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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggctataaaagcctaaattcttagtggcttatttattattttctgttttccacttatatcattaatcacttgtaagagtttgaaattgtttcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTGAGGATACAACAAAAATTAACCTGGGCTCGGAATCAACGACAAGCTGGCC

Basic information

species Glycine max
transcript GLYMA14G36610.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G36610.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0067g00180.t01 (Vitis vinifera), 3'ss of exon 5
----ggctataaaagcctaaattcttagtggcttat--ttattattttctgttttccacttatatcattaatcacttgtaagagtttgaaattgtttcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTGAGGATACAACAAAAATTAACCTGGGCTCGGAATCAACGACAAGCTGGCC
       |  || || |   ||  | || | |||    || |  | || | | ||   | |  ||  | ||  | | ||||   |||    ||  |  ||||||||||| |||| || |||||||| |||||||||||  |||| ||||| ||| ||||| |    |||||  |  | ||||| |   ||||||||||||||||||
atctaatttcaatagtc---atcataagagacttgcagttctcctgttatatctttttccttcattttcaaggaat-gtaatgctttt--ctttatgtttctccagTACACAGTTAAGAACTTGCAGTTTGCTCTGACTGTTGAACCAGATAATGTGAGGGTGGGGCAAAAGCTGTCATGGGCACAACATCAACGACAAGCTGGCC
















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|254347199|gb|GR856869.1|GR856869
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|151407616|gb|EV277431.1|EV277431
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAACCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|27426743|gb|CA938263.1|CA938263
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAG
EST: gi|151406931|gb|EV276746.1|EV276746
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|58017863|gb|CX704605.1|CX704605
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|192331092|gb|FK020312.1|FK020312
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|254333893|gb|GR848811.1|GR848811
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|298171750|gb|HO021342.1|HO021342
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|209706271|gb|BW676286.1|BW676286
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|58020634|gb|CX707376.1|CX707376
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|58017298|gb|CX704040.1|CX704040
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|209706270|gb|BW676285.1|BW676285
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAG
EST: gi|254333892|gb|GR848810.1|GR848810
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACCATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|208118431|gb|GD918282.1|GD918282
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|254345800|gb|GR859447.1|GR859447
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|208037472|gb|GD833539.1|GD833539
EST:     TACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTCGCTCTGACACTTGAGCCAGACAATTTG
genomic: TACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|151411907|gb|EV281718.1|EV281718
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|208268931|gb|GE069800.1|GE069800
EST:     ACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTCGCTCTGACACTTGAGCCAGACAATTTG
genomic: ACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|58021215|gb|CX707957.1|CX707957
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|254322038|gb|GR837452.1|GR837452
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|151402755|gb|EV272568.1|EV272568
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|151406677|gb|EV276492.1|EV276492
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|254334579|gb|GR844364.1|GR844364
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|254335322|gb|GR846819.1|GR846819
EST:     AACACTCGCTTCATTACCAAAGTCAACTCCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: AACACTCGCTTCATTACCAAAGTCAACT-CGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|254335321|gb|GR846818.1|GR846818
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
EST: gi|254340015|gb|GR858140.1|GR858140
EST:     TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAG                         TACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG
genomic: TAACACTCGCTTCATTACCAAAGTCAACTCGAGTATACTGTGGCCATGAGgtaaaaatct ... tcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttccacttatatcattaatcacttgtaagagtttgaaattgtttcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTGAGGATACAACAAAAATTAACCTGGGCTCGGAATCAACGACAAGCTGGCC
              cattaat  putative branch site (score: 3)
                                        ttgtttcttctcc  putative PPT
      acttatatcattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggctataaaagcctaaattcttagtggcttatttattattttctgttttccacttatatcattaatcacttgtaagagtttgaaattgtttcttctccagTACTCAGTGAACAACTTGCAATTTGCTCTGACACTTGAGCCAGACAATTTGAGGATACAACAAAAATTAACCTGGGCTCGGAATCAACGACAAGCTGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - gcctaaa
- - - - - - - - - - - -gtggctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagtttg