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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGACCTGCTGAATACAAGAGGTCTAGATTGCCTCGGAACCGCAGGACCGTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgctcaaaaagtctttagatgtttttgttgaaaattttcttagttgaagtaaatttacagccatttattcatggtatag

Basic information

species Glycine max
transcript GLYMA09G37360.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G37360.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os08g06040.1 (Oryza sativa), 5'ss of exon 3
TGAGACCTGCTGAATACAAGAGGTCTAGATTGCCTCGGAACCGCAGGACCGTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgctcaaaaagtctttagatgtttttgttgaaaattttcttagttgaagtaaatttacagccatttattcatggtatag
||||||||||||| ||||||||||| |||||| |  |||| ||||||||||| |||||  | ||||| |||||  | || ||    || || ||||| |||||       |||| |   |  |      ||| |||  |      | |||||  || ||   |   | || |   | | | |   
TGAGACCTGCTGAGTACAAGAGGTCCAGATTGTCAAGGAATCGCAGGACCGTGAACCGTCCTTACGGTGGTGTCCTGTCTGGTACTGCAGTCAGAGAGAGgtaaaccatccaaacacattacatgctcctttcttgcga------tcagttg--gtgaaccaat--ctatctgcacctcgcag--

upper sequence: GLYMA09G37360.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os08g33920.1 (Oryza sativa), 5'ss of exon 3
TGAGACCTGCTGAATACAAGAGGTCTAGATTGCCTCGGAACCGCAGGACCGTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgt----atgttgctcaaaaagtctttagatgtttttgttgaaaattttcttagttgaagtaa-atttacagccatttattcatggtatag
|||| |||||||| ||||||||||| || ||| || ||||||||||||| || |||||  | || || || ||  | || |||   || ||||| |||||||    |  |    | | |  |  | |  ||      || || || |   | || |   ||  |  | || |  |   |     |     
TGAGGCCTGCTGAGTACAAGAGGTCCAGGTTGTCTAGGAACCGCAGGACTGTGAACCGTCCATATGGTGGAGTGCTCTCTGGAACTGCAGTTAGGGAAAGgtcagtacataatgctagatattctgatgtgaaaactttcaagatctgtattgtggtcttattagctgcaactgtaactctgcag-----

upper sequence: GLYMA09G37360.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G032564_T01 (Zea mays), 5'ss of exon 3
TGAGACCTGCTGAATACAAGAGGTCTAGATTGCCTCGGAACCGCAGGACCGTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgctcaaaaagtctttagatgtttttgttgaaaattttcttagttgaagtaaatttacagccatttattcatggtatag
||||||||||||| ||||||||||| || ||| |  ||||||||||||| || |||||  | || || |||||| | || ||    || || ||||| ||||       ||         | |      |   ||||||   ||  | ||   | ||| |   | || || | |           
TGAGACCTGCTGAGTACAAGAGGTCCAGGTTGGCAAGGAACCGCAGGACTGTGAACCGTCCATATGGTGGTGTTCTGTCTGGTACCGCAGTGAGAGAGAGgtg-accattctttcgcaactcatgcccgtccattgaaatgattaatggtgatactaagtcacctgc-atgtctcag--------

upper sequence: GLYMA09G37360.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM5G820996_T01 (Zea mays), 5'ss of exon 3
TGAGACCTGCTGAATACAAGAGGTCTAGATTGCCTCGGAACCGCAGGACCGTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgctcaaaaagtctttagatgtttttgttgaaaatt---ttcttagttgaagtaaatttacagccatttattcatggtatag
|||||||||| || ||||||||||| || ||| || ||||||||||||| || |||||  | || || || ||  | || |||   |||||||| || ||||  ||   |  | | |     | ||  | ||||  ||        |||    |   ||||  |||    |   || ||   |||   
TGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAACCGCAGGACTGTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat--agaggcgggcatattgtgttgtgaaagcccaggatctgtcatcttgtaatcttatgagctactactctatgtag--

upper sequence: GLYMA09G37360.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv14s0108g00850.t01 (Vitis vinifera), 5'ss of exon 3
TGAGACCTGCTGAATACAAGAGGTCTAGATTGCCTCGGAACCGCAGGACCGTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgctcaaaaagtctttagatgtttttg--ttgaaaattttcttagttgaagtaaatttacagccatttattcatggtatag
          ||||||||||||||||||||||||  ||||||| ||||| || ||||| ||||| ||||||||||| || || || ||||| || || ||||||| | ||  ||| |  || |  | | |||   ||   || |    ||||||  ||   |    |   | || ||||        
----------TGAATACAAGAGGTCTAGATTGCCAAGGAACCGTAGGACTGTGAACCGGGCCTATGGAGGTGTTTTGTCGGGTGGTGCTGTCAGGGAGAGGTATGATCCTgtaaatgatttcaagtttatttcgtttcttaactgcactagttggggttt-tgattaataactttttcag-------

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|193405300|gb|FK371739.1|FK371739
EST:     GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAG                         GATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgct ... catggtatagGATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|5175487|gb|AI759820.1|AI759820
EST:     GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAG                         GATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgct ... catggtatagGATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|21600798|gb|BQ611129.1|BQ611129
EST:     GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAG                         GATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgct ... catggtatagGATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|31460083|gb|CD402111.1|CD402111
EST:     GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAG                         GATTATTCGTGCTTTCCTGGTTGAAGAGCATAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgct ... catggtatagGATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|33388640|gb|CA851847.1|CA851847
EST:     GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAG                         GATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgct ... catggtatagGATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|26059008|gb|CA801922.1|CA801922
EST:     GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAG                         GATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgct ... catggtatagGATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|41146454|gb|CK606665.1|CK606665
EST:     GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAG                         GATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgct ... catggtatagGATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|151395042|gb|EV264913.1|EV264913
EST:     GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAG                         GATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgct ... catggtatagGATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|192328957|gb|FK019684.1|FK019684
EST:     GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAG                         GATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgct ... catggtatagGATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|16104974|gb|BI892714.1|BI892714
EST:     GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAG                         GATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgct ... catggtatagGATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|192309351|gb|FK000559.1|FK000559
EST:     GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAG                         GATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgct ... catggtatagGATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|23732890|gb|BU764623.1|BU764623
EST:     GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAG                         GATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgct ... catggtatagGATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|254349282|gb|GR860080.1|GR860080
EST:     GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAG                         GATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgct ... catggtatagGATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|192328154|gb|FK020415.1|FK020415
EST:     GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAG                         GATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgct ... catggtatagGATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|193686812|gb|FK632477.1|FK632477
EST:     GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAG                         GATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgct ... catggtatagGATTATTCGTGCTTTCCTGGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGACCTGCTGAATACAAGAGGTCTAGATTGCCTCGGAACCGCAGGACCGTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgctcaaaaagtctttagatgtttttgttgaaaattttcttagttgaagtaaatttacagccatttattcatggtatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT