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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagtattccgaattcagagtcaatagaaataaaatcctttaactgcatttgtttggctgatttgtaagttttctgttactttttgttgaacatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATGCTATGACTATGTGCACGGCAAGAACAACTACTTTTTGTACCTCTTCCTT

Basic information

species Glycine max
transcript GLYMA17G05350.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G05350.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 8
ttagtattccgaattcagagtcaatagaaataaaatcctttaactgcatttgtttggctgatttgtaagttttctgttactttttgttgaacatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATGCTATGACTATGTGCACGGCAAGAACAACTACTTTTTGTACCTCTTCCTT
          | ||    | |   || | | ||||| || ||  ||   ||        |   |  |   |   ||  | | |  |||     ||  |||| |  ||  ||||||||||||||| || || ||| | ||| | || ||||||||||||| ||||||||| |||||||| |||||  | ||||| || |||
----------gtatgtttacttcctatatagaaaattctatatttgttattagaaactagggatacacactaaatg--attatgagttatttgtgt-cagATTGAATACATTGGAGCTTGGATTTGCGGCTTTCTTGTTCGTGTGCGGATGCTATGACTTTGTGCACGGGAAGAACAATTACTTCATCTACCTGTTTCTT
















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|193369498|gb|FK333974.1|FK333974
EST:     AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTCCCTTTGTGGATG
genomic: AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|298193613|gb|HO040261.1|HO040261
EST:     AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATCCGCTGCCTTCCTCTTCCTTTGTGGATG
genomic: AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|26056257|gb|CA799171.1|CA799171
EST:     AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
genomic: AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|207758279|gb|GD729739.1|GD729739
EST:     AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
genomic: AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|208229646|gb|GE026473.1|GE026473
EST:     AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCCTTGTGGATG
genomic: AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|208151943|gb|GD947872.1|GD947872
EST:     AAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
genomic: AAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|207804794|gb|GD778611.1|GD778611
EST:     AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
genomic: AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|208213146|gb|GE010553.1|GE010553
EST:     AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
genomic: AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|193563034|gb|FK520825.1|FK520825
EST:     AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
genomic: AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|208168934|gb|GD970507.1|GD970507
EST:     AGCAATGTCACCAAAGCAATCAGAAAATCTCGATACAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
genomic: AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|193549170|gb|FK510127.1|FK510127
EST:     CAATGTCACCAAAGCAATCAGAAAATCTCGATTACAAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
genomic: CAATGTCACCAAAGCAATCAGAAAATCTCGATT-CAAA-TTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|193630182|gb|FK585323.1|FK585323
EST:     AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
genomic: AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|298195915|gb|HO044306.1|HO044306
EST:     AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
genomic: AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|208317883|gb|GE117098.1|GE117098
EST:     GCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
genomic: GCAATGTCACCAAAGCAATCAGAAAATCTCGATTC-AAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|193698693|gb|FK635410.1|FK635410
EST:     AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGACTCGCTGCCTTCCTCTTCCTTTGTGGATG
genomic: AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|208252030|gb|GE046519.1|GE046519
EST:     AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
genomic: AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|193356210|gb|FK320515.1|FK320515
EST:     AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
genomic: AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|208087413|gb|GD886859.1|GD886859
EST:     AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
genomic: AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|207693852|gb|GD676365.1|GD676365
EST:     AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
genomic: AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|193721650|gb|FK661690.1|FK661690
EST:     AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
genomic: AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
EST: gi|208203438|gb|GD998822.1|GD998822
EST:     AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAG                         ACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG
genomic: AGCAATGTCACCAAAGCAATCAGAAAATCTCGATTCAAATTTGGTGAAAGgtcagttttg ... acatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatttgtttggctgatttgtaagttttctgttactttttgttgaacatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATGCTATGACTATGTGCACGGCAAGAACAACTACTTTTTGTACCTCTTCCTT
          ggctgat  putative branch site (score: 4)
                               ttacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagtattccgaattcagagtcaatagaaataaaatcctttaactgcatttgtttggctgatttgtaagttttctgttactttttgttgaacatgaacagACTTCATTTATTGGAGCTTGGATTCGCTGCCTTCCTCTTCCTTTGTGGATGCTATGACTATGTGCACGGCAAGAACAACTACTTTTTGTACCTCTTCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - tggctga