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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttcatactttcacttcattcgttttttgttttgttttgttttgtttgcagagatgctgaatcgtgcgttcccttttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAG

Basic information

species Glycine max
transcript GLYMA04G39250.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39250.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G112865_T02 (Zea mays), 3'ss of exon 1
-----------------------------------------------gttagttcatactttc--acttcattcgttttttgttttgttttgttttgt-ttgcagagatgctgaa-tcgtgcgttcccttttatc--tagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAG
                                                | || ||   ||||   ||      ||     ||| |  | ||| | ||  | ||   |  | |||  ||    | |   | |   |   || || ||||| |||||| |||||||||||||||||||||| || || || ||||||
gtaaattccgcaagcttggccgcgattactcccaacgcatctgcatgctcaggtctcgctttttaacccgcaccgacgcctgtatcctgttgctctgcgtcgccttgccgttgatctcactggatttgtctccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG

upper sequence: GLYMA04G39250.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G112865_T01 (Zea mays), 3'ss of exon 1
gttagttcatactttcacttcattcgttttttgttttgttttgttttgt-ttgcagagatgctgaa-tcgtgcgttcccttttatc--tagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAG
      ||    ||| ||      ||     ||| |  | ||| | ||  | ||   |  | |||  ||    | |   | |   |   || || ||||| |||||| |||||||||||||||||||||| || || || ||||||
---gtctcgctttttaacccgcaccgacgcctgtatcctgttgctctgcgtcgccttgccgttgatctcactggatttgtctccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG

upper sequence: GLYMA04G39250.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0044g00980.t01 (Vitis vinifera), 3'ss of exon 1
--gttagttcatactttcacttcattcgttttttgttttgt------tttgttttgtttgcagagatgctgaatcgtgcgttccc-ttttat----ctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAG
   | | ||||    |    ||      | ||  || ||        |  |   ||  || || | |  | ||   | | | |   ||||||      ||||| ||||| |||||||||||||||||||||||||| ||||| || || ||||||
gtttcaattcaattataagttttccaaatcttgggtcttaccagccgtacggactgaatgtagtgtttttaaaattttcttccttattttatgccttcagAACAATGGTGTCGCAGTTGGTGAAGCACGAGCGCATTGAAACCACCGTTGCCAAG

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|26268298|gb|CA819361.1|CA819361
EST:     GAATGTCCATGCTCAG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
genomic: GAATGTCCATGCTCAGgttagttcat ... ttttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
EST: gi|298187006|gb|HO034155.1|HO034155
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCAG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCAGgttagttcat ... ttttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
EST: gi|192311623|gb|FK003106.1|FK003106
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCAG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCAGgttagttcat ... ttttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
EST: gi|192310244|gb|FK002600.1|FK002600
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCAG                         AACCATGGTCTCGTAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCAGgttagttcat ... ttttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
EST: gi|192310245|gb|FK002601.1|FK002601
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCAG                         AACCATGGTCTCGTAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCAGgttagttcat ... ttttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
EST: gi|192311622|gb|FK003105.1|FK003105
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCAG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCAGgttagttcat ... ttttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
EST: gi|7587908|gb|AW703714.1|AW703714
EST:     CGAATGTCCATGCTCAG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
genomic: CGAATGTCCATGCTCAGgttagttcat ... ttttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
EST: gi|298174461|gb|HO014606.1|HO014606
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCAG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCAGgttagttcat ... ttttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
EST: gi|23064422|gb|BU579195.1|BU579195
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCAG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCAGgttagttcat ... ttttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
EST: gi|298189819|gb|HO038222.1|HO038222
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCAG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCAGgttagttcat ... ttttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
EST: gi|14009072|gb|BG725667.1|BG725667
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCAG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCAGgttagttcat ... ttttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
EST: gi|16343728|gb|BI969323.1|BI969323
EST:     CGAATGTCCATGCTCAG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC
genomic: CGAATGTCCATGCTCAGgttagttcat ... ttttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgttttgttttgtttgcagagatgctgaatcgtgcgttcccttttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAG
                                      cgttcccttttatct  CT-rich tract
      ttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttcatactttcacttcattcgttttttgttttgttttgttttgtttgcagagatgctgaatcgtgcgttcccttttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC