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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttaactatggctggtcaaagctatctgcatagaatgctaaaattaattcaatgatatttctaagggtgggctgacaagttcaatgtcttatcattcagGTCAAGCAACCTGGACTGGAGATGTCTACGGTTCAAAGTGAGCTTGACTTGTCATATGGACAACGGTATCAAGGAGTAACCATTCCTGAGGCTTATGAAC

Basic information

species Glycine max
transcript GLYMA16G06850.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G06850.3 (Glycine max), 3'ss of exon 13
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 13
---tgttaactatggctggtcaaagcta-tctgcatagaatgctaaaattaattcaatgatatttctaagggtgggctgacaagttcaatgtcttatcattcagGTCAAGCAACCTGGACTGGAGATGTCTACGGTTCAAAGTGAGCTTGACTTGTCATATGGACAACGGTATCAAGGAGTAACCATTCCTGAGGCTTATGAAC
    ||  |  |||      ||||  || | | |  |  |  || |  || |  || |    |     |    |   |     |   |   | ||   |  ||||| |||||||| || || || |||  ||| || |||||||| || |||||||| ||||| |||||||||||||| ||  | || |||||||| || || |
gtaagtatatgatgaacaaacaaacataatttactaattactctgaccttgaaccactacagtgaaccataacgctttt----ggctatgcttttgctacacagGTTAAGCAACCAGGTCTAGATATGAATACTGTGCAAAGTGAACTAGACTTGTCGTATGGGCAACGGTATCAAGGTGTCGCTATCCCTGAGGCATACGAGC

upper sequence: GLYMA16G06850.3 (Glycine max), 3'ss of exon 13
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 13
------tgttaactatggctggtcaaagctatctgcatagaatgctaaaattaattcaatgatatttctaagggtgggctgacaagttcaatgtcttatcattcagGTCAAGCAACCTGGACTGGAGATGTCTACGGTTCAAAGTGAGCTTGACTTGTCATATGGACAACGGTATCAAGGAGTAACCATTCCTGAGGCTTATGAAC
      |   | |      || | |    ||  || |||  ||      |  |||   | | |  |  |    |||  |||||   ||      ||| |||| ||||||||||| ||||| || || ||||| || || ||||| || || |||||||||||||||||||| ||||||||  | || ||||| |||||||||||||
tcattttaggatcctcaaatgat-attattacatgtataacattgcctcaggaatctgaaggttatcgtttatgtgcactgacgtatt-----acttctcatgcagGTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTGTCATATGGACAACGTTATCAAGGGTTTACAATTCCAGAGGCTTATGAAC
















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|15815763|gb|BI788038.1|BI788038
EST:     AGTGTGTTATCCGCCTACAGCCTTCAGAAGGTATTTACATGAAACTTACG                         GTCAAGCAACCTGGACTGG-GAATGTCTAC
genomic: AGTGTGTTATCCGCCTACAGCCTTCAGAAGCTATTTACATGAAGCTTACGgtgaggcaat ... tatcattcagGTCAAGCAACCTGGACTGGAGA-TGTCTAC
EST: gi|6566164|gb|AW233801.1|AW233801
EST:     AGTTTGTTATCCGCCTACAGCCTTCAGAAGCTATTTACATGAAGCTTACG                         GTCAAGCAACCTGGACTGGAGATGTCTACGGTTCAAAGTGAGCTTGACTTG
genomic: AGTGTGTTATCCGCCTACAGCCTTCAGAAGCTATTTACATGAAGCTTACGgtgaggcaat ... tatcattcagGTCAAGCAACCTGGACTGGAGATGTCTACGGTTCAAAGTGAGCTTGACTTG
EST: gi|37995859|gb|CF807448.1|CF807448
EST:     AGTTTGTTATCCGCCTACAGCCTTCAGAAGCTATTTACATGAAGCTTACG                         GTCAAGCAACCTGGACTGGAGATGTCTACGGTTCANAGTGAGCTTGACTTG
genomic: AGTGTGTTATCCGCCTACAGCCTTCAGAAGCTATTTACATGAAGCTTACGgtgaggcaat ... tatcattcagGTCAAGCAACCTGGACTGGAGATGTCTACGGTTCAAAGTGAGCTTGACTTG
EST: gi|37995462|gb|CF807051.1|CF807051
EST:     AGTTTGTTATCCGCCTACAGCCTTCAGAAGCTATTTACATGAAGCTTACG                         GTCAAGCAACCTGGACTGGAGATGTCTACGGTTCAAAGTGAGCTT
genomic: AGTGTGTTATCCGCCTACAGCCTTCAGAAGCTATTTACATGAAGCTTACGgtgaggcaat ... tatcattcagGTCAAGCAACCTGGACTGGAGATGTCTACGGTTCAAAGTGAGCTT
EST: gi|151395248|gb|EV265119.1|EV265119
EST:     AGTGTGTTATCCGCCTACAGCCTTCAGAAGCTATTTACATGAAGCTTACG                         GTCAAGCAACCTGGACTGGAGATGTCTACGGTTCAAAGTGAGCTTGACTTG
genomic: AGTGTGTTATCCGCCTACAGCCTTCAGAAGCTATTTACATGAAGCTTACGgtgaggcaat ... tatcattcagGTCAAGCAACCTGGACTGGAGATGTCTACGGTTCAAAGTGAGCTTGACTTG
EST: gi|37994622|gb|CF806296.1|CF806296
EST:     AGTTTGTTATCCGCCTACAGCCTTCAGAAGCTATTTACATGAAGCTTACG                         GTCAAGCAACCTGGACTGGAGATGTCTACGGTTCANAGTGAGCTTGACTTG
genomic: AGTGTGTTATCCGCCTACAGCCTTCAGAAGCTATTTACATGAAGCTTACGgtgaggcaat ... tatcattcagGTCAAGCAACCTGGACTGGAGATGTCTACGGTTCAAAGTGAGCTTGACTTG
EST: gi|15661712|gb|BI699083.1|BI699083
EST:     AGTTTGTTATCCGCCTACAGCCTTCAGAAGCTATTTACATGAAGCTTACG                         GTCAAGCAACCTGGACTGGAGATGTCTACGGTTCAAAGTGAGCTTGACTTG
genomic: AGTGTGTTATCCGCCTACAGCCTTCAGAAGCTATTTACATGAAGCTTACGgtgaggcaat ... tatcattcagGTCAAGCAACCTGGACTGGAGATGTCTACGGTTCAAAGTGAGCTTGACTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattcaatgatatttctaagggtgggctgacaagttcaatgtcttatcattcagGTCAAGCAACCTGGACTGGAGATGTCTACGGTTCAAAGTGAGCTTGACTTGTCATATGGACAACGGTATCAAGGAGTAACCATTCCTGAGGCTTATGAAC
                         ggctgac  putative branch site (score: 3)
                                          tcttatc  putative PPT
      aatgatatttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttaactatggctggtcaaagctatctgcatagaatgctaaaattaattcaatgatatttctaagggtgggctgacaagttcaatgtcttatcattcagGTCAAGCAACCTGGACTGGAGATGTCTACGGTTCAAAGTGAGCTTGACTTGTCATATGGACAACGGTATCAAGGAGTAACCATTCCTGAGGCTTATGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG