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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggacaggatacaagaatttcccaaaacaatttctgtgagaaatgtaacagtttatgttcttccatgcttgacattgtgaaaattttggttggtgttgcagATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCGCCAGAAGCCCTTGAAATTACAAGGAAGTTCATGA

Basic information

species Glycine max
transcript GLYMA08G20300.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20300.3 (Glycine max), 3'ss of exon 4
lower sequence: AT1G72730.1 (Arabidopsis thaliana), 3'ss of exon 4
ggacaggatacaagaatttcccaaa-acaatttctgtgagaaatgtaacagtttatgttcttccatgcttgacattgtgaaaattttggttggtgttgcagATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCGCCAGAAGCCCTTGAAATTACAAGGAAGTTCATGA
|   |   |     ||| |||||   ||| ||||| |      | |  | | | |  |     |||  |||   || | |    |||| ||  | |  ||||| || |||||||||||||| || || |||||  |||||||||| || ||||||||||||||||| || ||||||||||| || ||||||||||||||||
gtttaatcttgtttaatctcccattcacattttctttt-----tctctctgataaaatcaagtcat--ttgttcttataa----tttgatttctctgtcagATATACGACATCTTCCAGCTTCTTCCTTCCAAGGTTCAGGTTGGTGTTTTCTCTGCTACAATGCCTCCCGAAGCCCTTGAGATCACAAGGAAGTTCATGA

upper sequence: GLYMA08G20300.3 (Glycine max), 3'ss of exon 4
lower sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
ggacaggatacaagaatttcccaaaacaatttctgtgagaaatgtaacagtttatgttcttccatgcttgacattgtgaaaattttggttggtgttgcagATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCGCCAGAAGCCCTTGAAATTACAAGGAAGTTCATGA
        |     |  |||   |||   |   | |      |||     | | || | ||     ||||   |||||    |||  | ||   ||||||||||||||||| |||||||| || ||| | || ||||||||||||||||||||||| |||||||| || |||||  | || || ||||| || |||||||
-------gtttgttatcttcttcaaagtttgaatctaccctctgtggttatctctgatattg---acttggttttgtgttgttttctggtgaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA

upper sequence: GLYMA08G20300.3 (Glycine max), 3'ss of exon 4
lower sequence: AT3G13920.2 (Arabidopsis thaliana), 3'ss of exon 4
ggacaggatacaagaatttcccaaaacaatttctgtgagaaatgtaacagtttatgttcttccatgcttgacattgtgaaaattttggttggtgttgcagATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCGCCAGAAGCCCTTGAAATTACAAGGAAGTTCATGA
     | || |||  ||||| ||      |   |   |     || | ||||||            |||||   |       || ||| |  | || |||||||||||||| |||||||| || ||| | || || || ||||| |||||||| || |||||||| |||||||| ||||| || ||||||||||||||||
-----gtatgcaaatatttctcagtgtt-tcaattccattctcgttatagttta-----------acttgaatctcactggtttctgggt--tttttcagATCTATGACATATTCCAGCTTCTTCCACCAAAGATCCAAGTTGGTGTGTTCTCCGCAACAATGCCACCAGAAGCTCTTGAGATCACAAGGAAGTTCATGA

upper sequence: GLYMA08G20300.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g01760.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------------------------------------------------------ggacaggatacaagaatttcccaaaac-aatttctgtgagaaatgtaacagtttatgttcttccatgctt----gacattgtgaaaattttggttggtgttg-cagATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCGCCAGAAGCCCTTGAAATTACAAGGAAGTTCATGA
                                                                                        ||   |     ||| |  |   |    || |   | |  || ||   || |    |||   || ||    || | |     ||||||  ||| || || |||||||||||||| ||||||||||||||||| ||| | |||||||||||||||||||| |||||||| || || |||||||| || ||  | ||||||||||
gtctgttctattatatctctgtttctttactagttgtaatatttttgcatacttcatggtgaagaacattattttgctaattgttagaagttcatgctcattgcttattgctggatttttcaatatgtgcaagttttgactggctttgttgtttttctgataattcattaattttttttgctgctgtcagATCTATGACATTTTCCAGCTGCTGCCATCTAAAGTCCAGGTTGGAGTGTTCTCTGCCACAATGCCCCCTGAGGCCCTTGAGATCACTCGAAAGTTCATGA

upper sequence: GLYMA08G20300.3 (Glycine max), 3'ss of exon 4
lower sequence: PP1S31_150V6.5 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------ggacaggatacaagaatttcccaaaacaatttctgtgagaaatgta--------acagtttatgttcttccatgcttgacattg-tgaaa---attttggttggtgttgcagATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCGCCAGAAGCCCTTGAAATTACAAGGAAGTTCATGA
                                                  || | || |    ||      || ||||| ||     |  ||        | |   ||||        ||||  ||  |   ||||   |||  ||    |  ||||||| ||||||||||||||||| || |||   ||  |||| || || ||||| ||||| |||||||| || ||||| ||||| || || |||||||||||||
gtttgttcggagagtcctggaatggtagaagaaatttgtttttactcccaagaaaactaattgtttgtgtgactatttcagttctctaattatcctccttataagctatgagagatattgctcaacgctaacgaaattgattcgggcatcttctgcagATTTATGACATCTTCCAGCTTCTTCCACAGAAGCTTCAAGTGGGTGTGTTTTCTGCCACAATGCCACCCGAAGCGCTTGAGATCACCAGGAAGTTCATGA

upper sequence: GLYMA08G20300.3 (Glycine max), 3'ss of exon 4
lower sequence: PP1S383_1V6.3 (Physcomitrella patens), 3'ss of exon 3
-ggacaggatacaagaatttcccaaaacaatttctgtgagaaatgtaacagtttatgttcttccatgcttgacattgtgaaaattttggttggtgt-tgcagATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCGCCAGAAGCCCTTGAAATTACAAGGAAGTTCATGA
  |    |      || | |  |  |     || ||  ||   |||    |  | |     |  |       | |  |   | |  ||     |   ||||||| || |||||||| |||||||||||    ||  |||| || || || ||||||||||| ||||| || |||||||| || || ||||||||||||||||
gtgttgagtggtctgagtatgtcgcactg--ttttgataggggtgttggtgactgttacggtgaaaaggccgcttacttgcagtgatgtccaatacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTCTCTGCTACCATGCCTCCTGAAGCCCTCGAGATCACAAGGAAGTTCATGA

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|192296157|gb|FG989742.1|FG989742
EST:     TTGTTTTGGATGAG-CTGATGAAATGCTTTCACGTGGTTTCAAGGATCAG                         ATCTATGACATCTTCCAGCTGCTGCCATCCAAAAT
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAGgtttgttgtt ... ggtgttgcagATCTATGACATCTTCCAGCTGCTGCCATCCAAAAT
EST: gi|17964769|gb|BM271498.1|BM271498
EST:     GTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAG                         ATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
genomic: GTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAGgtttgttgtt ... ggtgttgcagATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
EST: gi|7925063|gb|AW831089.1|AW831089
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAG                         ATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAGgtttgttgtt ... ggtgttgcagATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
EST: gi|18041380|gb|BM309674.1|BM309674
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAG                         ATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAGgtttgttgtt ... ggtgttgcagATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
EST: gi|7285462|gb|AW597949.1|AW597949
EST:     GGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAG                         ATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
genomic: GGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAGgtttgttgtt ... ggtgttgcagATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
EST: gi|4396635|gb|AI495632.1|AI495632
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAG                         ATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAGgtttgttgtt ... ggtgttgcagATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
EST: gi|13312426|gb|BG406077.1|BG406077
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAG                         ATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAGgtttgttgtt ... ggtgttgcagATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
EST: gi|7686509|gb|AW757157.1|AW757157
EST:     GATGAAATGCTTTCACGTGGTTTCAAGGATCAG                         ATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
genomic: GATGAAATGCTTTCACGTGGTTTCAAGGATCAGgtttgttgtt ... ggtgttgcagATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
EST: gi|37994639|gb|CF806304.1|CF806304
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTNTCACGTGGTTTCAAGGATCAG                         ATCTATGACATCTTCCAGCTGC
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAGgtttgttgtt ... ggtgttgcagATCTATGACATCTTCCAGCTGC
EST: gi|6502132|gb|AW203505.1|AW203505
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAG                         ATCTATGACATCTTCCAGCTGCTGCCATTCAAAATTCAGGTTGGAGTGTTC
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAGgtttgttgtt ... ggtgttgcagATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacagtttatgttcttccatgcttgacattgtgaaaattttggttggtgttgcagATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCGCCAGAAGCCCTTGAAATTACAAGGAAGTTCATGA
                           attgtgaaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggacaggatacaagaatttcccaaaacaatttctgtgagaaatgtaacagtttatgttcttccatgcttgacattgtgaaaattttggttggtgttgcagATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCGCCAGAAGCCCTTGAAATTACAAGGAAGTTCATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - -cccaaaa
- - - - - - - - - - - - - - - ttctgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttga