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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttttctgttcttgtattctaatcaactgcaatccatgttagttctttaaccaaaggactgtcttttgattgttgcagAGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTAGAGTATAGGAGAGAGTGTGGTAGGGACAGTGTGCTGGATTCCCTGACTG

Basic information

species Glycine max
transcript GLYMA05G08060.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G08060.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 6
-----------gtatttttctgttctt---gtattctaatcaactgcaatccatg-ttagttc----tttaaccaaaggactgtcttttgattgttgcagAGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTAGAGTATAGGAGAGAGTGTGGTAGGGACAGTGTGCTGGATTCCCTGACTG
           |||| || |   |||    ||| |||      ||   ||  ||  ||    |    ||| |   || |      |  || ||||||||||||||||||| |||||||||||||||||| |||||||||||||||||| | ||||| ||||| |||||||| ||||||||||||||| | ||||| ||||
gtgattttcttgtatcttccaagtctaagagtactctgcatttcttttatttataatttacacacaatttgattgaaaggtctcatgatggttgttgcagAGTGCTCCACTGCCAATCTTGGAGAGTCACGAGCTTTCTTCCATGACTCTGGAGTACAGGAGGGAGTGTGGAAGGGACAGTGTGCTGCAGTCCCTCACTG
















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|16348974|gb|BI974569.1|BI974569
EST:     ATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAG                         AGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTA
genomic: ATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAGgtatttttct ... attgttgcagAGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTA
EST: gi|254345715|gb|GR859362.1|GR859362
EST:     ATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAG                         AGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTA
genomic: ATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAGgtatttttct ... attgttgcagAGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTA
EST: gi|10846299|gb|BF069222.1|BF069222
EST:     TCAATCAGCATGTCAACAATGTGAAGTACATNTGGCTGGGATTCTTGGAG                         AGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTT
genomic: TCAATCAGCATGTCAACAATGTGAAGTACAT-TGGCT-GGATTC-TGGAGgtatttttct ... attgttgcagAGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTT
EST: gi|298177960|gb|HO023809.1|HO023809
EST:     ATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAG                         AGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATAACTTTA
genomic: ATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAGgtatttttct ... attgttgcagAGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTA
EST: gi|254340121|gb|GR858246.1|GR858246
EST:     ATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAG                         AGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTA
genomic: ATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAGgtatttttct ... attgttgcagAGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTA
EST: gi|15662668|gb|BI700039.1|BI700039
EST:     ATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAG                         AGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTA
genomic: ATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAGgtatttttct ... attgttgcagAGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTA
EST: gi|254325646|gb|GR838527.1|GR838527
EST:     ATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAG                         AGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTA
genomic: ATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAGgtatttttct ... attgttgcagAGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTA
EST: gi|11274091|gb|BF324459.1|BF324459
EST:     ATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAG                         AGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTA
genomic: ATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAGgtatttttct ... attgttgcagAGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTA
EST: gi|4396532|gb|AI495529.1|AI495529
EST:     ATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAG                         AGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTA
genomic: ATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAGgtatttttct ... attgttgcagAGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caactgcaatccatgttagttctttaaccaaaggactgtcttttgattgttgcagAGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTAGAGTATAGGAGAGAGTGTGGTAGGGACAGTGTGCTGGATTCCCTGACTG
                   ttctttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttttctgttcttgtattctaatcaactgcaatccatgttagttctttaaccaaaggactgtcttttgattgttgcagAGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTAGAGTATAGGAGAGAGTGTGGTAGGGACAGTGTGCTGGATTCCCTGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA