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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGCACATACTACTTGCGTATGGTCGGCGCCATGGTTCTCTTCTTAAAAGTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAGgtaaaatgctctctctaaaaaaaaattctgatgtgaattgctcttatatctaaccaccctttgtattctgtataatcttttagtatgaggtaagtatgat...

Basic information

species Glycine max
transcript GLYMA19G35370.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G35370.3 (Glycine max), 5'ss of exon 11
lower sequence: AT1G04140.1 (Arabidopsis thaliana), 5'ss of exon 11
TGAGCACATACTACTTGCGTATGGTCGGCGCCATGGTTCTCTTCTTAAAAGTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAGgtaaaatgctctctctaaaa---aaaaattctgatgtgaattgctct---tatatctaaccaccctttgtatt-----ctgtataatcttttagtatgaggtaagtatgat------------------------------
 |||||||| || ||||| |||||||| || |||||||||||| | || || ||||| | ||||||||||||||||| || | | |  ||||| || |||||||  |     ||| |  |   |  ||||   |    |   |  |    | || |  |   |  ||| |||      || ||||  |||  | ||| |   |||  |                                 
CGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTTTCACAGTTTTGGAGgtaacgtctatgctccagtagttatgaatttctagaccagcagaacaatgtttagcagatgccattttatatcattaactatatacacttggaatatcatacaagagtttagactgtgtttttccctttctattccttcag

upper sequence: GLYMA19G35370.3 (Glycine max), 5'ss of exon 11
lower sequence: AT5G43930.1 (Arabidopsis thaliana), 5'ss of exon 11
TGAGCACATACTACTTGCGTATGGTCGGCGCCATGGTTCTCTTCTTAAAAGTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAGgtaaaatgctctctctaaaaaaaaattctgatgtgaattgctcttatatctaac-caccctttgtattctgtataatcttttagtatgaggtaagtatgat
 ||||| ||||||||||| ||||| ||||| |||||||||||| | |  || || || | |||||| |||||||||| || | | |  ||||| || ||||||||   ||    |||  |  | || |  ||||  |   ||   | || |||| ||    |||| || |||     |  | ||                 
GGAGCATATACTACTTGCATATGGGCGGCGTCATGGTTCTCTTTTGAGGAGCATCGTTAGTGATGGTGAAACAACATCACATTTTTTCACAGTATTGGAGgtaaagc-cttatgctactagtacatcc--atgttcagaacttggagatataacacagaacttgt-ttgtgtg-ggccggtcag-----------------

upper sequence: GLYMA19G35370.3 (Glycine max), 5'ss of exon 11
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 5'ss of exon 11
TGAGCACATACTACTTGCGTATGGTCGGCGCCATGGTTCTCTTCTTAAAAGTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAGgtaaaatgctctctctaaaaaaaaattctgatgtgaatt----------gctcttatatctaaccaccctttgtattctgtataatcttttagtatgaggtaagtatgat----------------------------------
||| |||||| ||||||| || |||||||| ||| ||||||| ||||||||  |||| || ||||| ||||| ||||||||||| || ||| | || ||||||| |         |  || |  |||  |  || |||           | |||   ||  ||   |   |    | || ||| |||| ||   ||        | ||||                                  
TGAACACATATTACTTGCCTACGGTCGGCGTCATAGTTCTCTCCTTAAAAGCCTTGTTATCGATGGGGAAACGACATTACCTATTTACACAATTTTGGAGgtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacaggctctttttgtcactcag

Mapped 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|151398183|gb|EV268061.1|EV268061
EST:     GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAG                         GTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
genomic: GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAGgtaaaatgct ... tgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
EST: gi|22928249|gb|BU545388.1|BU545388
EST:     GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAG                         GTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
genomic: GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAGgtaaaatgct ... tgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
EST: gi|15001188|gb|BI322002.1|BI322002
EST:     GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAG                         GTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
genomic: GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAGgtaaaatgct ... tgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
EST: gi|27446387|gb|CA953510.1|CA953510
EST:     GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAG                         GTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
genomic: GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAGgtaaaatgct ... tgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
EST: gi|193686900|gb|FK632523.1|FK632523
EST:     GTNTTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAG                         GTATACAGAGTGTCAGATA
genomic: GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAGgtaaaatgct ... tgtcttttagGTATACAGAGTGTCAGATA
EST: gi|15203207|gb|BI425975.1|BI425975
EST:     GTATTGT-TTTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAG                         GTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
genomic: GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAGgtaaaatgct ... tgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
EST: gi|12690329|gb|BG156665.1|BG156665
EST:     GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAG                         GTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
genomic: GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAGgtaaaatgct ... tgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
EST: gi|21676372|gb|BQ628723.1|BQ628723
EST:     GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAG                         GTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
genomic: GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAGgtaaaatgct ... tgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
EST: gi|16348103|gb|BI973698.1|BI973698
EST:     GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAG                         GTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
genomic: GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAGgtaaaatgct ... tgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGCACATACTACTTGCGTATGGTCGGCGCCATGGTTCTCTTCTTAAAAGTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAGgtaaaatgctctctctaaaaaaaaattctgatgtgaattgctcttatatctaaccaccctttgtattctgtataatcttttagtatgaggtaagtatgat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaccct