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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatctctttttactctctccatcagtcctcctcctatttttcttatgtgcatgtaggcagtggtcaaggtttttttattttattttgaattctgtttgaaaataactaagtcttttatttgctctggttcacttagGTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG

Basic information

species Glycine max
transcript GLYMA0048S00290.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0048S00290.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 3'ss of exon 5
gtaaatctctttttactctctccatcagtcctcctcctatttttct-tatgtgcatgtaggcagtggtcaaggtttttttattttattttgaattctgtttgaaaataactaagtcttttatttgctctggttcacttagGTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG
||||| ||||   |  | ||||  ||   | |    || |     | | ||||  |||  |  ||| |     | | | ||  || |  ||   ||| | ||  |||   ||  | | | |||   | |||    |  ||||||||||||| |||||||| ||||| || ||| ||||| |||| ||||||
gtaaacctctcact-ttatctctctcttgcattaatctgtaccagtgtgtgtgtgtgtgtgt-gtgtttttaatatatctaagttgtagtg---tctatctgttaatg-ttatatgtctcattgtttttggaattcc-agGTGCTTTGTGTCCATGGTGGTCTTTCACCTGACGTTCGAACAATTGATCAG
















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|209728247|gb|BW651682.1|BW651682
EST:     GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACT                         GTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG
genomic: GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACTgtaaatctct ... gttcacttagGTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG
EST: gi|298172509|gb|HO019549.1|HO019549
EST:     GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACT                         GTGTTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG
genomic: GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACTgtaaatctct ... gttcacttagGTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG
EST: gi|254340656|gb|GR854384.1|GR854384
EST:     GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACT                         GTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG
genomic: GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACTgtaaatctct ... gttcacttagGTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG
EST: gi|151410851|gb|EV280666.1|EV280666
EST:     GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACT                         GTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG
genomic: GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACTgtaaatctct ... gttcacttagGTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG
EST: gi|192323250|gb|FK018961.1|FK018961
EST:     GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACT                         GTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG
genomic: GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACTgtaaatctct ... gttcacttagGTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG
EST: gi|298178347|gb|HO024082.1|HO024082
EST:     GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACT                         GTGCTTTGTGTCCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG
genomic: GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACTgtaaatctct ... gttcacttagGTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG
EST: gi|192296025|gb|FG989419.1|FG989419
EST:     GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAGTTATAGATGGAACT                         GTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG
genomic: GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACTgtaaatctct ... gttcacttagGTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG
EST: gi|298187406|gb|HO034555.1|HO034555
EST:     GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACT                         GTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTC
genomic: GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACTgtaaatctct ... gttcacttagGTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTC
EST: gi|254340657|gb|GR854385.1|GR854385
EST:     GTACAGATG-TTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACT                         GTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG
genomic: GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACTgtaaatctct ... gttcacttagGTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG
EST: gi|193307179|gb|FK271075.1|FK271075
EST:     GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACT                         GTGCTTTGTGTTCATGGTGG
genomic: GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACTgtaaatctct ... gttcacttagGTGCTTTGTGTTCATGGTGG
EST: gi|298190555|gb|HO032676.1|HO032676
EST:     GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACT                         GTGCTTTGTGTTCATGGTGGCCTTT
genomic: GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACTgtaaatctct ... gttcacttagGTGCTTTGTGTTCATGGTGGCCTTT
EST: gi|16345163|gb|BI970758.1|BI970758
EST:     GTACAGATGTTTTTGACTATCTTACTCTTNNTGCAATTATAGATGGAACT                         GTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG
genomic: GTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACTgtaaatctct ... gttcacttagGTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttgaattctgtttgaaaataactaagtcttttatttgctctggttcacttagGTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG
                  aaataac  putative branch site (score: 2)
                                              ttcactt  putative PPT
                 aaaataactaagtctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatctctttttactctctccatcagtcctcctcctatttttcttatgtgcatgtaggcagtggtcaaggtttttttattttattttgaattctgtttgaaaataactaagtcttttatttgctctggttcacttagGTGCTTTGTGTTCATGGTGGCCTTTCTCCAGACATTCGATCAATAGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA