper sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------------------------------cattcaggttccatagaaatttgg-gctagacataatggatagcactatgacatttcctgtagtcctctgattatgttctaacaagctgcttgttgtttagGTGAGTCACCACCCAATGATTGTTGCTTGCCACTGTGAGGGGAGAGGCTGGAAGTTCTGGGCAGACTCTAATCTCAAAGGGAAGTTCTGGGGCCGTTCCA
|| || | |||| | | | | | | ||| | | | || | || ||| | |||||||||| ||||| | |||| ||||| || ||||||||||||||||| ||||||||||| || || |||||||| |||||||| |||||| | ||||| || |||||||| ||||| |
gtaactgggtttttcctttaacttttcaatcaaggttaatgggaatgagtcaaaatttacaggcaaatgcagcaacaataaactaaaatatttgttgcttcattattgtgttttgttgttgaatctgaaatagggcagtgatttgtgtgtcttatgctgctaattttcttctaacaagaagcttgct--ccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGATGGAAGTTTTGGGCAGATTCTAATTTGAAAGGAAAATTCTGGGGGCGTTCTA
upper sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G37650.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------------------------------------------cattcaggttccatagaaatttgggctagacataatggatagcactatgacatttcctgtagtcctctgattatgttctaacaagctgcttgttgtttagGTGAGTCACCACCCAATGATTGTTGCTTGCCACTGTGAGGGGAGAGGCTGGAAGTTCTGGGCAGACTCTAATCTCAAAGGGAAGTTCTGGGGCCGTTCCA
||||| | | | ||| || | || || || | || | | |||| | || ||| | ||||||||| ||||||| |||| ||||| || ||||||||||||||||| ||||||||||| || || |||||||| |||||||| |||||| | ||||| || |||||||| ||||| |
gtaactgggtttttccttttaacttttcaatcaaggttaatgggaatgagtcaaagtttacaggcaaatgcggcaaaaaatagactaataaatttgttgcttcattcttgcctttt-gttattgaatctgaa---aaagggcagtgatttg-tgtctattgtatgctgctaattttcatctaacaagaagcttgtt--ccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGTTGGAAGTTTTGGGCAGATTCTAATTTGAAAGGAAAATTCTGGGGGCGTTCTA
upper sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------------------------cattcaggttccatagaaatttgggctagacataatgga--tagcactat--gacatttcctgtagt----cctctgattatgttctaacaagctgcttgttgtttagGTGAGTCACCACCCAATGATTGTTGCTTGCCACTGTGAGGGGAGAGGCTGGAAGTTCTGGGCAGACTCTAATCTCAAAGGGAAGTTCTGGGGCCGTTCCA
||| || | | ||| || | ||| || || |||| ||||| | ||| |||| || | | | | || | || ||||| |||||||||| || || ||||||||||||||||| |||||||| ||| ||||| ||||||| |||||| ||| ||||||| || || ||||| || || |
gcaagtcaaccatcacatcattctaatgtagaagttgtattgaaaaatcatgcatgaatgtgaaaaactttaacacttcattatctttttaaatctatcagacatatataatagcaacccctcaccttctttgccaccataattctc-ttgttcagGTGAGTCATCATCCTATGATTGTTGCTTGCCATTGTGAGGGACAAGGGTGGAATTTCTGGGGAGACTCAAATATCAAAGGAAAATTTTGGGGACGGTCAA
upper sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S67_260V6.1 (Physcomitrella patens), 3'ss of exon 5
---cattcaggttccatagaaatttgggctagacataatggatagcactatgacatttcctgtagtcctctgattatgttctaacaagctgc-ttgttgtttagGTGAGTCACCACCCAATGATTGTTGCTTGCCACTGTGAGGGGAGAGGCTGGAAGTTCTGGGCAGACTCTAATCTCAAAGGGAAGTTCTGGGGCCGTTCCA
|| || | |||| || | | | | || | | || || ||| || ||||| | || | ||| | | |||||||||| || ||||||||||| || || || || ||||| ||||||||||| ||||||| ||| ||| | ||| | ||||| ||||| ||||| |
ggagatattaatttgcaacctctttgtcatatctttcgagctttagattaagtaaaagt---taatcatcttgc-atcttctatctccctacgttgctttgcagGTGAGTCATCATCCAATGATTGTGGCATGTCATTGCGAGGGCAGAGGCTGGAAATTCTGGGGTGACAGCAATTTGAAAAGCAAGTTTTGGGGTCGTTCAAMapped 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|110419051|gb|EC985243.1|EC985243EST: CCTATGAGGCTGATTATCCTGATAAAGGTCTTCGCTTCTTCTCTGAAAAA GTGAGTCACCACCCAATGATTGTTGCTTGCCACTGTGAGGGGAGAGGCTGG
genomic: CCTATGAGGCTGATTATCCTGATAAAGGTCTTCGCTTCTTCTCTGAAAAAgtaattccct ... tgttgtttagGTGAGTCACCACCCAATGATTGTTGCTTGCCACTGTGAGGGGAGAGGCTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgacatttcctgtagtcctctgattatgttctaacaagctgcttgttgtttagGTGAGTCACCACCCAATGATTGTTGCTTGCCACTGTGAGGGGAGAGGCTGGAAGTTCTGGGCAGACTCTAATCTCAAAGGGAAGTTCTGGGGCCGTTCCA
ttctaac putative branch site (score: 1)
attatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cattcaggttccatagaaatttgggctagacataatggatagcactatgacatttcctgtagtcctctgattatgttctaacaagctgcttgttgtttagGTGAGTCACCACCCAATGATTGTTGCTTGCCACTGTGAGGGGAGAGGCTGGAAGTTCTGGGCAGACTCTAATCTCAAAGGGAAGTTCTGGGGCCGTTCCA
cattcag
- - - - - - atagaaa
- - - - - - - - - - - gggctag
- - - - - - - - - - - - - - - - - -tggatag
- - - - - - - - - - - - - - - - - - - - - cactatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaacaa