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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtcctaaatatagtggatggaatttatccatccattttcagcttaaattcctttctagttggatctataaacccataaagggaaaactgtttgtagttggtttttctaactgttacatgttgctttgcagGTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCCGACTCTAGCCTTGTCTGGGATGATGGATAAGCAACAAAATGTGGCTAAT

Basic information

species Glycine max
transcript GLYMA08G45020.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G45020.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g23890.2 (Oryza sativa), 3'ss of exon 5
gcaagtcctaaatatagtggatggaatttatccatccattttcagcttaaattcctttctagttggatctataaacccataaagggaaaactgtttgtagttggtttttctaactgttacatgttgctttgcagGTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCCGACTCTAGCCTTGTCTGGGATGATGGATAAGCAACAAAATGTGGCTAAT---
                 || | ||| | |    |   |  ||  |   ||||    |  |  |    ||||||    ||||       |  ||   ||| |   ||| |||   | || | |||| ||    ||||||||||||| ||| || ||||| ||||||||||||||||| |||||||| |   |||| ||||||||||||||||| ||   ||| | || | |||||   
-----------------tgcacggagtgtgctga---agcttgtgtgcaaatgatatgttc-tccattctata---tcatattctatcagttga--gtaatca-tttctct---tttttcctgttact----agGTACCAGAAGAAGGTTTCGAACATAATTGATGATGTTCTTGAGTGGTCTCCAAAGTTAGCTTTGTCTGGGATGATGGAAAA---ACATACTGGGACTAATGCA

upper sequence: GLYMA08G45020.1 (Glycine max), 3'ss of exon 4
lower sequence: AC217358.3_FGT011 (Zea mays), 3'ss of exon 4
gcaagtcctaaatatagtggatggaatttatccatccattttcagcttaaattcctttctagttggatctataaacccataaagggaaaactgtttgtagttggtttttcta-actgttacatgttgctttgcagGTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCCGACTCTAGCCTTGTCTGGGATGATGGATAAGCAACAAAATGTGGCTAAT---
                                 | | |  |||    |||| |     |      ||  | | |     |     |||    | || || |     |||||| | |||| |   |  |||  ||||||||| |||| ||| |||||||| || ||||| |||||||||||||||||||   ||||  | ||||| ||||| || |||||    | || ||||||    
-----------------------------tggtagcgaccttcg---taaactgtcaccagcaatgaaatttgattgagtgttctgaa--tcgctt-tattaaccctttctatattgttgcccctctcttgccagGTACCAAAAGAAGGTTTCTAACATAATCGATGACGTTCTTGAATGGTCTCCGAAGTTAGCTATTTCTGGAATGATTGAAAAGCAC---ACTGGGGCTAACATT

upper sequence: GLYMA08G45020.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g02280.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------------gcaagtcctaaatatagtggatggaatttatccatccattttcagcttaaattcctttctagttggatctataaacccataaagggaa--------aactgtttgtagttggtttttctaactgttacatgttgct-ttgcagGTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCCGACTCTAGCCTTGTCTGGGATGATGGATAAGCAACAAAATGTGGCTAAT
                                      |  |       | || |||    |    |||||| ||| |||    |    ||| |   |        |   | ||||  |  |||         || ||||||   |  || | ||| |       ||  | || ||||||||| |||||| |||| || ||||| || |||||||||||||| ||||| || |   | || |||||||| |||||||| ||||| |||   || | | ||
gtaagtttcactattaatgctacacatgtattgggaaactggcttgtgttgtaatggtctaag---atccatacatcttccaaatgtcatccatgacatgaaatcttgggagcccaggagtggattatatcttaattgtttgccatgtgtctgtctgaagtgattattctactcttgcagGTATCAGAAGCGGGTCTCAAACATAATAGATGATGTTCTTGAGTGGTCACCAAGATTGGCTTTGTCTGGAATGATGGAGAAGCAGCAACCAGTAGTTGAT

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|193621273|gb|FK566799.1|FK566799
EST:     TTCATATTATTGCTGAGGCATCATGCACCCGATGAAGCTGCCAGAGCAAG                         GTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCC
genomic: TTCATATTATTGCTGAGGCATCATGCACCCGATGAAGCTGCCAGAGCAAGgcaagtccta ... tgctttgcagGTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCC
EST: gi|193428447|gb|FK396699.1|FK396699
EST:     TTCATATTATTGCTGAGGCATCATGCACCCGATGAAGCTGCCAGAGCAAG                         GTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCC
genomic: TTCATATTATTGCTGAGGCATCATGCACCCGATGAAGCTGCCAGAGCAAGgcaagtccta ... tgctttgcagGTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCC
EST: gi|6566302|gb|AW233975.1|AW233975
EST:     TTCATATTATTGCTGAGGCATCATGCACCCGATGAAGCTGCCAGAGCAAG                         GTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCC
genomic: TTCATATTATTGCTGAGGCATCATGCACCCGATGAAGCTGCCAGAGCAAGgcaagtccta ... tgctttgcagGTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCC
EST: gi|193361277|gb|FK328637.1|FK328637
EST:     TCATTATTATTGCTGAGGCATCATGCACCCGATGAAGCTGCCAGAGCAAG                         GTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCC
genomic: TCA-TATTATTGCTGAGGCATCATGCACCCGATGAAGCTGCCAGAGCAAGgcaagtccta ... tgctttgcagGTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCC
EST: gi|26268170|gb|CA819233.1|CA819233
EST:     ATCATGCACCCGATGAAGCTGCCAGAGCAAG                         GTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCC
genomic: ATCATGCACCCGATGAAGCTGCCAGAGCAAGgcaagtccta ... tgctttgcagGTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCC
EST: gi|207680211|gb|GD662705.1|GD662705
EST:     TTCATATTATTGCTGAGGCATCATGCACCCGATGAAGCTGCCAGAGCAAG                         GTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCC
genomic: TTCATATTATTGCTGAGGCATCATGCACCCGATGAAGCTGCCAGAGCAAGgcaagtccta ... tgctttgcagGTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCC
EST: gi|20497862|gb|BQ272792.1|BQ272792
EST:     AGCTGCCAGAGCAAG                         GTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCC
genomic: AGCTGCCAGAGCAAGgcaagtccta ... tgctttgcagGTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCC
EST: gi|193351636|gb|FK318360.1|FK318360
EST:     TTCATATTATTGCTGAGGCATCATGCACCCGATGAAGCTGCCAGAGCAAG                         GTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCC
genomic: TTCATATTATTGCTGAGGCATCATGCACCCGATGAAGCTGCCAGAGCAAGgcaagtccta ... tgctttgcagGTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaagggaaaactgtttgtagttggtttttctaactgttacatgttgctttgcagGTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCCGACTCTAGCCTTGTCTGGGATGATGGATAAGCAACAAAATGTGGCTAAT
                            ttctaac  putative branch site (score: 1)
                                            ttgcttt  putative PPT
                         tttttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagtcctaaatatagtggatggaatttatccatccattttcagcttaaattcctttctagttggatctataaacccataaagggaaaactgtttgtagttggtttttctaactgttacatgttgctttgcagGTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCCGACTCTAGCCTTGTCTGGGATGATGGATAAGCAACAAAATGTGGCTAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA