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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattggagttttggcctcgatgatttatttaatagaacatgtgtagtactttacctcgtttttgtactgaggatttgataggcttaacatcttccgtagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAACCAAGGTGTTGAAAAG

Basic information

species Glycine max
transcript GLYMA02G36530.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G36530.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g24650.1 (Oryza sativa), 3'ss of exon 6
ttattggagt--tttggcctcgatgatttatttaatagaacatgtgtagtact----ttacctcgtttttgtactgaggatttgataggcttaacatcttccgtagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAACCAAGGTGTTGAAAAG
     |||||  | | |    | | ||     |  |  |  ||  ||| | ||    | ||   ||| || |  |   | | |  |     || ||  ||    ||||  ||||||||||||| ||||| || ||||| || || |||||| |||||||||| ||||| |  |||||||| |||
--gagggagtaatattgtgatgcttatcctgcttctcaattatcagtaatgctaagatcacactgttcttatcgtccagttcttgt----ctatcactttgttcagGTGGACAACACTGATGCAGAAGGAAGGCTTACACTTGCTGATGCTTTGGTATATGCCTGTAAACTGGGTGTTGACAAG

upper sequence: GLYMA02G36530.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G178958_T01 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------------------------ttatt-ggagttttggcctcgatgatttatttaatagaacatgtgtagtactttacctcgtttttgtactgaggatttgataggcttaacatcttccgtagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAACCAAGGTGTTGAAAAG
                                                                             |  || ||| | | | | |  |  | | ||  |  | |     | |  | | |  |  |   |||  ||| |   |||| |    | ||| | || |  |||| || |||||||| || ||||| || || || || || |||||| |||| |||||||| ||||||||||||||||||
gtatgttttttttttccaacttgttataaatgaccagaacgtgcatgattcatgaagctttgttataagggatctgctcgttcggaatgtagtcttttagcagtcatagatcatagtccttctgctccatgtctgctagttttcactaaacttttgcttt-ttgaacgtatttc--agGTAAATAACACTGACGCAGAAGGAAGGCTAACACTTGCTGATGCTTTGGTCTATGCTTGCAACCAAGGTGTTGAAAAG

upper sequence: GLYMA02G36530.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G043893_T01 (Zea mays), 3'ss of exon 6
--------------ttattggagttttggcctcgatgatttatt-taatagaacatgtgtagtactttacctcgtttttgtactgaggatttgataggcttaacatcttccgtagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAACCAAGGTGTTGAAAAG
              ||   | |||   |   |  |  |    |  |  |    |   | | |||   | | | || |||||| | |    ||   |  | |     ||||   ||||  | ||||| ||||| || || || ||||| ||||| || ||| |||| ||||||||||||||||||||||| |||
gtacatattttctcttgcagtagtaacgcgtttcagaacccgtcattgtcctgctaatttcgtagcgttcattgtctttgtattcatatgttagcacacatg----cttcttcagGTAGATAACACGGATGCGGAGGGGAGGCTTACACTGGCTGACGCTTTGGTCTATGCTTGTAACCAAGGTGTTGACAAG

upper sequence: GLYMA02G36530.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G178958_T02 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------------------------ttatt-ggagttttggcctcgatgatttatttaatagaacatgtgtagtactttacctcgtttttgtactgaggatttgataggcttaacatcttccgtagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAACCAAGGTGTTGAAAAG----------------------
                                                                             |  || ||| | | | | |  |  | | ||  |  | |     | |  | | |  |  |   |||  ||| |   |||| |    | ||| | || |  |||| || |||||||| || ||||| || || || || || |||||| |||| |||||||| ||||||||||||||||||                      
gtatgttttttttttccaacttgttataaatgaccagaacgtgcatgattcatgaagctttgttataagggatctgctcgttcggaatgtagtcttttagcagtcatagatcatagtccttctgctccatgtctgctagttttcactaaacttttgcttt-ttgaacgtatttc--agGTAAATAACACTGACGCAGAAGGAAGGCTAACACTTGCTGATGCTTTGGTCTATGCTTGCAACCAAGGTGTTGAAAAGGTAATGAAGCTTCATTTGGAAG

upper sequence: GLYMA02G36530.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 6
ttattggagttttggcctcgatgatttatttaatagaacatgtgtagtactttacctcgttt-ttgtactgaggatttgataggcttaacatcttccgtagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAACCAAGGTGTTGAAAAG
 |||   |     |   || || ||  ||| |     | | |  | |  |||| | | |||  || |||     | |   |  |  |   ||     | |||| |||||||| |||||||||||| |||| || || ||||||||| | || |||||||| ||||| ||||| || |||
gtatcataacaccg-tttccat-atgaattcagcttcaaaaggttcgagctttccattgttagttttacgccaaactaattgtgggtggtatt----gcagGTCAACAACACCGATGCTGAAGGTCGACTAACACTTGCAGATGCTTTAGTTTATGCTTGCAACCAGGGTGTCGATAAG

upper sequence: GLYMA02G36530.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 7
ttattggagttttggcctcgatgatttatttaatagaacatgtgtagtactttacctcgtttttgtactgaggatttgataggcttaacatcttccgtagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAACCAAGGTGTTGAAAAG
             |     |||||||| ||       |   | || |  ||||  ||  ||||  ||   |    |   |       |     |  |||||| |||||||| |||||||||||| | || || || ||||||||||| || ||||||||||||||||| || || |||
-------------gtatctgatgattttttccccctca---gagttgagcttttactgtttttcctatgaaatgctaattgttggcgatggtgtgtgtagGTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAG

upper sequence: GLYMA02G36530.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv11s0037g00180.t01 (Vitis vinifera), 3'ss of exon 6
--ttattggagttttggcc-tcgatgatttatttaatagaacatgtgtagtactttacctcgtttttgtactgaggatttgataggcttaacatcttccgtagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAACCAAGGTGTTGAAAAG
  |   |   |||  | || | ||  |  |  || || | | ||||||  |  ||      |  ||  || || |   ||| | |     |  ||| | | |||| || ||||| ||||| || || ||||| || || ||||| ||| ||||||||||||||||||||||||| || |||
agtccattttgttaagtccatggagaaactgattgattgcatatgtgttatgtttatttatgaattcctaatgtg---ttgttggctcccatctctactgcagGTCAATAACACAGATGCAGAGGGCAGACTCACACTTGCAGACGCTTTGGTATATGCTTGTAACCAAGGTGTAGAGAAG

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|151406149|gb|EV275964.1|EV275964
EST:     GTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAG                         GTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTA
genomic: GTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAGgtgaggattt ... tcttccgtagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTA
EST: gi|192304831|gb|FG997041.1|FG997041
EST:     GTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAG                         GTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTA
genomic: GTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAGgtgaggattt ... tcttccgtagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTA
EST: gi|21677539|gb|BQ629890.1|BQ629890
EST:     GTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAG                         GTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTA
genomic: GTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAGgtgaggattt ... tcttccgtagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtactttacctcgtttttgtactgaggatttgataggcttaacatcttccgtagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAACCAAGGTGTTGAAAAG
                                     gcttaac  putative branch site (score: 3)
                                           catcttcc  CT-rich tract
              tttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattggagttttggcctcgatgatttatttaatagaacatgtgtagtactttacctcgtttttgtactgaggatttgataggcttaacatcttccgtagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAACCAAGGTGTTGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - -acatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tactgag