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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattctcacttttcacaacccaatcacatagcttgaaactagtttgcttgttattttacttgatggtttctctttgacattgttagGTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTACTGGAGAAACTACTTTGAGCAAACAGATGGTTTGGTTTGGGTGGTTGAC

Basic information

species Glycine max
transcript GLYMA11G07330.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G07330.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g22140.1 (Oryza sativa), 3'ss of exon 3
-gtaattctcacttt--tcacaac-ccaatcacatagcttgaaactagtttgcttgttatt-----ttacttgatggt-ttctctttgacattgt--tagGTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTACTGGAGAAACTACTTTGAGCAAACAGATGGTTTGGTTTGGGTGGTTGAC
  | ||  |  | |    || ||| | |  || |    ||  |  |   || |||     |     ||| |  ||  | ||   |||| ||||||   |||||  |  | || ||||||||| | || || ||||| || ||  ||||||||||||| || |||||||||||||| |||||  | |||||||||||||| 
actgatcattgcatcagccaaaacactaggcatagcaattccatttgtattacttcagggtggaaattaatgaataatgtttgttttgtcattgtggcagGTACTCATTGAACATATGGGATATCGGTGGACAGAAGACTATCCGATCTTACTGGAGGAATTACTTTGAGCAAACTGATGGACTAGTTTGGGTGGTTGAT

upper sequence: GLYMA11G07330.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G154890_T03 (Zea mays), 3'ss of exon 3
------gtaattctcacttttcacaacccaatcacatagcttgaaactagtttgct---tgttattttacttgatggttt---ctctttgacattgttagGTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTACTGGAGAAACTACTTTGAGCAAACAGATGGTTTGGTTTGGGTGGTTGAC
       ||| |  ||    |  |||  |   ||   |   |    |||  || ||    ||   | |  || |   |||    |  ||||   |  ||| ||  |  | || |||||||||||||| || ||||| ||||| || |||||||||||||||||||||||||| || ||||| || |||||||| ||||| 
cattttctaaataccagacattgcaaatctggcaaccacgctttttctatgttactgcaggtgggtctgattaactatttaaatttattgattatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTACTGGAGAAACTACTTTGAGCAGACTGATGGATTAGTTTGGGTTGTTGAT

upper sequence: GLYMA11G07330.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G18390.1 (Arabidopsis thaliana), 3'ss of exon 2
--------gtaattctcacttttcacaacccaat------caca--tagctt-gaaactagtttg--cttgttattttacttgatg-gtttctctttgacattgt-----tagGTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTACTGGAGAAACTACTTTGAGCAAACAGATGGTTTGGTTTGGGTGGTTGAC
         || |||||   | |   |      |      || |  | | || | || |   | |  | ||||||      ||||| |||| |  |  | | |||     ||||||||| |||||||||||||||||||| || || || || |||||||| || ||||| || ||||||||||| || ||||||||||||||||||||||| 
gtaaagctctatttctctgctcttgtagtttcgtgttcttcagagttggtttaggaatttcatcgaacatgttataggcaatgatgagtttgtggtgaataatgtgtgtgtagGTATACGCTAAATATATGGGATGTTGGTGGGCAAAAGACTATAAGATCGTATTGGAGGAATTACTTTGAGCAGACTGATGGTTTGGTTTGGGTGGTTGAT

upper sequence: GLYMA11G07330.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g01820.t01 (Vitis vinifera), 3'ss of exon 3
--gtaattctcacttttcacaacccaatcacatagcttgaaactagtttgcttgttattttactt-gatg-----gtttctctttgacat-----tgttagGTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTACTGGAGAAACTACTTTGAGCAAACAGATGGTTTGGTTTGGGTGGTTGAC
    || |   | |  | | |     |||     | || | ||   |||  | |  |||    |  || |      || |  ||||  ||     ||  |||||||| || ||||||||||||||||||||||| | ||| |||||||||||||||||||||||||| || ||||| ||||||||||| ||||| ||||| 
ttacaactgata-tgcttatagattgatcctgaggttttatacctatttattgggcattgggttgagacgctgaaattccattttggtatgaatctgacagGTATACTCTTAATATATGGGATGTTGGGGGCCAAAGAACCATAAGATCTTACTGGAGAAACTACTTCGAACAAACTGATGGTTTGGTATGGGTCGTTGAT

upper sequence: GLYMA11G07330.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S62_133V6.2 (Physcomitrella patens), 3'ss of exon 2
---------gtaattctcacttttcacaa------cccaatcacatagcttgaaactagtttgcttgttattttacttgatggtttctctttgacattgt--tagGTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTACTGGAGAAACTACTTTGAGCAAACAGATGGTTTGGTTTGGGTGGTTGAC
          | | | |  ||| | |||         | | | | | |||||||| |  || |  | |||||  |||  |    |||  | ||| ||||   ||| |    ||| || || |||||  |||| || || || ||  |  ||||||||||||||||||||| |||||||||||||||  |||| ||||| ||||| 
ggacctgttttcactattgcttgttacatggttctttcgagctctttgcttgaaatt--ttagtcttttattc-act--aaaacttccatatgaaattgaaatagTTTCCGCCTCAACATTTGGGACATTGGCGGGCAAAAGACTTTGCGATCTTACTGGAGAAACTACTATGAGCAAACAGATGGCATGGTATGGGTAGTTGAT

upper sequence: GLYMA11G07330.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ10782 (Selaginella moellendorffii), 3'ss of exon 2
gtaattctcacttttcacaacccaatcacatagcttgaaactagtttgcttgttattttacttgatggtttctctttgacattgttagGTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTACTGGAGAAACTACTTTGAGCAAACAGATGGTTTGGTTTGGGTGGTTGAC
                                    | || |  || ||  |   | || | |||| ||  ||| | |   |  | |||||||  ||||| || ||||||||||| ||||| |||||  | ||||| |||||||| || ||||  |||||||| |||||| |||| |||||||| |||
------------------------------------gtaagtgattcgc--gacctctttcgtgatcgtaactcatcgctttcttcagGTATAGGCTAAACATTTGGGATGTTGGTGGCCAAAAAACTCTGAGATCGTACTGGAGGAATTACTACGAGCAAACGGATGGTCTGGTGTGGGTGGTCGAC

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|192324311|gb|FK018287.1|FK018287
EST:     GTCATCAGTCCCACGCTCGGCTTCAACATCAAAACCATAACTTACCAAAA                         GTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTA
genomic: GTCATCAGTCCCACGCTCGGCTTCAACATCAAAACCATAACTTACCAAAAgtaattctca ... acattgttagGTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTA
EST: gi|192299303|gb|FG988703.1|FG988703
EST:     GTCATCAGTCCCACGCTCGGCTTCAACATCAAAACCATAACTTACCAAAA                         GTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTA
genomic: GTCATCAGTCCCACGCTCGGCTTCAACATCAAAACCATAACTTACCAAAAgtaattctca ... acattgttagGTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTA
EST: gi|151394539|gb|EV264410.1|EV264410
EST:     GTCATCAGTCCCACGCTCGGCTTCAACATCAAAACCATAACTTACCAAAA                         GTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTA
genomic: GTCATCAGTCCCACGCTCGGCTTCAACATCAAAACCATAACTTACCAAAAgtaattctca ... acattgttagGTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTA
EST: gi|298163052|gb|HO011785.1|HO011785
EST:     GTCATCAGTCCCACGCTCGGCTTCAACATCAAAACCATAACTTACCAAAA                         GTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTA
genomic: GTCATCAGTCCCACGCTCGGCTTCAACATCAAAACCATAACTTACCAAAAgtaattctca ... acattgttagGTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTA
EST: gi|192330133|gb|FK020493.1|FK020493
EST:     GTCATCAGTCCCACGCTCGGCTTCAGCATCAAAACCATAACTTACCAAAA                         GTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTA
genomic: GTCATCAGTCCCACGCTCGGCTTCAACATCAAAACCATAACTTACCAAAAgtaattctca ... acattgttagGTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTA
EST: gi|192313863|gb|FK010311.1|FK010311
EST:     GTCATCAGTCCCACGCTCGGCTTCAACATCAAAACCATAACTTACCAAAA                         GTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTA
genomic: GTCATCAGTCCCACGCTCGGCTTCAACATCAAAACCATAACTTACCAAAAgtaattctca ... acattgttagGTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTA
EST: gi|254337626|gb|GR849472.1|GR849472
EST:     GTCATCAGTCCCACGCTCGGCTTCAACATCAAAACCATAACTTACCAAAA                         GTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTA
genomic: GTCATCAGTCCCACGCTCGGCTTCAACATCAAAACCATAACTTACCAAAAgtaattctca ... acattgttagGTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTA
EST: gi|151393722|gb|EV263597.1|EV263597
EST:     GTCATCAGTCCCACGCTCGGCTTCAACATCAAAACCATAACTTACCAAAA                         GTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTA
genomic: GTCATCAGTCCCACGCTCGGCTTCAACATCAAAACCATAACTTACCAAAAgtaattctca ... acattgttagGTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgaaactagtttgcttgttattttacttgatggtttctctttgacattgttagGTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTACTGGAGAAACTACTTTGAGCAAACAGATGGTTTGGTTTGGGTGGTTGAC
                                        ctttgac  putative branch site (score: 4)
                ttgttattttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattctcacttttcacaacccaatcacatagcttgaaactagtttgcttgttattttacttgatggtttctctttgacattgttagGTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTACTGGAGAAACTACTTTGAGCAAACAGATGGTTTGGTTTGGGTGGTTGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG