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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgatagtactgccgaaatctatagatgtcttggaattatatgcactaattttagttctgctttggtacttctagtaggtatttacattttgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCCATCATGACATTGCTAATGAAATTCCAATTCATCTTCAAAAATTGCAATA

Basic information

species Glycine max
transcript GLYMA07G31090.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G31090.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 5
atgatagtactgccgaaatctatagatgtcttggaatta-tatgca-ctaattttagttctgctttggtacttctagtaggtatttacattttgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCCATCATGACATTGCTAATGAAATTCCAATTCATCTTCAAAAATTGCAATA
 ||    |  |   |||   |||   |  | ||   ||| |||  | || |||||  ||| |   | |     ||  ||  | ||   ||||||||| |||||||| |||||  |||||||||| |||||||| |||||| | ||| | ||||||||||| ||  | ||||| || || | ||| ||||||| | |||||||
ctgggccttgtcatgaagattatttgttccatgtttttaatataaagctcattttgtttcagaggttgctaagct--tacattttattattttgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA

upper sequence: GLYMA07G31090.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G448715_T01 (Zea mays), 3'ss of exon 5
atgatagtactgccgaaatctatagatgtcttggaattatatgcactaattttagttctgctttggtacttcta-gtaggtattt-acattttgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCCATCATGACATTGCTAATGAAATTCCAATTCATCTTCAAAAATTGCAATA
   |  | | || |   |    ||  |   |     || |    |  || || | ||    |       ||||| |     |||| |   ||||||| |||||||| |||||  |||||||||| |||||||| |||||| | ||| | ||||||||||| ||    ||||| || || | ||| ||||||| | |||||||
--cagggcattggcatgaaaattattttgatccatgtttttaagataaagttcattttgtttcacaagtttctaagcttacatttcattatttgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCCATCATGATATCATCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA

upper sequence: GLYMA07G31090.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 5
atgatagtactgccgaaatctatagatgtcttggaattatatgcactaattttagttctgctttggtacttctagtaggtatttac-attttgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCCATCATGACATTGCTAATGAAATTCCAATTCATCTTCAAAAATTGCAATA
 | |||  | |   ||  | |  |  |  ||   |  |  |  |||     |||||| | |  ||  | ||    |     ||| | | |||||||| ||||||||||||||||||||||||| |||||||| || || |||||||| ||||||||||| ||||| |||||||| || |||||||| ||||| ||||| ||
ctaataacattatggacttattcaatttcctcaaacctccaaacaccc-cattagtttttccatgcaatttacgtttcaagttttctactttgttttccagCTGGAATTGTTCTTGAGGAGAAAAATTGGCCACCATTCTTCCCAATTATCCATCATGATATTGCGAATGAAATACCGATTCATCTACAAAAGTTGCAGTA

upper sequence: GLYMA07G31090.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ28229 (Selaginella moellendorffii), 3'ss of exon 4
atgatagtactgccgaaatctatagatgtcttggaattatatgcactaattttagttctgctttggtacttctagtaggtatttacattttgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCCATCATGACATTGCTAATGAAATTCCAATTCATCTTCAAAAATTGCAATA
                                              |||  |  || | | |||  ||  |||   | | ||  |||  ||  | ||||||||||||  |||| ||||||||||| ||||| || |||||||| || ||||  |||||||||  |   || |||||| | |||||||||    | || ||
---------------------------------------------gtaagct--gtccagatttattatgtcttcgatg-ataaacaagtt--tatgcagCTGGAATCTTTCTAGAGGAGAAGAACTGGCCTCCCTTTTTCCCGATCATCCGCCATGACATTCGTCGCGACATTCCATTGCATCTTCAACGCCTACAGTA

upper sequence: GLYMA07G31090.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ29726 (Selaginella moellendorffii), 3'ss of exon 1
--------------------------------------------atgatagtactgc--cgaaatctatagatgtcttggaattata---tgcactaatttta--gttctgctttggtacttctagtaggtatttacattttgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCCATCATGACATTGCTAATGAAATTCCAATTCATCTTCAAAAATTGCAATA
                                            ||| |     ||   |   | ||    | |   |||||  | |   ||| | |  |     || | | |||  ||  ||| | | | ||  |||  ||  | ||||||||||||  |||| ||||||||||| ||||| || |||||||| || ||||  |||||||||  |   || |||||| | |||||||||           
gtagtcctctgttggaaatttttttcttccctccttaaagagaaatgcttactttgtttcaggagctgcgaaagc--tggaagcacaagctgcgcgaggtaagctgtccagatttattatgtcttggatg-ataaacaagTT--TATGCAGCTGGAATCTTTCTAGAGGAGAAGAACTGGCCTCCCTTTTTCCCGATCATCCGCCATGACATTCGTCGCGACATTCCATTGCATCTTCAACG---------

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|20812614|gb|BQ297092.1|BQ297092
EST:     GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAG                         CTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
genomic: GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAGgtgatttaca ... tgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
EST: gi|192297701|gb|FG989591.1|FG989591
EST:     GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAG                         CTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
genomic: GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAGgtgatttaca ... tgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
EST: gi|7146910|gb|AW508832.1|AW508832
EST:     GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAG                         CTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTGTTCCCAATAATCC
genomic: GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAGgtgatttaca ... tgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
EST: gi|19453024|gb|BM954434.1|BM954434
EST:     GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAG                         CTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
genomic: GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAGgtgatttaca ... tgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
EST: gi|9259727|gb|BE347874.1|BE347874
EST:     GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAG                         CTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
genomic: GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAGgtgatttaca ... tgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
EST: gi|19934355|gb|BQ079383.1|BQ079383
EST:     GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAG                         CTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
genomic: GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAGgtgatttaca ... tgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
EST: gi|42722448|gb|CK768347.1|CK768347
EST:     GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAG                         CTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
genomic: GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAGgtgatttaca ... tgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
EST: gi|16996884|gb|BM086256.1|BM086256
EST:     GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAG                         CTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
genomic: GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAGgtgatttaca ... tgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
EST: gi|13311994|gb|BG405645.1|BG405645
EST:     CAGGAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAG                         CTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
genomic: CAGGAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAGgtgatttaca ... tgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
EST: gi|151409246|gb|EV279054.1|EV279054
EST:     GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAG                         CTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
genomic: GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAGgtgatttaca ... tgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
EST: gi|254315266|gb|GR830259.1|GR830259
EST:     GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAG                         CTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC
genomic: GAAGTGAGACGGAAAGAAGAAGCTGCTTCACGAGgtgatttaca ... tgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaattttagttctgctttggtacttctagtaggtatttacattttgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCCATCATGACATTGCTAATGAAATTCCAATTCATCTTCAAAAATTGCAATA
 cactaat  putative branch site (score: 2)
                                          ttttgtttt  putative PPT
                                  tatttacattttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgatagtactgccgaaatctatagatgtcttggaattatatgcactaattttagttctgctttggtacttctagtaggtatttacattttgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCCATCATGACATTGCTAATGAAATTCCAATTCATCTTCAAAAATTGCAATA

- - - -tactgcc
- - - - - - - - - - - - - tgtcttg
- - - - - - - - - - - - - - - - - - - -tatgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttctag