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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcaagtgctgtattaatcttatatctccttcaacataattaccacatattgatgataatatataaagtaatgagttgaaatgaaattggtgatgtgtagGGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTTAGCTGTACAAAAGAGCGTCGGAGAAGAGAACGAGAAGAACAGCAGCAGC

Basic information

species Glycine max
transcript GLYMA03G31530.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G31530.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G138268_T01 (Zea mays), 3'ss of exon 1
----ttcaagtgctgtat-taatcttatatctccttcaacataattaccacatattgatgataatatataaagtaatgagttgaaatgaaattggtgatgtgtagGGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTTAGCTGTACAAAAGAGCGTCGGAGAAGAGAACGAGAAGAACAGCAGCAGC
     || | ||||| || |      |  ||||  ||     |  ||||   | |   |  | |  | | |   |  ||| |  | || |  |    |  || ||||| |||||||| || |||||||| || ||||| ||||||||||||||  |  | || ||      |   || |  |    ||  ||   |  ||    |
ataaatctaatgctggatctggatggacgtctcagtct---catctaccgtgtgtacgttttgagttttgacagagggaggtatattgtatatac--acctgcagGGCTCAGGTGGTGGGATGGCCACCGGTCCGGTCGTTCCGGAAGAACATCATGTCCGTGCAGTCCGACAAGGGCGCCGCCGCCGCCAACGGCGACAAGTCC

upper sequence: GLYMA03G31530.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0141g00290.t01 (Vitis vinifera), 3'ss of exon 1
-ttcaagtgctgtattaatcttatatctccttcaacataattaccaca--tattgatgataatatataaagtaatgagttgaaatgaaattggtgatgtgtagGGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTTAGCTGTACAAAAGAGCGTCGGAGAAGAGAACGAGAAGAACAGCAGCAGC
 ||    || |  |   |  |  | ||    | ||   | | || | |   ||  || | |||| |  | || |  | || |   ||||||||  |  | |||||||||||| || || |||||||| || ||||||||||||||||||||||| || |  || ||| ||| | | || ||    ||||||   ||| ||| |
tttttcctgttaaaaacagttgttctcataataaagtcattaactaaaaccatacataaaaataaagcaggtgaataattcatg-gaaattgg--aattttagGGCACAGGTTGTGGGGTGGCCACCGGTTCGGTCCTTCCGGAAGAACATGTTGGCCGGGCAGAAGGGCGGCAGCGAGGAAGGGGAGAAGGTGAGCTGCAAC
















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|213593271|gb|DB966096.1|DB966096
EST:     CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCCAA                         GGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttaat ... tgatgtgtagGGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|193488445|gb|FK457584.1|FK457584
EST:     AAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAAGACCAAA                         GGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGT
genomic: AAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCC-AG-CC-AAgtaagttaat ... tgatgtgtagGGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGT
EST: gi|151394543|gb|EV264414.1|EV264414
EST:     CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCCAA                         GGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttaat ... tgatgtgtagGGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|9987128|gb|BE661236.1|BE661236
EST:     CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCCAA                         GGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttaat ... tgatgtgtagGGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|193380966|gb|FK348825.1|FK348825
EST:     CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCCAA                         GGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttaat ... tgatgtgtagGGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|207807742|gb|GD778091.1|GD778091
EST:     CCTGCTAAGCCTCCAGCCAA                         GGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTGCTAAGCCTCCAGCCAAgtaagttaat ... tgatgtgtagGGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|207713784|gb|GD694899.1|GD694899
EST:     CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCGAA                         GGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttaat ... tgatgtgtagGGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|209699149|gb|BW652892.1|BW652892
EST:     CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCCAA                         GGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttaat ... tgatgtgtagGGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|10709892|gb|BF009616.1|BF009616
EST:     CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCCAA                         GGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttaat ... tgatgtgtagGGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|151406946|gb|EV276761.1|EV276761
EST:     CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCCAA                         GGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttaat ... tgatgtgtagGGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|14125492|gb|BG789930.1|BG789930
EST:     CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCCAA                         GGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttaat ... tgatgtgtagGGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
EST: gi|151394747|gb|EV264618.1|EV264618
EST:     CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCCAA                         GGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT
genomic: CCTAAGGAGAAGACTCTTCTGCCTGCAGATCCTGCTAAGCCTCCAGCCAAgtaagttaat ... tgatgtgtagGGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catattgatgataatatataaagtaatgagttgaaatgaaattggtgatgtgtagGGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTTAGCTGTACAAAAGAGCGTCGGAGAAGAGAACGAGAAGAACAGCAGCAGC
  tattgat  putative branch site (score: 3)
          ataatatataaagtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcaagtgctgtattaatcttatatctccttcaacataattaccacatattgatgataatatataaagtaatgagttgaaatgaaattggtgatgtgtagGGCACAGGTGGTAGGTTGGCCACCTGTGCGGTCCTTCCGGAAGAACATGTTAGCTGTACAAAAGAGCGTCGGAGAAGAGAACGAGAAGAACAGCAGCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - tgctgta
- - - - - - - - - - - - -ctccttc
- - - - - - - - - - - - - - - - - - - - - ccacata
- - - - - - - - - - - - - - - - - - - - - - - - - tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatgaaa