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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgcatttatagtttatactggttgtcctaattgtatggactggatgctgttaacacttgtacacctccttaaatgtttgcttcctgttgttacaatagGTATAAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAGGAGCAGCCTCTTCAG

Basic information

species Glycine max
transcript GLYMA07G05220.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 2
----gttgcatttatagtttatactggttgtcctaattgta--tggactggatgctgttaacacttgtacacctcctt---aaatgtttgcttc--ctgttgttacaat--agGTATAAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAGGAGCAGCCTCTTCAG
    ||     | | | | | | ||  |     ||| | ||  ||  ||  | | || |  | ||  | || ||   |   | ||| |    |   |||||  |  | |  ||| || || |||||||| ||||| || ||| |||| ||||||||||| ||||| || |||||||| ||||||||||||||||| || || |||
gtgtgtgctcgtcaaattctttgcttctcaatttaaatataactgtgctacagg-tgcttgcgctattccaacttgctgcaacatgctcatctgaactgttaatgaattgcagGAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTGTATCCGATAAGCAGATGATGCAGGAGGAGCAACCCCTGCAG

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 2
------------gttgcatttatagtttatactggttgtcctaattgtatggactggatgctgttaacacttgtacacctccttaaatgtttgcttcctgttgttacaatagGTATAAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAGGAGCAGCCTCTTCAG
            ||||  | |  | ||||| | | ||||  ||||  || | |   | | || || | |   | | ||||    | |||| |   || | |  | |    ||||||||||||||||||||| || || ||| |||| |||||||||||| | ||||| ||||| || |||||||| || || || ||  | || 
attttgttctatgttgt-tctgcaatttat-cagtttgttttaatgctaggaa---ggtccttttga-atcagcatacctg---agatgtgt---tcttatactaaatgcagGTATAAAGGAGTCTGATACAGGGTTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAACAGATGATGCAAGAAGAACAACCGTTACAA

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 2
--------gttgcat-ttatagtttatactggttgtcctaattgtatggactggatgctgttaacacttgtacacctccttaaatgtttgcttcctgttgttacaatagGTATAAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAGGAGCAGCCTCTTCAG
         |   || || |    |  |   | ||   |||  ||   ||   | | || || | | | | | ||||    | ||||   ||     |  |||    ||| ||||||||||||||||| ||  | ||| |||| |||||||||||| | ||||| |||||||| |||||||| || || || ||  | || 
agttctctatcaaatgttcttccattcatcagctgctttaaaggttaaga--aggtccttttga-attagcatacctg---agatgtgccctc---atacttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------------------------------------------------------------------gttgcatttatagtttatactggttgtcctaattgtatggactggatgctgttaacacttgtacacctccttaaatgtttgct----tcctgttgttacaatagGTATAAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAGGAGCAGCCTCTTCAG
                                                                                                |||  ||    |||||  |     |   |   |  ||||| |||  |   | |   |     |||| || | ||||  | ||     |  |  | ||| || |||||| ||||| ||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
gtatgtttcttattcgtgatatttccaatgtatagtgctatttgataaactgggcatgtattatgttgatccatgttgaaaatagtagtagccaaggttatatgagaagttttgataaactaggcatgtattatgggctgattatggcttgaata---acacttcatgaaattatagcaatgattttcatcttataacagGTATCAAGGAATCTGATACTGGCTTAGCTGCACCAAGTCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAGGAGCAGCCTCTTCAG

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 2
gttgcatttatagtttatactggttgtcctaattgtatggactggatgctgttaacac-ttgtacacctccttaaatgtttgcttcctgttgttacaatagGTATAAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAGGAGCAGCCTCTTCAG
                                                         | |||    | | ||    | |||    | || | || ||   || || |||||||| || |||||| |||| || || |||||||||||||| || |||||||||||||||||||| || |||||||| || || 
------------------------------------------------------gtgcgttgcgatcttgctgggcttttttgagcgtgcttttcca---gGGATCAAGGAGTCCGACACTGGTCTAGCAGCTCCTAGCCAGTGGGATCTGGTGTCTGATAAGCAAATGATGCAAGAAGAGCAGCCACTGCAA

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ13722 (Selaginella moellendorffii), 3'ss of exon 2
gttgcatttatagtttatactggttgtcctaattgtatggactggatgctgttaacacttgtacacctccttaaatgtttgcttcctgttgttacaatagGTATAAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAGGAGCAGCCTCTTCAG
                                           |   | ||   |   |  |   | |  || |  ||    ||||            ||| || |||||||| || |||||| |||| || || |||||||||||||| || |||||||||||||||||||| || |||||||| || || 
-------------------------------------------gtgcgttgc-gattttgctgggcttttttgagcgtgcttttcc------------agGGATCAAGGAGTCCGACACTGGTCTAGCAGCTCCTAGCCAGTGGGATCTGGTGTCTGATAAGCAAATGATGCAAGAAGAGCAGCCACTGCAA

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|193682744|gb|FK621784.1|FK621784
EST:     GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTG                         GTATAAAGGAGTCTGATACTGGTTTAG
genomic: GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTGgtatgtgcaa ... gttacaatagGTATAAAGGAGTCTGATACTGGTTTAG
EST: gi|298168532|gb|HO009462.1|HO009462
EST:     GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTG                         GTATAAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTG
genomic: GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTGgtatgtgcaa ... gttacaatagGTATAAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTG
EST: gi|192302201|gb|FG997281.1|FG997281
EST:     GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTG                         GTATAAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTG
genomic: GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTGgtatgtgcaa ... gttacaatagGTATAAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTG
EST: gi|209711453|gb|BW665205.1|BW665205
EST:     GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTG                         GTATAAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTG
genomic: GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTGgtatgtgcaa ... gttacaatagGTATAAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTG
EST: gi|193722902|gb|FK657912.1|FK657912
EST:     GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTG                         GTATAAAGGAGTCTGATACTGGTTTAG
genomic: GGCGGAGAAGGAAATCAAAGATATGGCCAAGAAAGTGAATGACTTATGTGgtatgtgcaa ... gttacaatagGTATAAAGGAGTCTGATACTGGTTTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctgttaacacttgtacacctccttaaatgtttgcttcctgttgttacaatagGTATAAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAGGAGCAGCCTCTTCAG
    tgttaac  putative branch site (score: 2)
                         ttaaatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgcatttatagtttatactggttgtcctaattgtatggactggatgctgttaacacttgtacacctccttaaatgtttgcttcctgttgttacaatagGTATAAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAGGAGCAGCCTCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG