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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGGAGCGCTGGGCCATCCCCCACCGGATTCCCCCACCCTCGATTCCTCCGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctattagaattcttcttttctcttctcgatcccttcactggtccacttttcctttgtttttgtttttgtctgataattttcaaaaccctaatttctgtgtag

Basic information

species Glycine max
transcript GLYMA14G08940.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G08940.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv18s0001g10820.t01 (Vitis vinifera), 5'ss of exon 1
GGTGGAGCGCTGGGCCATCCCCCACCGGATTCCCCCACCCTCGATTCCTCCGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgta---------cgctattagaattcttcttttctcttctcgatcccttcactggtccacttttc-ctttgtttttgt-ttttgtctgataattttcaaaaccctaatttctgtgtag-----------------
|| || ||  |||| || || || |||||||| || || || || || || |||||||| ||||| ||||| ||||| || ||||||||||||||||||||||         ||| |  | || | || |||    ||   |    |||      |    | ||| | |   ||        |   |     |||||||     |   || ||  | |                 
GGAGGGGCATTGGGGCACCCTCCGCCGGATTCGCCGACTCTGGACTCGTCGGAGCAGGTTTACATTTCCTCTCTCGCTCTCCTCAAAATGCTCAAACACGgtaacatcttgacgccaagacaagttttatttcaattttagggctgctttgtgatttttttattcgcatcacttccaaaccctaattagggtttttcaatttgttttcttttgatttggggattgggaataatag

upper sequence: GLYMA14G08940.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S46_324V6.1 (Physcomitrella patens), 5'ss of exon 1
GGTGGAGCGCTGGGCCATCCCCCACCGGATTCCCCCACCCTCGATTCCTCCGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctattagaattcttcttttctcttctcgatcccttcactggtccacttttcctttgtttttgtttttgtctgataattttcaaaaccctaatttctgtgtag
|| ||  |    ||    || |  || ||||| |||  | | ||||| || ||||| || ||||| ||||| || || || ||||||||||||||||| ||||||||  | ||||  |  | | |    |  || |  ||      |    | | |  |||     |   || |      | ||    ||   |  ||  |   | |
GGCGGTTCTGGAGGTGGACCGCATCCAGATTCACCCCTCGTTGATTCGTCGGAGCAAGTGTACATTTCCTCTCTGGCGCTGCTCAAAATGCTCAAACATGgtacgctgcttgaatcataatatac----caggaccgttttgtcatttttatgtccaattgcaggcgaacttcttgtgcgaattc---aattattgttcttacttgg

upper sequence: GLYMA14G08940.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ37436 (Selaginella moellendorffii), 5'ss of exon 1
GGTGGAGCGCTGGGCCATCCCCCACCG-GATTCCCCCACCCTCGATTCCTCCGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctattagaa--ttcttcttttctcttctcgatcccttcactggtccacttttcctttgtttttgtttttgtctgataattttcaaaaccctaatttctgtgtag
 | ||   || | | ||| || ||||  ||||| |||  | ||||  | ||||||||||||||||||||||| || || || |||||||||||||| ||||||| |     |||    ||  | |||   | || || |  | | ||  |                                                            
-GCGGGCGGCGGTGGCATGCCTCACCCCGATTCGCCCCTCGTCGACACGTCCGAGCAGGTCTACATCTCCTCGCTAGCGCTGCTCAAAATGCTCAAGCACGgtaaggagggagagagctccgcattttcgtgctagagctttgcgcttctttcgcag-----------------------------------------------------

upper sequence: GLYMA14G08940.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ16494 (Selaginella moellendorffii), 5'ss of exon 1
GGTGGAGCGCTGGGCCATCCCCCA-CCGGATTCCCCCACCCTCGATTCCTCCGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctattagaattcttcttttctcttctcgatcccttcactggtccacttttcctttgtttttgtttttgtctgataattttcaaaaccctaatttctgtgtag-
|| |||| |  | ||   ||| || || || || ||     ||||| | || ||||| ||||||||||| || ||||| |||||||| |||||||| ||||||| |   ||  ||   |   ||||| | |  |||   ||| || |    |||| | |   ||  || |   |    ||  || | |   |  |  |||    ||   
GGAGGAG-GAGGCGCTGGCCCGCATCCCGACTCGCCGCTGGTCGATACGTCGGAGCAAGTCTACATCTCATCGCTCGCGCTTCTCAAGATGCTCAAGCACGgtaggtccttgaaaacttagatttct-tgcgggat---ttcgcttggat-ctttccataccttgctgctcgagc---atgtttctaagcgcagtgctttgctcgttcc

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|33390193|gb|CA853400.1|CA853400
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACG                         GAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctatt ... ttctgtgtagGAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
EST: gi|298190679|gb|HO032800.1|HO032800
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACG                         GAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctatt ... ttctgtgtagGAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
EST: gi|12773252|gb|BG238179.1|BG238179
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACG                         GAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctatt ... ttctgtgtagGAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
EST: gi|192300390|gb|FG991462.1|FG991462
EST:     CGAGCAGGCCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACG                         GAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctatt ... ttctgtgtagGAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
EST: gi|151394289|gb|EV264160.1|EV264160
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACG                         GAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGCTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctatt ... ttctgtgtagGAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
EST: gi|213602552|gb|DB956572.1|DB956572
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACG                         GAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctatt ... ttctgtgtagGAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
EST: gi|254326087|gb|GR840679.1|GR840679
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACG                         GAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctatt ... ttctgtgtagGAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
EST: gi|120494533|gb|EH222700.1|EH222700
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACG                         GAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctatt ... ttctgtgtagGAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
EST: gi|6341699|gb|AW164585.1|AW164585
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACG                         GAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctatt ... ttctgtgtagGAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
EST: gi|213599137|gb|DB962230.1|DB962230
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACG                         GAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctatt ... ttctgtgtagGAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
EST: gi|192303126|gb|FG994244.1|FG994244
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACG                         GAAGAGCTGGGG-ACCCATGGAAGTGATGGGTCTGATGT-GGGGGA
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctatt ... ttctgtgtagGAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGA
EST: gi|8669760|gb|BE190867.1|BE190867
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACG                         GAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctatt ... ttctgtgtagGAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
EST: gi|23725587|gb|BU760753.1|BU760753
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACG                         GAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctatt ... ttctgtgtagGAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
EST: gi|298182393|gb|HO026568.1|HO026568
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACG                         GAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctatt ... ttctgtgtagGAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
EST: gi|209698688|gb|BW656513.1|BW656513
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACG                         GAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctatt ... ttctgtgtagGAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
EST: gi|298190950|gb|HO038429.1|HO038429
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACG                         GAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctatt ... ttctgtgtagGAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
EST: gi|298195630|gb|HO044021.1|HO044021
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACG                         GAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctatt ... ttctgtgtagGAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
EST: gi|151394039|gb|EV263910.1|EV263910
EST:     CGAGCAGGTCTACATCTCCTCCATCGCCCTTCTCAAAATGCTCAAACACG                         GAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctatt ... ttctgtgtagGAAGAGCTGGGGTACCCATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGGAGCGCTGGGCCATCCCCCACCGGATTCCCCCACCCTCGATTCCTCCGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACGgtacgctattagaattcttcttttctcttctcgatcccttcactggtccacttttcctttgtttttgtttttgtctgataattttcaaaaccctaatttctgtgtag

- - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC