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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgatttgcttttacacaagtgtcatgctgtaagtatgaccaagtcttgatatgttgcttgggtgcattctaagtggtttttatgtgttccttttgcagATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTGCTGTTCTTGTTTCGGATGATATTGAGGAAAAGTTGATAACCATGGACAC

Basic information

species Glycine max
transcript GLYMA10G40340.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G40340.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G14740.2 (Arabidopsis thaliana), 3'ss of exon 1
tgtgatttg--cttttacacaagtgtcatgctgtaagtatgaccaagtcttgatatgttgcttgggtgcattctaagtggtttttatgtgttccttttgcagATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTGCTGTTCTTGTTTCGGATGATATTGAGGAAAAGTTGATAACCATGGACAC
 ||  ||    || |||| |||  |   || |   | |     | | || |  || | |   |  |||   |    || ||| || | ||||  || || |||||| ||||| ||||||||||||||||| |||||||| || || |||||||||||||||||  | ||| || |||| |||   ||||| || ||||| ||
-gtacttcaatctcttactcaatcgatttgattcgattcgattcgattcct--tagggtttataagtgttgtt---gttgttgttgt-tgttg-ttgtgtagATTGTTTCTTCGCTTTGAAGGTATGGAACGCACAGAAAGCAGGTGCTTCTGCTGTTCTTGTAGCTGATAATGTTGATGAACCTTTGATTACAATGGATAC

upper sequence: GLYMA10G40340.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G14720.2 (Arabidopsis thaliana), 3'ss of exon 2
tgtgatttgcttttacacaagtgtcatgctgtaagtatgaccaagtcttgatatgttgcttgggtgcattctaagtggtttttatgtgttccttttgcagATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTGCTGTTCTTGTTTCGGATGATATTGAGGAAAAGTTGATAACCATGGACAC
                ||     || |    | | |  ||    || | |||  | | | |  | |  ||   | | ||  || |       || || |||||| ||||| ||||||||||||||||| |||||||| || || |||||||||||||||||  | ||| || |||| ||    ||||| || ||||| ||
--------------gtactttcatcttttcttcaat-cgatttcgt-tagattcgattccttagggtttttatacttgtggttgt-----tattgtgtagATTGTTTCTTCGCTTTGAAGGTATGGAACGCACAGAAAGCAGGTGCTTCTGCTGTTCTTGTAGCTGATAATGTTGATGAGCCTTTGATTACAATGGATAC

upper sequence: GLYMA10G40340.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 1
tgtgatttgcttttacacaagtgtcatgctgtaagtatgaccaagtcttgatatgttgcttgggtg--cattctaagtggtttttatgtgttccttt---tgcagATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTGCTGTTCTTGTTTCGGATGATATTGAGGAAAAGTTGATAACCATGGACAC
      ||| | |      |  |||      |   | | | |     |||  |     |  | |    | || |||  | |||  || | |  ||||   |||||||||||| ||||| || ||||| |||||||| ||||| || || |||||||| || |||||| | ||| | |||||||||    |||||||||||||| |
-----gttggtctcctgtgatagtctaagccttcatcttatctgtcattgccacacaacaggaggaacccttttaacagatttaaatatttgtctttctttgcagATTGCTTTTTTGCGTTAAAGGTTTGGAATGCCCAGAATGCAGGTGCTTCTGCAGTGCTTGTTGCAGATAACATTGAGGAACCACTGATAACCATGGACTC

upper sequence: GLYMA10G40340.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ30872 (Selaginella moellendorffii), 3'ss of exon 1
tgtgatttgcttttacacaagtgtcatgctgtaagtatgaccaag-tcttgatatgttgcttgggtgcattctaagtggtttttatgtgttccttttgcagATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTGCTGTTCTTGTTTCGGATGATATTGAGGAAAAGTTGATAACCATGGACAC
                                  ||  | ||| | |  |   || |||||  | |  ||||||       |  || |||||  | | ||||||| | ||| ||||||||||| ||||| ||||| || ||||||||  ||||||| || ||| |||||||||     ||     |||| ||||||||| |
----------------------------------gtgagcccacgattcttccattttgct--gctcaattcta------ctaaatttgttc--tctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTGCTGTACTGGTTGCGGATGATAGATCCGAGCCTCTGATCACCATGGACTC

upper sequence: GLYMA10G40340.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ22768 (Selaginella moellendorffii), 3'ss of exon 1
tgtgatttgcttttacacaagtgtcatgctgtaagtatgaccaagtcttgatatgttgcttgggtgcattctaagtggtttttatgtgttccttttgcagATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTGCTGTTCTTGTTTCGGATGATATTGAGGAAAAGTTGATAACCATGGACAC
                                                     ||       | | | ||         |  ||  | || || |  ||||||| | ||| ||||||||||| ||||| ||||| || ||||||||  ||||||| || ||| |||||||||     ||     |||| ||||||||| |
----------------------------------------------------gtgagctcacgattctttgctcacttctactaaatttttctctc-cagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTGCTGTACTGGTTGCGGATGATAGAACCGAGCCTCTGATCACCATGGACTC

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|207715533|gb|GD696647.1|GD696647
EST:     CAAATCCAAACCCGGTGCTCTTCCCACTATCGTTT-GCTCGATCGAGGAA                         ATTGCTTCTTTGCTTT
genomic: CAAATCCAAACCCGGTGCTCTTCCCACTATCGTTTTGCTCGATCGAGGAAgtaagattcc ... ccttttgcagATTGCTTCTTTGCTTT
EST: gi|16997121|gb|BM086493.1|BM086493
EST:     CAAATCCAAACCCGGTGCTCTTCCCACTATCGTTTTGCTCGATCGAGGAA                         ATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTG
genomic: CAAATCCAAACCCGGTGCTCTTCCCACTATCGTTTTGCTCGATCGAGGAAgtaagattcc ... ccttttgcagATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTG
EST: gi|193441370|gb|FK404577.1|FK404577
EST:     CAAATCCAAACCCGGTGCTCTTCCCACTATCGTTTTGCTCGATCGAGGAAAA                        
genomic: CAAATCCAAACCCGGTGCTCTTCCCACTATCGTTTTGCTCGATCGAGG--AAgtaagattcc ... ccttttgca
EST: gi|208280650|gb|GE080974.1|GE080974
EST:     CAAATCCAAACCCGGTGCTCTTCCCACTATCGTTTTGCTCGATCGAGGAA                         ATTGCTTCTTT
genomic: CAAATCCAAACCCGGTGCTCTTCCCACTATCGTTTTGCTCGATCGAGGAAgtaagattcc ... ccttttgcagATTGCTTCTTT
EST: gi|6916299|gb|AW397829.1|AW397829
EST:     CAAATCCAAACCCGGTGCTCTTCCCACTATCGTTTTGCTCGATCGAGGAA                         ATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTG
genomic: CAAATCCAAACCCGGTGCTCTTCCCACTATCGTTTTGCTCGATCGAGGAAgtaagattcc ... ccttttgcagATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTG
EST: gi|208155166|gb|GD957087.1|GD957087
EST:     CAAATCCAAACCCGGTGCTCTTCCCACTATCGTTTTGCTCGATCGAGGAA                         ATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTG
genomic: CAAATCCAAACCCGGTGCTCTTCCCACTATCGTTTTGCTCGATCGAGGAAgtaagattcc ... ccttttgcagATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTG
EST: gi|207819682|gb|GD791282.1|GD791282
EST:     CAAATCCAAACCCGGTGCTCTTCCCACTATCGTTTTGCTCGATCGAGGAA                         ATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAAGAAGGCTGGAGCTTCT
genomic: CAAATCCAAACCCGGTGCTCTTCCCACTATCGTTTTGCTCGATCGAGGAAgtaagattcc ... ccttttgcagATTGCTTCTTTGCTTTGAAGGTATGGAATGCACA-GAAGGCTGGAGCTTCT
EST: gi|193670205|gb|FK613211.1|FK613211
EST:     CAAATCCAAACCCGGTGTTCTTCCCACTATCGTTTTGCTCGATCGAGGAA                         ATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTG
genomic: CAAATCCAAACCCGGTGCTCTTCCCACTATCGTTTTGCTCGATCGAGGAAgtaagattcc ... ccttttgcagATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTG
EST: gi|207811527|gb|GD785226.1|GD785226
EST:     CAAATCCAAACCCGGTGCTCTTCCCACTATCGTTTTACTCGATCGAGGAA                         ATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTG
genomic: CAAATCCAAACCCGGTGCTCTTCCCACTATCGTTTTGCTCGATCGAGGAAgtaagattcc ... ccttttgcagATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgatatgttgcttgggtgcattctaagtggtttttatgtgttccttttgcagATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTGCTGTTCTTGTTTCGGATGATATTGAGGAAAAGTTGATAACCATGGACAC
 tcttgat  putative branch site (score: 4)
                                         tgttcctttt  putative PPT
                                 tttttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgatttgcttttacacaagtgtcatgctgtaagtatgaccaagtcttgatatgttgcttgggtgcattctaagtggtttttatgtgttccttttgcagATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTGCTGTTCTTGTTTCGGATGATATTGAGGAAAAGTTGATAACCATGGACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- tgatttg
- - - - - - - - - - - -tcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcattct