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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acacatttttatcaccgttttctgttttcagtgaaaatgaaaacagaaaacaaccaaaccaaacacccctaatattttgttatgatctgatcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTATTAAGGATTTTATGATTCAGGCTGGTGATTTTGTAAAG

Basic information

species Glycine max
transcript GLYMA13G26260.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G26260.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0084g00620.t01 (Vitis vinifera), 3'ss of exon 1
acacatttttatcaccgttttctgttttcagtgaaaatgaaaa---cagaaaacaaccaaaccaaacacccctaatattttgttatgatc----tgatcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTATTAAGGATTTTATGATTCAGGCTGGTGATTTTGTAAAG
        || | |   ||||||   |||| | |   |   |    ||| |      |           |  |  | || | | ||||      | ||  | | ||| ||||| ||| | ||||||||||||||||| || || || || || || || || ||||| ||||||||||||||||||||||| |||
-------gtttttattcttttctaacttcactcattttcttattttcaggatgatttccttttctttttctttcttcttatttgatgaatacaataatgatttgcagAAAAGCTGGATTACCTGTTGGTTACAAGGGATGCCAGTTCCACAGGGTCATCAAAGATTTCATGATTCAGGCTGGTGATTTTGTCAAG
















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|58015177|gb|CX701919.1|CX701919
EST:     GGCAGTTCTGCACTGGGGAATACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|58025427|gb|CX712168.1|CX712168
EST:     GGCAGTTCTGCACTGGGGAATACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|298164520|gb|HO014165.1|HO014165
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|151408761|gb|EV278569.1|EV278569
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|298179325|gb|HO027796.1|HO027796
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|298174291|gb|HO017627.1|HO017627
EST:     GGCAGTTCTGCACTAGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|58021016|gb|CX707758.1|CX707758
EST:     GGCAGTTCTGCACTGGGGAATACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|298170313|gb|HO018937.1|HO018937
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|31561148|gb|CD486986.1|CD486986
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|209704174|gb|BW664792.1|BW664792
EST:     TGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: TGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|298180377|gb|HO025578.1|HO025578
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|208029483|gb|GD827899.1|GD827899
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|192333246|gb|FK026127.1|FK026127
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|16348066|gb|BI973661.1|BI973661
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|298172532|gb|HO019572.1|HO019572
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|151393429|gb|EV263304.1|EV263304
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|298183104|gb|HO028367.1|HO028367
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|163923182|gb|EH038294.1|EH038294
EST:     GGCAGTTCTGCACTGGGGAATACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|209704173|gb|BW664791.1|BW664791
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|58021929|gb|CX708670.1|CX708670
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
EST: gi|192298333|gb|FG992108.1|FG992108
EST:     GGCAGTTCTGCACTGGGGAGTACAG                         GAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT
genomic: GGCAGTTCTGCACTGGGGAATACAGgtactggaac ... tcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaacaaccaaaccaaacacccctaatattttgttatgatctgatcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTATTAAGGATTTTATGATTCAGGCTGGTGATTTTGTAAAG
                        taatattttgttatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acacatttttatcaccgttttctgttttcagtgaaaatgaaaacagaaaacaaccaaaccaaacacccctaatattttgttatgatctgatcttatacagGAAAGCAGGACTGCCTGTTGGTTACAAGGGTTGTCAATTTCATAGAGTTATTAAGGATTTTATGATTCAGGCTGGTGATTTTGTAAAG

- - - - - - - - - -ttctgtt
- - - - - - - - - - - - - ttcagtg
- - - - - - - - - - - - - - - - - aaatgaaa
- - - - - - - - - - - - - - - - - - - - - - - aaaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -ccaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttatg