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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgcaacattttgtttaccttaagaactcttcattatctagtacttatctgttaaatgatggccatcatagtcacttgtatgaatttctttgtcaacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTCTGGGTATTTTAATTCAGAATTGGAGGAGTATGTGGAAATTCCCAGTGAC

Basic information

species Glycine max
transcript GLYMA09G40690.1
intron # 5
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 5
lower sequence: LOC_Os05g40420.1 (Oryza sativa), 3'ss of exon 6
-tttgcaacattttgtt-taccttaagaactcttcattatctagtactta-tctgttaaatgatggccatcatagtcacttgtatgaatttctttgtcaacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTCTGGGTATTTTAATTCAGAATTGGAGGAGTATGTGGAAATTCCCAGTGAC
  |  ||  |||      || ||||      |    | || |  | || | |||   || |  || ||| | |       || ||  | |  |||||   |||||| ||||| || || || || |||||||| ||||||||||||||||||||||| || ||  ||  |  |  ||| |||||||||||||| || ||||||
agtaacataattggaaaataacttatagttgcactgtaatttctttctaactctaccaatt--tgtccaactttacttactgaattgactcatttgttc-cagTGAAACTGTGAAGTTCGGCCATGTCACATTTTTCTGGAATGGAAACCGCTCTGGATACTTCGATGAAACAAAGGAAGAGTATGTGGAAATCCCTAGTGAC

upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G003385_T02 (Zea mays), 3'ss of exon 6
------------tttgcaacattttgtttaccttaagaactcttcattatctagtacttatctgttaaatgatggccatcatagtcacttgtatgaatttctttgtcaacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTCTGGGTATTTTAATTCAGAATTGGAGGAGTATGTGGAAATTCCCAGTGAC
              || | |||  |  |      ||   |  ||| | || |  |  |  | | || | | ||| |    | | | | |||| ||             |||||||||| || |||||||| || |||||||| ||||||||||| |||||||| || || ||| ||  |     ||| |||||||| ||| |||| ||||||
gattgactcattgatgtatcatccttgtgcttgcaatggcatttcttcattttttcttcttatttttacttatg-ctgcaacattgatttgtgtg-----------tgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTCGGGATACTTTGATGAAACTAAGGAAGAGTATGTAGAAGTTCCTAGTGAC

upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 6
tttgcaacattttgtttaccttaagaactcttcattatctagtacttatctgttaaatgatggccatcatagtcacttgtatgaatttctttgt---caacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTCTGGGTATTTTAATTCAGAATTGGAGGAGTATGTGGAAATTCCCAGTGAC
    ||   || | |   ||||  |    |  ||| |||||    ||  ||  |   |      |    || | |         |||  |||||     |||||||||| ||||||||||| || |||||||| |||||||| || ||||| || || || ||| || ||     |||||||||||| ||| | || ||||||
---tcattgttgtatcatccttgtgcttgcaacatgatctacattttcccttctctctctctctctctctacttatgcagcaacattgttttgtgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTCGGGATACTTTGATGCAACTAAGGAGGAGTATGTAGAAGTACCTAGTGAC

upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------------------tttgcaacattttgtttacct-----taagaactcttcattatctagtacttatctgttaa------atgatggccatcatagtcacttgtatgaatttctttgtc---aacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTCTGGGTATTTTAATTCAGAATTGGAGGAGTATGTGGAAATTCCCAGTGAC
                                                    || | |   ||    || | |     | | |  |||  | |||    | | | | ||  ||      || | |       |  |||  | ||| ||| | | || |   ||||||||||| || || ||||| || ||||| ||||||||||||||||| || ||||| ||||| ||     |||||||||||||||| ||||| || ||||||
gtatttcaacttctgtccttttctcactttgagtaatggttatatgctttgtttagtatagttccagttgcttgctcattataggtctatactatgctttgcatttttgccaatagtgtatcacgcttgaactgatcatatatattaatgtatgtgactgaaacagTGAGACCGTCAAGTTTGGGCATGTCACCTTCTTCTGGAATGGAAATCGATCTGGATATTTCAACGAGAAATTGGAGGAGTATGTTGAAATCCCAAGTGAC

upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 4
tttgcaacattttgtttaccttaagaactcttcattatctagtacttatctgttaaatgatggccatcatagtcacttgtatgaatttctttgtc----aacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTCTGGGTATTTTAATTCAGAATTGGAGGAGTATGTGGAAATTCCCAGTGAC
 |  |    | ||| | |  |||   ||  || ||  |    ||| ||  |  | |||||   |     || | || | |   |||||  ||       |||||||||||||| || ||||| || || || |||||||||||||| ||||||||||| ||||| |||  | | || || ||||| || || ||||| ||||| 
ctcactttttcttgatgagatta--taccgttgatggttagttacata--taatgaatgaattctcagctattaacctattaaaattttatttcactgaaacagTGAGACTGTGAAGTTTGGCCATGTAACCTTCTTCTGGAATGGCAACCGCTCTGGATATTTCAATGAAAAGTTAGAAGAGTACGTTGAGATTCCAAGTGAT

upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 5
tttgcaacattttgtttaccttaagaactcttcattatctagtacttatctgttaaatgatggccatcatagtcacttgtatgaatttctttgtcaacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTCTGGGTATTTTAATTCAGAATTGGAGGAGTATGTGGAAATTCCCAGTGAC
   |    ||||  |      | | |  |  |  || |  | | |     | || |||      |      |||           ||  ||  | |||||||||||||| ||||||||||| || || || |||||||||||||| ||||| ||||||||| || ||    ||||||| ||||| |||||||||||||| 
gagggtttatttcatggttagtgataggttctttttcttcaattcaccagtttttaataccattctctgctgtctaactctctttttctttctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTCAGGGTATTTTGATCCAAGTATGGAGGAATATGTAGAAATTCCCAGTGAT

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|7925554|gb|AW831589.1|AW831589
EST:     ACTTCTGGTGAATATTTAGTGTATAATGGTATTCGGACTTTTGCTTGCAG                         TGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTC
genomic: ACTTCTGGTGAATATTTAGTGTATAATGGTATTCGGACTTTTGCTTGCAGgtagttgtct ... ttgtcaacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTC
EST: gi|33387910|gb|CA851117.1|CA851117
EST:     ACTTCTGGTGAATATTTAGTGTATAATGGTATTCGGACTTTTGCTTGCAG                         TGAGACTGTTAAATTTGGCCACGTCACATTCTTCTGGAATGGAAACCGCTC
genomic: ACTTCTGGTGAATATTTAGTGTATAATGGTATTCGGACTTTTGCTTGCAGgtagttgtct ... ttgtcaacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTC
EST: gi|298197962|gb|HO039501.1|HO039501
EST:     ACTTCTGGTGAATATTTAGTGTATAATGGTATTCGGACTTTTGCTTGCAG                         TGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTC
genomic: ACTTCTGGTGAATATTTAGTGTATAATGGTATTCGGACTTTTGCTTGCAGgtagttgtct ... ttgtcaacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTC
EST: gi|151401069|gb|EV270883.1|EV270883
EST:     ACTTCTGGTGAATATTTAGTGTATAATGGTATTCGGACTTTTGCTTGCAG                         TGAGACTGTTAAATTTGGTCACGTCACATTCCTCTGGAATGGAAACCGCTC
genomic: ACTTCTGGTGAATATTTAGTGTATAATGGTATTCGGACTTTTGCTTGCAGgtagttgtct ... ttgtcaacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTC
EST: gi|10845255|gb|BF068411.1|BF068411
EST:     ACTTCTGGTGAATATTTAGTGTATAATGGTATTCGGACTTTTGCTTGCAG                         TGAGACTGTTAAATTTGGCCACGTCACATTCTTCTGGAATGGAAACCGCTC
genomic: ACTTCTGGTGAATATTTAGTGTATAATGGTATTCGGACTTTTGCTTGCAGgtagttgtct ... ttgtcaacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTC
EST: gi|254344788|gb|GR855552.1|GR855552
EST:     ACTTCTGGTGAATATTTAGTGTATAATGGTATTCGGACTTTTGCTTGCAG                         TGAGACTGTTAAATTTGGCCACGTCACATTCTTCTGAAATGGAAACCGCTC
genomic: ACTTCTGGTGAATATTTAGTGTATAATGGTATTCGGACTTTTGCTTGCAGgtagttgtct ... ttgtcaacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTC
EST: gi|33390329|gb|CA853524.1|CA853524
EST:     ACTTCTGGTGAATATTTAGTGTATAATGGTATTCGGACTTTTGCTTGCAG                         TGAGACTGTTAAATTTGGCCACGTCACATTCTTCTGGAATGGAAACCGCTC
genomic: ACTTCTGGTGAATATTTAGTGTATAATGGTATTCGGACTTTTGCTTGCAGgtagttgtct ... ttgtcaacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTC
EST: gi|10845312|gb|BF068459.1|BF068459
EST:     CGGACTTTTGCTTGCAG                         TGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTC
genomic: CGGACTTTTGCTTGCAGgtagttgtct ... ttgtcaacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTC
EST: gi|254346934|gb|GR856656.1|GR856656
EST:     ACTTCTGGTGAATATTTAGTGTATAATGGTATTCGGACTTTTGCTTGCAG                         TGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTC
genomic: ACTTCTGGTGAATATTTAGTGTATAATGGTATTCGGACTTTTGCTTGCAGgtagttgtct ... ttgtcaacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatctgttaaatgatggccatcatagtcacttgtatgaatttctttgtcaacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTCTGGGTATTTTAATTCAGAATTGGAGGAGTATGTGGAAATTCCCAGTGAC
                                        tttctttgtc  CT-rich tract
       ttaaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgcaacattttgtttaccttaagaactcttcattatctagtacttatctgttaaatgatggccatcatagtcacttgtatgaatttctttgtcaacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTCTGGGTATTTTAATTCAGAATTGGAGGAGTATGTGGAAATTCCCAGTGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- tgcaaca
- - - - - - - - - - - - - -ctcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - atgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatga