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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactaaatggttcaccgtgattttgggaatcgtgatctaattaaacttttatttactctcttattttgtctgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATTGAAGCAACAGTTGTGGCTTGCAAGGCAGCTGATGCTGCTGTGAAG

Basic information

species Glycine max
transcript GLYMA09G40690.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g60190.1 (Oryza sativa), 3'ss of exon 7
gtaactaaatggttcaccgtgattttgggaatcgtg-atctaattaaacttttatttactctcttattttgtctgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATTGAAGCAACAGTTGTGGCTTGCAAGGCAGCTGATGCTGCTGTGAAG
|||  ||| || |||  ||    |  |   |  ||    |||  |||| | ||  |||   | ||  ||  ||| ||    ||||||| |||||||| || |||||||||||||| || || || ||||| |||||||| || || || ||||||||||||||||| |  || || |||
gtaggtaattgtttcgtcggtgctcagatgactgtttgcctatataaaatgttgcttaaaatttttattactctttt----agGTACGTGTCAACCTGCCGAATGGTGACATGGTTGGTCACACTGGTGATATTGAAGCCACGGTAGTTGCTTGCAAGGCAGCTGACGAAGCCGTTAAG

upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g40420.1 (Oryza sativa), 3'ss of exon 7
gtaactaa--atggttcaccgtgattttgggaatcgtgatctaattaaacttttatttactctcttattttgtctgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATTGAAGCAACAGTTGTGGCTTGCAAGGCAGCTGATGCTGCTGTGAAG
||||  ||      ||    | || ||||  |    ||   ||| | |  |     | |   |||||   |     |  || |||| ||||| ||||| ||||||||||| |||||||| || || ||||||||||| || ||||| || |||||||| || |||||||  ||||| |||
gtaaaaaacagcacttgtgtgcgactttgataggtttg--ttaaattatttacccctaaaattcttaacattctgttcttacagGTCCGCGTTAACCTCCCAAATGGTGATATGGTGGGTCACACTGGTGACATTGAGGCCACAGTGGTTGCTTGCAAAGCTGCTGATGAGGCTGTCAAG

upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G003385_T02 (Zea mays), 3'ss of exon 7
gtaactaaatggttcaccgtgattttgggaatcgtgatctaattaaacttttatttactctcttattttgtctgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATTGAAGCAACAGTTGTGGCTTGCAAGGCAGCTGATGCTGCTGTGAAG
     |||||  ||    |  ||||     |  |   |||  ||    ||  ||||   ||||||   |     |  || ||||||| |||||||| ||||||||||||||||| || || || || || ||||| || || ||||| |||||||||||||||||||  ||||| |||
----gtaaataattt---gaaatttctattagaggagtct--tttggtttccattt---ctcttagcataatgttgttacagGTACGTGTCAACCTGCCAAATGGTGACATGGTTGGTCACACTGGGGATATTGAGGCTACCGTTGTTGCTTGCAAGGCAGCTGATGAAGCTGTTAAG

upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 7
gtaactaaatggttcaccgtgatt--ttgggaatcgtgatctaattaaacttttatttactctcttattttgtct---gttgt-atagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATTGAAGCAACAGTTGTGGCTTGCAAGGCAGCTGATGCTGCTGTGAAG
                  || | |  || | | |    ||   |  |  ||||   || | || ||  || | ||   ||||| | ||||||| |||||||| ||||||||||||||||| || || || ||||| ||||| || || || || |||||||||||||||||||  ||||| |||
------------------gtaaataatttgaagtttctattagagcactctttcggtttccctgttgcttagcctagcgttgttacagGTACGTGTCAACCTGCCAAATGGTGACATGGTTGGTCACACTGGTGATATTGAGGCCACCGTAGTTGCTTGCAAGGCAGCTGATGAAGCTGTTAAG

upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 5
gtaactaaatggttcaccgtgattttgggaatcgtgatctaattaaacttttatttactc--tcttattttgtctgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATTGAAGCAACAGTTGTGGCTTGCAAGGCAGCTGATGCTGCTGTGAAG
      |  ||  |   | |        | |||   | | | | ||||  ||   | ||   | |  |       | | |  |||| || || ||||| |||||||| || |||||||||||||| ||||| ||||||||||| ||||| || ||  | || ||||||  |||||||| |
---gtaaggtgtattctcttatcacattgtatc--aacccattaaaacaattggcttctgagtttggtgccaatggattttcagGTGCGTGTAAACCTGCCAAATGGAGATATGGTGGGGCATACTGGTGATATTGAAGCAACTGTTGTTGCCTGTGAAGCTGCTGATCGTGCTGTGAGG

upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 4
-----gtaactaaatggttcaccgtgattttgggaatcgtgatctaattaaacttttatttactctcttattttgt----ctgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATTGAAGCAACAGTTGTGGCTTGCAAGGCAGCTGATGCTGCTGTGAAG
      |   |  || ||      |||| ||   |      |||  |  |||     | | |   |||||| ||       || | |  |||| || || ||| |||||||||| || |||||||| ||||||||||| |||||||| || ||||| || ||| |||| ||||||  ||||||||||
gtgagatggatgcatagtc--ttatgatcttataatcgaacatcccaggaaataagcagtgatcatcttatgtttcaatattgattttcagGTGCGAGTTAACATTCCAAATGGAGATATGGTGGGTCATACAGGTGATATTGAAGCCACGGTTGTTGCATGCGAGGCTGCTGATCTTGCTGTGAAG

upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 6
gtaactaaatggttcaccgtg----attttgggaatcgtgatctaa-ttaaacttttatttactctcttattttgtctgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATTGAAGCAACAGTTGTGGCTTGCAAGGCAGCTGATGCTGCTGTGAAG
|||| ||   |  |   | |     ||||  |  | | || |  ||  | |||   |||||  | | || |    ||| |||| ||||| || || ||||| ||||||||||||||||||||||| || ||||| ||||| || ||| |||| ||||||||||| |||||||  ||||| |||
gtaattagtggacttggcatagggtatttgagacaacatggttcaagctgaacaaatatttgatttgtt-tcacatct-ttgtttagGTTCGTGTTAACCTACCAAATGGTGACATGGTGGGGCACACTGGTGATATTGAGGCTACAATTGTAGCTTGCAAGGCTGCTGATGAAGCTGTCAAG

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|6134275|gb|AW132668.1|AW132668
EST:     AGGGATGCTATTCTTAGCGGGAAATTTGATCAG                         GTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
genomic: AGGGATGCTATTCTTAGCGGGAAATTTGATCAGgtaactaaat ... tgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
EST: gi|17964652|gb|BM271384.1|BM271384
EST:     AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAG                         GTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
genomic: AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAGgtaactaaat ... tgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
EST: gi|7925554|gb|AW831589.1|AW831589
EST:     AGATTGCTGAAAAGGCTANGGATGCTATTCTTAGCGGGAAATNTGATCAG                         GTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
genomic: AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAGgtaactaaat ... tgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
EST: gi|33387910|gb|CA851117.1|CA851117
EST:     AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAG                         GTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
genomic: AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAGgtaactaaat ... tgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
EST: gi|254346935|gb|GR856657.1|GR856657
EST:     AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAG                         GTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
genomic: AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAGgtaactaaat ... tgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
EST: gi|151401069|gb|EV270883.1|EV270883
EST:     AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAG                         GTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
genomic: AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAGgtaactaaat ... tgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
EST: gi|254346385|gb|GR856107.1|GR856107
EST:     AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAG                         GTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
genomic: AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAGgtaactaaat ... tgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
EST: gi|10845255|gb|BF068411.1|BF068411
EST:     AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAG                         GTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
genomic: AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAGgtaactaaat ... tgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
EST: gi|17401042|gb|BM177824.1|BM177824
EST:     CTGAAAAGGCTAGGGATGCTATTCTTAGCGAGAAATTTGATCAG                         GTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
genomic: CTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAGgtaactaaat ... tgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
EST: gi|298181410|gb|HO022849.1|HO022849
EST:     AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAG                         GTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAAGTGACATT
genomic: AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAGgtaactaaat ... tgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
EST: gi|254321595|gb|GR824912.1|GR824912
EST:     AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAG                         GTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
genomic: AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAGgtaactaaat ... tgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
EST: gi|254344788|gb|GR855552.1|GR855552
EST:     AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAG                         GTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
genomic: AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAGgtaactaaat ... tgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
EST: gi|10845312|gb|BF068459.1|BF068459
EST:     AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAG                         GTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
genomic: AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAGgtaactaaat ... tgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
EST: gi|254346934|gb|GR856656.1|GR856656
EST:     AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAG                         GTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT
genomic: AGATTGCTGAAAAGGCTAGGGATGCTATTCTTAGCGGGAAATTTGATCAGgtaactaaat ... tgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaatcgtgatctaattaaacttttatttactctcttattttgtctgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATTGAAGCAACAGTTGTGGCTTGCAAGGCAGCTGATGCTGCTGTGAAG
         atctaat  putative branch site (score: 3)
                              ctctcttattttgtct  putative PPT
            taattaaacttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactaaatggttcaccgtgattttgggaatcgtgatctaattaaacttttatttactctcttattttgtctgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATTGAAGCAACAGTTGTGGCTTGCAAGGCAGCTGATGCTGCTGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT