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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTAACAACATCCGTTACTATATTCTTCCTGACAGCTTGAATCTTGAGACCTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgtttatagtttgactacaaaattttcatccatactcaattcactctaattgtttcttggtgagttccccaggttttaattttagcatattttcattacatttccag

Basic information

species Glycine max
transcript GLYMA02G10640.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G10640.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os02g37430.1 (Oryza sativa), 5'ss of exon 3
GGTAACAACATCCGTTACTATATTCTTCCTGACAGCTTGAATCTTGAGACCTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgtttatagtttgactacaaaattttcatccatactcaattcactctaattgtttcttggtgagttccccaggttttaattttagcatattttcattacatttccag
|| |||||||| || || || ||||||||||||||||| || || ||||| |||||||| || || ||||| | | ||||  | |||||||||||||| |||  || | || ||||     |   |  || ||   |||| |  |      || ||||| |   |||      ||    |||||      | |                  
GGAAACAACATTCGCTATTACATTCTTCCTGACAGCTTAAACCTGGAGACATTGCTGGTTGAGGATACACCGAGGGTCAAGGCTAAGAAGCCAACTGCAGgt-ttgataattgttttgtctctctaagttgattt-tactgagctg--ctgaactgtttgtc--tga-----tcaaaccttaatccggaaacag-----------------

upper sequence: GLYMA02G10640.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G416061_T01 (Zea mays), 5'ss of exon 4
GGTAACAACATCCGTTACTATATTCTTCCTGACAGCTTGAATCTTGAGACCTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgtttatagtttgactacaaaattttcatccatactcaattcactctaattgtttcttggtgagttccccaggttttaattttagcatattttcattacatttccag
|| ||||||||||| || ||||| |||||||||||| | || || ||||| |||||||| || || ||||| | | |||| || |||||||| ||| |||||       | ||||           |||||  ||||  ||||    |   | ||    | || |            || | |||| | |  || ||||| | |   ||||
GGAAACAACATCCGCTATTATATCCTTCCTGACAGCCTAAACCTGGAGACTTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTGgt------cagagttct---------ttttctcccat-ttcaaccttcgagatttaccacctgctagc--------attatcatttcatc-catcttcatcaaaaa-ccag

upper sequence: GLYMA02G10640.1 (Glycine max), 5'ss of exon 4
lower sequence: AT4G02840.2 (Arabidopsis thaliana), 5'ss of exon 4
GGTAACAACATCCGTTACTATATTCTTCCTGACAGCTTGAATCTTGAGACCTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgtttatagtttgactacaaaattttcatccatactcaattcactctaattgtttcttggtgagttccccaggttttaattttagcatattttcattacatttccag
|| |||||||| || || ||||||||||| ||||| |||||||| ||||| |||||||| ||||| || || |  ||||||||||| ||||||||||| ||||                 ||||||  ||  |   | || || |    ||   | ||| ||  ||  ||  |   |  | |  |||    | || || ||    |  |||
GGAAACAACATTCGCTATTATATTCTTCCGGACAGTTTGAATCTGGAGACTTTGCTGGTTGAAGACACTCCAAGAATCAAACCCAAAAAGCCAACTGCAGgta-----------------acaaaacatttcttttttctgaactatgcctttgtttttgtttttgtttttgcttagactcatctttctattgttctctttg--gtatcag

upper sequence: GLYMA02G10640.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 5
GGTAACAACATCCGTTACTATATTCTTCCTGACAGCTTGAATCTTGAGACCTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgtttatagtttgactacaaaattttcatccatactcaattcactctaattgtttcttggtgagttccccaggttttaattttagcatattttcattacatttccag
|| |||||||| || || ||||| ||||| ||||||||||||||||||||| |  |||||||||||||||| | | |||| |||||||||||||| || |||| || |       |  ||       | | || | ||  || ||   | | |||         |  |||||||  |||||||||||     ||  |  || |  || |||
GGCAACAACATTCGGTATTATATCCTTCCCGACAGCTTGAATCTTGAGACCCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctc------tatctctttggctctaattc-tatgcattttcgtatgatt---------tatgttccccttgttttaattttttttaatgcttttttccatttcag

upper sequence: GLYMA02G10640.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv19s0015g01330.t01 (Vitis vinifera), 5'ss of exon 3
GGTAACAACATCCGTTACTATATTCTTCCTGACAGCTTGAATCTTGAGACCTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgtttatag----tttgactacaaaattttcatccatactcaattcactctaattgtttcttggtgagttccccaggttttaattttagcatattttcattacatttccag
|| ||||| || || || ||||| ||||| |||||| | ||||| ||||| |||||||||||||||||||| | | |||| |||||||||||||||||||||| ||  |||      |||||||   | |  ||     | | | ||| |  | |||   ||| ||  | | | || |    | ||| |  ||                      
GGCAACAATATTCGGTATTATATACTTCCCGACAGCATAAATCTGGAGACATTGCTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACTGCTGgtattgcatatttcccttttgacttatataccttgtgatagatt-aatactttttaaaattttttt--ttaatgcctc----tataaatccag----------------------

upper sequence: GLYMA02G10640.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ29766 (Selaginella moellendorffii), 5'ss of exon 3
GGTAACAACATCCGTTACTATATTCTTCCTGACAGCTTGAATCTTGAGACCTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgtttatagtttgactacaaaattttcatccatactcaattcactctaattgtttcttggtgagttccccaggttttaattttagcatattttcattacatttccag
|| ||||||||||| ||||| ||||| || |||||||||||||| |||||  |||| ||||| || || ||||   | || |  ||||| ||| | || |||| || | ||   |||          || | || | | |       || |  ||  |||  |                                                
GGGAACAACATCCGCTACTACATTCTACCCGACAGCTTGAATCTCGAGACGCTGCTCGTGGACGATACGCCCAGAGTGAAGCAGAAGAAACCAGCGGCGGgta-tgatcatc-cttgttcttcgtgcttgcttctaaatttgtgctgcttttcttccttccag------------------------------------------------

upper sequence: GLYMA02G10640.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ08912 (Selaginella moellendorffii), 5'ss of exon 3
GGTAACAACATCCGTTACTATATTCTTCCTGACAGCTTGAATCTTGAGACCTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgtttatagtttgactacaaaattttcatccatactcaattcactctaattgtttcttggtgagttccccaggttttaattttagcatattttcattacatttccag
|| ||||||||||| ||||| ||||| || |||||||||||||| |||||  |||| ||||| || || ||||   | || |  ||||| ||| | || |||| || | ||  ||   || |    ||       | | |       || |  ||  |||  |                                                
GGGAACAACATCCGCTACTACATTCTACCCGACAGCTTGAATCTCGAGACGCTGCTCGTGGACGATACGCCCAGAGTGAAGCAGAAGAAACCAGCGGCGGgta-tgatcatccttgttcttcgtgcttgcttctaaaatttgtgctgcttttcttccttccag------------------------------------------------

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|7285068|gb|AW597555.1|AW597555
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|192326454|gb|FK015941.1|FK015941
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|120496339|gb|EH224506.1|EH224506
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|23727600|gb|BU761836.1|BU761836
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|19052973|gb|BM731640.1|BM731640
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|192315263|gb|FK007721.1|FK007721
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|298192845|gb|HO033279.1|HO033279
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|58015388|gb|CX702130.1|CX702130
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|7284502|gb|AW597091.1|AW597091
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|192301565|gb|FG994777.1|FG994777
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|10847035|gb|BF069805.1|BF069805
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|58025133|gb|CX711874.1|CX711874
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|22932348|gb|BU549487.1|BU549487
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|58018364|gb|CX705106.1|CX705106
EST:     CTTGCTGGT---AGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|22541357|gb|BU091200.1|BU091200
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|192314297|gb|FK007035.1|FK007035
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|18714299|gb|BM522772.1|BM522772
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|19268713|gb|BM884969.1|BM884969
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|192301564|gb|FG994776.1|FG994776
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|58015707|gb|CX702449.1|CX702449
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|9902219|gb|BE611187.1|BE611187
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACAAGGAAGGGGCCGTGGCCATGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
EST: gi|298187789|gb|HO031746.1|HO031746
EST:     CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTG                         GCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC
genomic: CTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgttta ... acatttccagGCAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGCCGTGGTCGTGGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTAACAACATCCGTTACTATATTCTTCCTGACAGCTTGAATCTTGAGACCTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgtttatagtttgactacaaaattttcatccatactcaattcactctaattgtttcttggtgagttccccaggttttaattttagcatattttcattacatttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC