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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggaaaaatttctataatgtttttagcatgtgatgtccaatcaattataaatcgtgtattcctctttaaattgaatgctctattctgttctgctgggcagGTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATTTATTGCATTTGTATCAACCGAGGCAGAGACAGATCAGCCAGCAATTGAA

Basic information

species Glycine max
transcript GLYMA08G13300.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13300.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv05s0094g01550.t01 (Vitis vinifera), 3'ss of exon 10
tggaaaaatttctataatgtttttagc-atgtgatgtccaatcaattataaatcgtgtattcctctttaaattgaatgctctattctgttctgc---tgggcagGTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATTTATTGCATTTGTATCAACCGAGGCAGAGACAGATCAGCCAGCAATTGAA
    || ||||          |  ||  || | ||||    |    | |   || | ||||  | ||   | | |||  | ||      |||     || | ||||| || || |||||||| ||| |||||||||||||||| ||||| ||||| |||||||||||||| |||||||||||||| ||||| || |    ||||
---caagatttagcagtcaactaaagttatttaatgtgtctttttgtttctttcctctattt-tgttgggactaaatcttgtaaatacctctatgattgtgtagGTATCTTTTCTGTTGTTCTTATTCTCACAATGTTGCTCCCAAGGGCAAATTCATTGCATTTGTATCGACCGAGGCAGAGACTGATCATCCTGAGTCTGAA
















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|6567090|gb|AW234717.1|AW234717
EST:     TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACAT                         GTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
genomic: TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACATgtaagtttac ... tgctgggcagGTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
EST: gi|10843935|gb|BF067288.1|BF067288
EST:     TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACAT                         GTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
genomic: TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACATgtaagtttac ... tgctgggcagGTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
EST: gi|8404346|gb|BE059980.1|BE059980
EST:     TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACAT                         GTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATN
genomic: TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACATgtaagtttac ... tgctgggcagGTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
EST: gi|208035181|gb|GD836407.1|GD836407
EST:     TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACAT                         GTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
genomic: TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACATgtaagtttac ... tgctgggcagGTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
EST: gi|26048272|gb|CA784798.1|CA784798
EST:     TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACAT                         GTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
genomic: TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACATgtaagtttac ... tgctgggcagGTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
EST: gi|193547656|gb|FK504601.1|FK504601
EST:     TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACAT                         GTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
genomic: TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACATgtaagtttac ... tgctgggcagGTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
EST: gi|4283991|gb|AI440725.1|AI440725
EST:     GGTGCAAATTATTTTACCACAGGAACCAGT-GGGTTCG-AAGTCAGACAT                         GTACCTATTTTGTTGT
genomic: GGTGCAAATTATTTTACCACAGAAAC-AGTTGGGT-CGGAAGTCAGACATgtaagtttac ... tgctgggcagGTACCTATTTTGTTGT
EST: gi|16105598|gb|BI893338.1|BI893338
EST:     TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACAT                         GTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
genomic: TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACATgtaagtttac ... tgctgggcagGTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
EST: gi|26268738|gb|CA819801.1|CA819801
EST:     TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACAT                         GTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
genomic: TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACATgtaagtttac ... tgctgggcagGTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
EST: gi|192327651|gb|FK020670.1|FK020670
EST:     TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACAT                         GTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
genomic: TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACATgtaagtttac ... tgctgggcagGTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
EST: gi|58015032|gb|CX701774.1|CX701774
EST:     TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACAT                         GTACCTATTTTGTTGTTCATATACTCACAATGTTGTTCCAAAGGGAAAATT
genomic: TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACATgtaagtttac ... tgctgggcagGTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
EST: gi|15203704|gb|BI426472.1|BI426472
EST:     TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACAT                         GTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
genomic: TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACATgtaagtttac ... tgctgggcagGTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
EST: gi|58016818|gb|CX703560.1|CX703560
EST:     TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACAT                         GTACCTATTTTGTTGTTCATATACTCACAATGTTGTTCCAAAGGGAAAATT
genomic: TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACATgtaagtttac ... tgctgggcagGTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
EST: gi|22521741|gb|BU080552.1|BU080552
EST:     TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACAT                         GTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
genomic: TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACATgtaagtttac ... tgctgggcagGTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
EST: gi|208038580|gb|GD833290.1|GD833290
EST:     TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACAT                         GTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT
genomic: TCGGTGCAAATTATTTTACCACAGAAACAGTTGGGTCGGAAGTCAGACATgtaagtttac ... tgctgggcagGTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataaatcgtgtattcctctttaaattgaatgctctattctgttctgctgggcagGTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATTTATTGCATTTGTATCAACCGAGGCAGAGACAGATCAGCCAGCAATTGAA
                                ctctattctgttct  CT-rich tract
                 tctttaaattgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggaaaaatttctataatgtttttagcatgtgatgtccaatcaattataaatcgtgtattcctctttaaattgaatgctctattctgttctgctgggcagGTACCTATTTTGTTGTTCATATACTCACAATGTTGCTCCAAAGGGAAAATTTATTGCATTTGTATCAACCGAGGCAGAGACAGATCAGCCAGCAATTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA