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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatggaggaaaattctgtttacttttcatctatcatttgctatgtgccatccttgaatatgcattatgcatcctaattgcttggataattttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTATGTATATATGTTTTTGCATTTTGCTGGGTCTACATTGTAAGAATTATGGCAT

Basic information

species Glycine max
transcript GLYMA19G27160.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G27160.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
------------------------------------------aatggaggaaaattctgtttacttttcatctatcatttgctatgtgccatcc-ttgaatatgcattatg-catcctaattg----cttggataattttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTATGTATATATGTTTTTGCATTTTGCTGGGTCTACATTGTAAGAATTATGGCAT-
                                            | |   | |  | ||  || || |      | |||      ||||  | | ||||     | | |   || | | |       | |  |  || |||  |||||||||||||||||||||||| ||||||||| ||||| || ||| |||| ||  | || || ||||| || || ||||| |||||  | |  |||| |  || 
gtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTA-GAAATG

upper sequence: GLYMA19G27160.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G821611_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------aatggaggaaaattctgtttacttttcatctatcatttgctatgtgccatccttgaatatgcattatgc--atcctaattgcttggataattttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTATGTATATATGTTTTTGCATTTTGCTGGGTCTACATTGTAAGAATTATGGCAT
                                                                               |||   | |  | || |||     |    | ||||||  |        |   | | | |  ||| ||   | ||| ||       |||    ||| ||||||||||||||||||||||||  |||||||| ||||| || ||  | || ||  | ||||| ||||| || || ||||| ||  |  | |  ||||  ||  
gtaagttactcgagatgctagctgttttaatagcgtccttatattagaacaatcgcggtgtgcacatacacttgaattgatgtttggaggtactctttctgggtagattttcatttttttaagttgttgactaactttctattctgttaagcctgatcatcaacata----tttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGCCTCTATGTATTTGCCTTCTGTTGGGTGTATGTGATCAAGATTAGAGCTG

upper sequence: GLYMA19G27160.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G068657_T02 (Zea mays), 3'ss of exon 3
----------------------------------------------aatggag--gaaaattctgtttacttttcatctat-catttgctatgtgccatccttgaatatgcattatgcatcctaattgcttggataattttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTATGTATATATGTTTTTGCATTTTGCTGGGTCTACATTGTAAGAATTATGGCAT
                                              | | ||   || | ||     |||| ||  |   | |||||  | ||     |   | | | |  ||| ||  |    | ||       |  | ||| ||||||||||||||||||||||||  |||||||| | ||| || ||  | || ||  | ||||| ||||| || || ||||| ||  |  | |  ||||  ||| 
gtaagttacacaagattactaggtgtttcataggcgtcctcatattacttgaattgatatttagagctactatttctgggtacattttttttgaatgttgactaactttctattttg--ttaagactgaccatcaatgtatttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATCCTCGACAACATTGCTCTGCCTGTATGTATTTGCCTTCTGTTGGGTGTATGTGATCAAGATTAGAGCAG

upper sequence: GLYMA19G27160.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G41060.1 (Arabidopsis thaliana), 3'ss of exon 3
aatggaggaaaattct--gtttacttttcatctatcatttgctatgtgccatccttgaatatgcattatgcatcctaattgcttggataattttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTATGTATATATGTTTTTGCATTTTGCTGGGTCTACATTGTAAGAATTATGGCAT
      | ||  ||||  ||||    ||   || ||  ||  | | || ||||    | | |  || || ||||  | |  | | |  |||||     |||| | || ||||| ||||||||||||||||||||||| || || || || ||| ||||||| || || ||||| || ||||||||    |  || |  |  |
------gtaagtttctcggtttttcgttttcctgtccgttagtttctgacatc----agtctatataattcatctcattctccttgggaattt-----gcagAGAAACTATCGATTCTTCTTCATGTTTGTCTTCTCCACGACTCTTCTCTGTGTATATGTGTTCGCCTTTTGTTGTGTCTACATAAAGAAGATCAAAGAGT

upper sequence: GLYMA19G27160.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G26935.1 (Arabidopsis thaliana), 3'ss of exon 3
aatggaggaaaattctgtttacttttcatctatcatttgc-tatgtgccatccttgaatatgcattatgcatcctaattgcttggataattttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTATGTATATATGTTTTTGCATTTTGCTGGGTCTACATTGTAAGAATTATGGCAT
  |     ||||| |   | |       | ||   | | |  ||   ||||  ||   ||   ||    ||||  |  |  |  |||  || ||   |||| | || || || |||||||||||||| |||||||| || || || |||||||||||||| ||||| || ||||||||||| ||   ||  ||||||| ||
-gtaagtcaaaatccaactgatcccgtctttaagctatccacataaaccatagtttcctaaatat----catctca--tattctgatggttgtt---gcagAGGAACTACCGATTCTTCTTCATGTTCGTCTTCTCCACGACCCTTCTATGTATATATGTGTTTGCCTTCTGCTGGGTCTATATAAGAAAGATTATGGAAT

upper sequence: GLYMA19G27160.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 3
aatggaggaaaattctgtttacttttcatctatcat--ttgctatg-tgc-catccttgaatatgca--ttatgcat---cctaattgcttggataattttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTATGTATATATGTTTTTGCATTTTGCTGGGTCTACATTGTAAGAATTATGGCAT
            | | |||  | | |   | | |||  | |  ||| |||   | ||||||| ||      ||||||    || |   |||  | |||| |   |||||||||||||||| || |||||||||||||||||||| || || || || ||||||||||| ||||  || ||||||||||| |||   || || ||||  |
---------ttttccagttgtcatcttcaccaacatgataggaatgatgcatgtgcttgaatttgtgggcaatgcatgaatctgaacactttcacaattctgggtgcagCGTAATTATCGATTTTTCTTCATGTTTGTCTTCTCGACGACTCTTCTTTGTATATATGTGTTTGGGTTCTGCTGGGTCTATATTAAGAGGATCATGGATT

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|17518880|gb|BM187922.1|BM187922
EST:     TGGAACGGTTTGATCATCACTGTCCTTGGGTTGGGCAGTGTATTGGGCTG                         CGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTATGT
genomic: TGGAACGGTTTGATCATCACTGTCCTTGGGTTGGGCAGTGTATTGGGCTGgtaagttgga ... ttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTATGT
EST: gi|151412254|gb|EV282066.1|EV282066
EST:     TGGAACGGTTTGATCATCACTGTCCTTGGGTTGGGCAGTGTATTGGGCTG                         CGTAATTACCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTATGT
genomic: TGGAACGGTTTGATCATCACTGTCCTTGGGTTGGGCAGTGTATTGGGCTGgtaagttgga ... ttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccatccttgaatatgcattatgcatcctaattgcttggataattttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTATGTATATATGTTTTTGCATTTTGCTGGGTCTACATTGTAAGAATTATGGCAT
                         tcctaat  putative branch site (score: 2)
                                           ttttttat  putative PPT
                                   ttggataattttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatggaggaaaattctgtttacttttcatctatcatttgctatgtgccatccttgaatatgcattatgcatcctaattgcttggataattttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTATGTATATATGTTTTTGCATTTTGCTGGGTCTACATTGTAAGAATTATGGCAT

- tggagga
- - - - - - ttctgtt
- - - - - - - - - - - - - - - - - - -tgctatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgg