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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtttccttgataagtgtcctcagggtcttagttagaatttgactaatttgttttccttgggtacaataatttaatactataaatccttgttcaaacagGTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCGCCATATTACAGCGAGTTATCTGAGAAATACACATCTATGATGTTCTTGT

Basic information

species Glycine max
transcript GLYMA09G40970.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G40970.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g07376.1 (Oryza sativa), 3'ss of exon 3
ttgtttccttgataagtgtcctcagggtcttagttagaatttgactaatttgttttccttgggtacaata-atttaatactataaatccttgttcaa---acagGTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCGCCATATTACAGCGAGTTATCTGAGAAATACACATCTATGATGTTCTTGT
|||   |||  ||| || | ||         ||| ||||  ||     ||| | ||||     ||||||  | |  | |  |  |||   ||  | |     ||||||||||||||||||||||  |||||||||| || ||     | ||||| ||    ||    ||| | ||  ||| |||| |     | ||||||||| 
ttgcg-cctgcatatgttttcttcttaatgaagtaagaaagtgtgatctttatgttccc---atacaatgtactataaataaagaattggtggaccatttgtagGTGATTGCAAATTTCAGTGCTGCATGGTGTGGACCATGCCGTGTCATTGCACCTGTATATGCTGAGATGTCACAGACATACCCCCAGTTCATGTTCTTGA

upper sequence: GLYMA09G40970.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G08710.1 (Arabidopsis thaliana), 3'ss of exon 3
---ttgtttccttgataagtgtcctcagggtcttagttagaatttgactaatttgttttccttgggtacaataatttaatactataaatccttgttcaaacagGTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCGCCATATTACAGCGAGTTATCTGAGAAATACACATCTATGATGTTCTTGT
    | ||||| |  |   | |        ||| |  |||  ||    |  ||| |    ||   |          |||||   |   | ||  || ||||||||| ||||||| |||||||| |||||||||||||| ||||| ||  | || |||| || || |||| | || |||||| |  | ||| | |||||| |  
gtaatttttccctttttgatatttctcttctctcatgtagtgttgtgtttgtttctcaatctcatgc---------taatatcttctcttctc-ttgaaacagGTGGTTGCAAACTTCAGTGCGACATGGTGTGGTCCGTGTAAAATTGTGGCACCATTTTTCATCGAGCTCTCAGAGAAACATTCTTCTCTTATGTTCCTTC

upper sequence: GLYMA09G40970.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0040g00020.t01 (Vitis vinifera), 3'ss of exon 3
ttgtttccttgataagtgtcctcagggtcttagttagaatttgactaatttgttttccttgg--gtacaataattt---aat----acta--taaatccttgt-tcaaacagGTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCGCCATATTACAGCGAGTTATCTGAGAAATACACATCTATGATGTTCTTGT
     | |||||  | |        | ||||  ||  ||||||| | || || |    |  |  |||||||| |||   |||    ||||  |  | |    | |   |||||||||||||||||| |||||||||||||||||||||||||| |||||||| ||||  ||| ||||  ||||||||  | || | ||| |||||||  |  
-----tgcttgaggaatt-------gctcttcattgcaatttgatttatctggtgagttcagttgtacaatatttttccaattttcactaattggagctgcatattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCACCATTCTACTGCGAACTATCTGAGGCACACCCTTCTCTGATGTTTCTAA

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|15201232|gb|BI424764.1|BI424764
EST:     AAGAAGCGTGGGACCAATCTTTGGAAGAAGCAAGGAGGGGTGGCAAAATT                         GTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCG
genomic: AAGAAGCGTGGGACCAATCTTTGGAAGAAGCAAGGAGGGGTGGCAAAATTgttagttttc ... gttcaaacagGTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCG
EST: gi|15203337|gb|BI426105.1|BI426105
EST:     AAGAAGCGTGGGACCAATCTTTGGAAGAAGCAAGGAGGGGTGGCAAAATT                         GTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCG
genomic: AAGAAGCGTGGGACCAATCTTTGGAAGAAGCAAGGAGGGGTGGCAAAATTgttagttttc ... gttcaaacagGTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCG
EST: gi|13479405|gb|BG508748.1|BG508748
EST:     AAGAAGCGTGGGACCAATCTTTGGAAGAAGCAAGGAGGGGTGGCAAAATT                         GTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCG
genomic: AAGAAGCGTGGGACCAATCTTTGGAAGAAGCAAGGAGGGGTGGCAAAATTgttagttttc ... gttcaaacagGTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCG
EST: gi|7478449|gb|AW666269.1|AW666269
EST:     AAGAAGCGTGGGACCAATCTTTGGAAGAAGCAAGGAGGGGTGGCAAAATT                         GTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCG
genomic: AAGAAGCGTGGGACCAATCTTTGGAAGAAGCAAGGAGGGGTGGCAAAATTgttagttttc ... gttcaaacagGTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCG
EST: gi|21257008|gb|BQ453896.1|BQ453896
EST:     AAGAAGCGTGGGACCAATCTTTGGAAGAAGCAAGGAGGGGTGGCAAAATT                         GTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCG
genomic: AAGAAGCGTGGGACCAATCTTTGGAAGAAGCAAGGAGGGGTGGCAAAATTgttagttttc ... gttcaaacagGTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCG
EST: gi|13790090|gb|BG652681.1|BG652681
EST:     AAGAAGCGTGGGACCAATCTTTGGAAGAAGCAAGGAGGGGTGGCAAAATT                         GTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCG
genomic: AAGAAGCGTGGGACCAATCTTTGGAAGAAGCAAGGAGGGGTGGCAAAATTgttagttttc ... gttcaaacagGTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttgttttccttgggtacaataatttaatactataaatccttgttcaaacagGTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCGCCATATTACAGCGAGTTATCTGAGAAATACACATCTATGATGTTCTTGT
                         atttaat  putative branch site (score: 4)
                                        tccttgttc  putative PPT
                  tacaataatttaatac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtttccttgataagtgtcctcagggtcttagttagaatttgactaatttgttttccttgggtacaataatttaatactataaatccttgttcaaacagGTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCGCCATATTACAGCGAGTTATCTGAGAAATACACATCTATGATGTTCTTGT

-tgtttcc
- - - - - - - - tgtcctc