Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgttgaaataatggtgtcaattgtcagatcccccttgtggtgttgtgatattagcagtggttaacatgctgagttttgggtcttgtgtttttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTCCTCCATCCCCACTGTGTGATCTGATCCTAAATCCTATAGCCATGACTAC

Basic information

species Glycine max
transcript GLYMA07G31030.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G31030.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G21560.2 (Arabidopsis thaliana), 3'ss of exon 2
gtgttgaaataatggtgtcaattgtcagatcccccttgtggtgttgtgatattagcagtggttaacatgctgagtt---ttgggtcttgtgtttttcct-tcagTGAAGAAGAACCCTTCT------------CTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTCCTCCATCCCCACTGTGTGATCTGATCCTAAATCCTATAGCCATGACTAC
 | |  |  |  |    |||  ||    ||  | |||||  || |  ||| |||    |  |||   || |   ||   ||||  ||  || ||||  | ||||  | ||||     | ||            ||||||||||||||| |||||||||||||   ||| | ||    |  |||  | || |||  || |  | ||||  |      
ttttctatcttctatgatcacctgc---atttctcttgttttggttagatgttaatc-tccttagtgtgatttattaacttggtactattgattttgatatcagCTAGGAAGCTTTTTGCTTTTTGTTTTCGTCTTTGCGCGTGTCCCATTCTCTTCTCCAAAGTTCC-CTATA---ATAGTGAAAGCTCATC--AAGTTATTTAGCTCT------
















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|192331108|gb|FK020328.1|FK020328
EST:     GAACCTCACTCGCTACCATTCGATTACAACGTCTTCTGGTTCTT                         TGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
genomic: GAACCTCACTCGCTACCATTCGATTACAACGTCTTCTGGTTCTTgtaagcccct ... tttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
EST: gi|192305965|gb|FG993611.1|FG993611
EST:     CTCGCTACCATTCGATTACAACGTCTTCTGGTTCTT                         TGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
genomic: CTCGCTACCATTCGATTACAACGTCTTCTGGTTCTTgtaagcccct ... tttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
EST: gi|208280723|gb|GE075909.1|GE075909
EST:     AACAACGAACCTCACTCGCTACTATTCGATTACAACGTCTTCTGGTTCTT                         TGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
genomic: AACAACGAACCTCACTCGCTACCATTCGATTACAACGTCTTCTGGTTCTTgtaagcccct ... tttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
EST: gi|298186159|gb|HO036792.1|HO036792
EST:     AACGTCTTCTGGTTCTT                         TGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
genomic: AACGTCTTCTGGTTCTTgtaagcccct ... tttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
EST: gi|151410248|gb|EV280063.1|EV280063
EST:     GATTACAACGTCTTCTGGTTCTT                         TGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
genomic: GATTACAACGTCTTCTGGTTCTTgtaagcccct ... tttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
EST: gi|19938409|gb|BQ081706.1|BQ081706
EST:     CTCGCTACCATTCGATTACAACGTCTTCTGGTTCTT                         TGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
genomic: CTCGCTACCATTCGATTACAACGTCTTCTGGTTCTTgtaagcccct ... tttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
EST: gi|298183291|gb|HO028504.1|HO028504
EST:     GCTACCATTCGATTACAACGTCTTCTGGTTCTT                         TGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
genomic: GCTACCATTCGATTACAACGTCTTCTGGTTCTTgtaagcccct ... tttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
EST: gi|298199231|gb|HO042594.1|HO042594
EST:     AACAACGAACCTCACTCGCTACCATTCGATTACAACGTCTTCTGGTTCTT                         TGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
genomic: AACAACGAACCTCACTCGCTACCATTCGATTACAACGTCTTCTGGTTCTTgtaagcccct ... tttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
EST: gi|192311844|gb|FK004503.1|FK004503
EST:     AACAACGAACCTCACTCGCTACCATTCGATTACAACGTCTTCTGGTTCTT                         TGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
genomic: AACAACGAACCTCACTCGCTACCATTCGATTACAACGTCTTCTGGTTCTTgtaagcccct ... tttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
EST: gi|298171949|gb|HO021541.1|HO021541
EST:     ACCATTCGATTACAACGTCTTCTGGTTCTT                         TGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
genomic: ACCATTCGATTACAACGTCTTCTGGTTCTTgtaagcccct ... tttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
EST: gi|192302748|gb|FG993768.1|FG993768
EST:     AACAACGAACCTCGCTCGCTACCATTCGATTACAACGTCTTCTGGTTCTT                         TGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
genomic: AACAACGAACCTCACTCGCTACCATTCGATTACAACGTCTTCTGGTTCTTgtaagcccct ... tttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
EST: gi|209699913|gb|BW661169.1|BW661169
EST:     AACGAACCTCACTCGCTACCATTCGATTACAACGTCTTCTGGTTCTT                         TGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
genomic: AACGAACCTCACTCGCTACCATTCGATTACAACGTCTTCTGGTTCTTgtaagcccct ... tttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
EST: gi|192297217|gb|FG990593.1|FG990593
EST:     ACTCGCTACCATTCGATTACAACGTCTTCTGGTTCTT                         TGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
genomic: ACTCGCTACCATTCGATTACAACGTCTTCTGGTTCTTgtaagcccct ... tttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
EST: gi|19348590|gb|BM893122.1|BM893122
EST:     CGATTACAACGTCTTCTGGTTCTT                         TGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
genomic: CGATTACAACGTCTTCTGGTTCTTgtaagcccct ... tttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
EST: gi|19271212|gb|BM887468.1|BM887468
EST:     CATTCGATTACAACGTCTTCTGGTTCTT                         TGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
genomic: CATTCGATTACAACGTCTTCTGGTTCTTgtaagcccct ... tttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
EST: gi|192311843|gb|FK004502.1|FK004502
EST:     AACAACGAACCTCACTCGCTACCATTCGATTACAACGTCTTCTGGTTCTT                         TGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
genomic: AACAACGAACCTCACTCGCTACCATTCGATTACAACGTCTTCTGGTTCTTgtaagcccct ... tttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
EST: gi|9564690|gb|BE474199.1|BE474199
EST:     GTCTTCTGGTTCTT                         TGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
genomic: GTCTTCTGGTTCTTgtaagcccct ... tttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
EST: gi|14125451|gb|BG789889.1|BG789889
EST:     AACAACGAACCTCACTCGCTACCATTCGATTACAACGTCTTCTGGTTCTT                         TGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC
genomic: AACAACGAACCTCACTCGCTACCATTCGATTACAACGTCTTCTGGTTCTTgtaagcccct ... tttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatattagcagtggttaacatgctgagttttgggtcttgtgtttttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTCCTCCATCCCCACTGTGTGATCTGATCCTAAATCCTATAGCCATGACTAC
              ggttaac  putative branch site (score: 3)
                                    tcttgtgtttttcctt  putative PPT
                ttaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttgaaataatggtgtcaattgtcagatcccccttgtggtgttgtgatattagcagtggttaacatgctgagttttgggtcttgtgtttttccttcagTGAAGAAGAACCCTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTCCTCCATCCCCACTGTGTGATCTGATCCTAAATCCTATAGCCATGACTAC

-tgttgaa
- - - - - - tggtgtc
- - - - - - - - - - - - - - atccccc
- - - - - - - - - - - - - - - - - - - -ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - agtggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcttgtg