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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctatcgacatgttctaaaaatttagttttgaccatactgctttctgaaacttgttttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCTGGAGGCGGTGCTACAGAGTTGACGGTGTCGGCTGCCTTGAAACAAAAGA

Basic information

species Glycine max
transcript GLYMA09G28650.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G28650.2 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 10
-------gtaagctatcgacatgttctaaaaatttagttttgac-catactgctttctgaaacttgtt-ttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCTGGAGGCGGTGCTACAGAGTTGACGGTGTCGGCTGCCTTGAAACAAAAGA
        |||  |  |        ||  || |||   |   |     ||   |  |     ||| || || |||||||||||||||||||||||||||||||||| | ||||| || |||||| | |||||||| |||||||| ||| |||| || || || ||  |||| |||||||
gtatttgttaatgttcctgtggtacctgtaattttgcatgccatgttcaccaataaccatttcttattctttttgacagGATGCCATGTCTGTTGCAAGGAACATTTTGAAAAACCCAAAACTTTTACCTGGAGGTGGTGCTACCGAGCTGACTGTATCAGCAGCACTGAAGCAAAAGA

upper sequence: GLYMA09G28650.2 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G175510_T01 (Zea mays), 3'ss of exon 10
---------------------------gtaagctatcgacatgttctaaaaattta---gttttgaccatactgctttctgaaacttgttttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCTGGAGGCGGTGCTACAGAGTTGACGGTGTCGGCTGCCTTGAAACAAAAGA
                            | | |  | |      || ||  || |    |||| | | |   |  |            |||||    ||||||||||||||||||||||| |||||| | |||||||| |||||  |||||||||| |||||||||||| |||| || || ||  |  |||| |||||||
gaattacatggagcccaactacctgtaatgaacacttgtttccctcaaagcatgtcgatgtttaggctaacataatggtatgtgtacattttcaatgcagGATGCCATGTCTGTTGCAAGAAACATTTTGAAAAATCCGAAACTCCTTCCTGGAGGTGGTGCTACAGAGCTGACTGTATCAGCAACACTGAAGCAAAAGA

upper sequence: GLYMA09G28650.2 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G069765_T05 (Zea mays), 3'ss of exon 10
---------------------------gtaagctatcgacatgttctaaaaattt---agttttgaccatactgctttctgaaacttgttttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCTGGAGGCGGTGCTACAGAGTTGACGGTGTCGGCTGCCTTGAAACAAAAGA
                              | | |||       || || ||| |   ||||  ||| |   |  |    |       |||||    |||||||||||||| ||||||||||||||| | |||||||| |||||  |||||||||| || ||||||||| |||| || || ||  |  |||| |||||||
attttgtcaggaacccaactatttgtaaagaacaatcatttccctcgaagaatgtccaagttcagactaatataatggtcgctgtacattttcaatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCTGGAGGTGGCGCTACAGAGCTGACTGTATCAGCAACACTGAAGCAAAAGA

upper sequence: GLYMA09G28650.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 9
gtaagctatcgacatgttctaaaaatttagtt---ttgaccatactgctttctgaaac-ttgttttctt--gacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCTGGAGGCGGTGCTACAGAGTTGACGGTGTCGGCTGCCTTGAAACAAAAGA
|||     | ||  |  | |     |  |  |   |  ||  ||  |  |||||||   ||||||||||   |||||||||||||||||| ||||| ||||| ||||| ||||| || ||||||||||| || |||||||||||||| || || || ||| || | ||||| || |
gtatctccttgatttaatttgctgttacatatagatcaactctatggagttctgaagtattgttttcttttaacagGATGCCATGTCTGTGGCAAGAAACATGATAAAGAATCCAAAGCTTGTTCCTGGTGGGGGTGCTACAGAGTTAACTGTTTCAGCTACCCTAAAACAGAAAA

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|207735261|gb|GD711112.1|GD711112
EST:     TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAG                         GATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCT
genomic: TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAGgtaagctatc ... ttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCT
EST: gi|208278764|gb|GE077983.1|GE077983
EST:     TAAGGGGTGCTAGTAAGGATCTATCAAATGAAGTTGAAAGAAACCTACAG                         GATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
genomic: TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAGgtaagctatc ... ttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
EST: gi|193547528|gb|FK501465.1|FK501465
EST:     TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAG                         GATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
genomic: TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAGgtaagctatc ... ttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
EST: gi|58017480|gb|CX704222.1|CX704222
EST:     ATTAAATGAAGTTGAAAGAAACCTACAG                         GATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
genomic: ATTAAATGAAGTTGAAAGAAACCTACAGgtaagctatc ... ttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
EST: gi|209714673|gb|BW674236.1|BW674236
EST:     GAAACCTACAG                         GATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
genomic: GAAACCTACAGgtaagctatc ... ttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
EST: gi|10842929|gb|BF066288.1|BF066288
EST:     TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAG                         GATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCAAAACTTGTTCCT
genomic: TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAGgtaagctatc ... ttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
EST: gi|26058880|gb|CA801794.1|CA801794
EST:     TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAG                         GATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCAAAACTTGT
genomic: TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAGgtaagctatc ... ttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGT
EST: gi|192309232|gb|FG999123.1|FG999123
EST:     TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAG                         GATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
genomic: TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAGgtaagctatc ... ttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
EST: gi|26048688|gb|CA785141.1|CA785141
EST:     TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAG                         GATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
genomic: TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAGgtaagctatc ... ttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
EST: gi|193493510|gb|FK460092.1|FK460092
EST:     TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAG                         GATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTT
genomic: TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAGgtaagctatc ... ttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTT
EST: gi|7590571|gb|AW706320.1|AW706320
EST:     TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAG                         GATGCCATGTCTGTTG
genomic: TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAGgtaagctatc ... ttcttgacagGATGCCATGTCTGTTG
EST: gi|208059831|gb|GD857833.1|GD857833
EST:     TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAG                         GATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
genomic: TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAGgtaagctatc ... ttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
EST: gi|208336139|gb|GE139138.1|GE139138
EST:     TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAG                         GATGCCATGTCTGTTGCAAGGAACATTATAAAAA
genomic: TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAGgtaagctatc ... ttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAA
EST: gi|207803832|gb|GD772791.1|GD772791
EST:     TAAGGGGTGCTAGTAAGGATCTATCAAATGAAGTTGAAAGAAACCTACAG                         GATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
genomic: TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAGgtaagctatc ... ttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
EST: gi|15199729|gb|BI423980.1|BI423980
EST:     TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAG                         GATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
genomic: TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAGgtaagctatc ... ttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
EST: gi|208270977|gb|GE067801.1|GE067801
EST:     TAAGGGGTGCTAGTAAGGATCTATCAAATGAAGTTGAAAGAAACCTACAG                         GATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT
genomic: TAAGGGGTGCTAGTAAGGATCTATTAAATGAAGTTGAAAGAAACCTACAGgtaagctatc ... ttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctaaaaatttagttttgaccatactgctttctgaaacttgttttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCTGGAGGCGGTGCTACAGAGTTGACGGTGTCGGCTGCCTTGAAACAAAAGA
                                       cttgttttctt  CT-rich tract
     aaaaatttagttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctatcgacatgttctaaaaatttagttttgaccatactgctttctgaaacttgttttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCTGGAGGCGGTGCTACAGAGTTGACGGTGTCGGCTGCCTTGAAACAAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG