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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtattataattaaatataatatgttttcatcaaccaattaattaagttattctcaaactgaattatctgatttatcattgttgcagATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGGAATCCATGCCCTCGAGCATACTACAGATGCACTATGGCAGTTGGTTGCC

Basic information

species Glycine max
transcript GLYMA09G00820.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G00820.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0116g01200.t01 (Vitis vinifera), 3'ss of exon 4
gtacgtatt--ataattaaatataatatgttttcatcaaccaattaattaagttattctcaaactg--------aattatctgatttatcattgttgcagATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGGAATCCATGCCCTCGAGCATACTACAGATGCACTATGGCAGTTGGTTGCC
||| | || ||||| | | | | | | | |||| | | || | ||| | || |||| || | | ||||||| | |||||| ||||||||| | || ||||| || |||||||| |||||||| |||||||| ||||| |||||| |||| || ||||||||||| ||||
gtaagaatccaataataatgtttgaaaattcaactagaacccctctgatttgtagtcgtcacagtgtggattgggattaatcgaatatgtgtaactgcagATCACTGATGGATGCCAATGGCGCAAGTATGGGCAGAAAATGGCGAAGGGGAACCCATGCCCGCGAGCCTACTACCGATGTACCATGGCAGTTGGCTGCC

upper sequence: GLYMA09G00820.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S246_89V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------------gtacgtattataattaaatataatatgttttcatcaaccaattaat-taagttattctcaaactgaattatctgatttatcattgttgcagATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGGAATCCATGCCCTCGAGCATACTACAGATGCACTATGGCAGTTGGTTGCC
|| ||| || | | | | | | || || || || | || | || | | || ||| ||| | || ||||||| || || ||||| |||||||||||||| || || |||||||| |||||||| |||||||| ||||| ||| | |||||| | ||| || |
gtgagaacttggagttctttaaatacttcaacagctactctcatcgcattgcttttgtagcttcaaagccagctttaagcagttgatatgtgtaagtccctggattaacatggtgagatattttgttttcagATTAACGACGGATGCCAGTGGAGAAAATATGGTCAGAAGATGGCTAAAGGGAATCCTTGCCCTCGCGCATATTACCGCTGCACTGTTATGTCTGGCTGTC
















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|15814711|gb|BI786986.1|BI786986
EST:     CAATGAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATG                         ATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAA
genomic: CAATGAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATGgtacgtatta ... attgttgcagATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAA
EST: gi|13478414|gb|BG507901.1|BG507901
EST:     CAATGAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATG                         ATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGG
genomic: CAATGAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATGgtacgtatta ... attgttgcagATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGG
EST: gi|16349454|gb|BI975049.1|BI975049
EST:     CAATGAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATG                         ATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGG
genomic: CAATGAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATGgtacgtatta ... attgttgcagATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGG
EST: gi|17401365|gb|BM178147.1|BM178147
EST:     CAATGAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATG                         ATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGG
genomic: CAATGAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATGgtacgtatta ... attgttgcagATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGG
EST: gi|8282721|gb|BE020282.1|BE020282
EST:     CAATGAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATG                         ATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGG
genomic: CAATGAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATGgtacgtatta ... attgttgcagATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGG
EST: gi|23732895|gb|BU764626.1|BU764626
EST:     CAATGAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATG                         ATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGG
genomic: CAATGAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATGgtacgtatta ... attgttgcagATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGG
EST: gi|17964331|gb|BM271068.1|BM271068
EST:     AATGAGAAAAGCTCGTGTCTCAGATCGTGCCCGATCAAAAAGCTCCCATG                         AATAGTGAATGGGTGCCCAATG
genomic: AATGAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAA-GCTCCCATGgtacgtatta ... attgttgcagATTAGTGA-TGGGTGCC-AATG
EST: gi|254326714|gb|GR832866.1|GR832866
EST:     TCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATG                         ATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGG
genomic: TCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATGgtacgtatta ... attgttgcagATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGG
EST: gi|7925908|gb|AW831934.1|AW831934
EST:     CAATGAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATG                         ATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGG
genomic: CAATGAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATGgtacgtatta ... attgttgcagATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGG
EST: gi|192299784|gb|FG987800.1|FG987800
EST:     GAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATG                         ATTAGTGATGGGTGCCAATGGAGAAAATATGGACNNNNNNNTGGCTAAGGG
genomic: GAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATGgtacgtatta ... attgttgcagATTAGTGATGGGTGCCAATGGAGAAAATATGGAC-AAAAAATGGCTAAGGG
EST: gi|13563033|gb|BG551253.1|BG551253
EST:     CAATGAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATG                         ATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGG
genomic: CAATGAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATGgtacgtatta ... attgttgcagATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGG
EST: gi|17023955|gb|BM094989.1|BM094989
EST:     CAATGAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATG                         ATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGG
genomic: CAATGAGAAAAGCTCGTGTCTCAGTTCGTGCCCGATCAGAAGCTCCCATGgtacgtatta ... attgttgcagATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccaattaattaagttattctcaaactgaattatctgatttatcattgttgcagATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGGAATCCATGCCCTCGAGCATACTACAGATGCACTATGGCAGTTGGTTGCC
     attaattaagttattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtattataattaaatataatatgttttcatcaaccaattaattaagttattctcaaactgaattatctgatttatcattgttgcagATTAGTGATGGGTGCCAATGGAGAAAATATGGACAAAAAATGGCTAAGGGGAATCCATGCCCTCGAGCATACTACAGATGCACTATGGCAGTTGGTTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG