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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgaaataaagatctggactctacagttcatattagtttggctgcatagtagcgcaaatctttgctgttatattttttcttatagtgatgattttcattattctatttcatggacatgtgaattttctagagataattgttgtgatttttaagcagGTGATGATGCAATAGAGAAGAGGAGCAAACTTGTTCCTGACTTAAATGATCTTACTGGAGAAGGAAATATTGAAAGTATGCTTTCAGTTGAAATGGGACT

Basic information

species Glycine max
transcript GLYMA10G44630.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G44630.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G126266_T01 (Zea mays), 3'ss of exon 10
gcatgaaataaagatctggactctacagttcatattagtttggctgcatagtagcgcaaatctttgctgttatattttttcttatagtgatgattttcattatt-ctatttcatggacatgtgaattttctagagataattgttgtgatt---tttaagcagGTGATGATGCAATAGAGAAGAGGAGCAAACTTGTTCCTGACTTAAATGATCTTACTGGAGAAGGAAATATTGAAAGTATGCTTTCAGTTGAAATGGGACT---
                                                       |||| |  ||||     || |  || ||||| | | | | |  ||| |   |||| ||||  ||    ||||      | ||||||| |   | |   || | | ||||||  |||   |  |   ||| |  |||||||  |  ||  | | |||| | |  |||||||| ||||| || || |||||||||||||||||||| ||   
-------------------------------------------------------gcaagt--ttgcatccttaatccttattatatttaagctgtagattttagttattccatg--caccccaatt------aaataattgcttcaaatttattcatgtagGTGACAATG---TTCAAGGGAGAAATAAACTTGCACGAGAAATGAGTGATGTAATGGGAGAAGGCAATATAGAGAGCATGCTTTCAGTTGAAATGGGCCTTAG

upper sequence: GLYMA10G44630.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G13260.1 (Arabidopsis thaliana), 3'ss of exon 11
gcatgaaataaagatctggactctacagttcatattagtttggctgcatagtagcgcaaatctttgctgttatattttttcttatagtgatgattttcattattctatttcatggacatgtgaattttctagagataattgttgtgatttttaagcagGTGATGATGCAATAGAGAAGAGGAGCAAACTTGTTCCTGACTTAAATGATCTTACTGGAGAAGGAAATATTGAAAGTATGCTTTCAGTTGAAATGGGACT
                           |     | |   |       ||        ||   | || ||| |||   ||   ||||     || | |||   ||||  ||  || | ||     || |||   | |   | |    |  | | | |||    ||| |  |  |||||||||||| | || ||||  ||  |||||||||| || |||||||||||||||||||||||||| || || |||||||| ||
---------------------------gcaagcaatcactcaatcatatttc----taagattctgttgtgataacattc--tataactccgagtatcac--ttctcgttactgtatat-----ttatct---gttggctatgaaaacatctgaccagAATCTGAGGAGAACGAGAAGAGGAGCCAGCTCGTTCAAGATATAAATGATCTAACAGGAGAAGGAAATATTGAAAGTATGCTCTCTGTGGAAATGGGTCT

upper sequence: GLYMA10G44630.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv01s0244g00070.t01 (Vitis vinifera), 3'ss of exon 11
gcatgaaataaagatctggactctacagttcata--ttagtttggctgcatagtagcgcaaatc-------tttgctgttatattttttcttatagtgatgat----tttcattattctatttcatggacatg-tgaattttctagagataattgttgtgatttttaagcagGTGATGATGCAATAGAGAAGAGGAGCAAACTTGTTCCTGACTTAAATGATCTTACTGGAGAAGGAAATATTGAAAGTATGCTTTCAGTTGAAATGGGACT
||  | |||     | ||  || | |  || ||   ||  |     |  |  || ||  |||         || | | ||  | |||   | | |||    ||    |||||| ||| |||    |  || || | || ||   | |  |      |   |   || ||||||||| ||||     ||||  ||||||||||| ||||  ||||| |||||||| |||||||| ||||| ||||| |||||||||||||||||||||||  |
gctagtaatccctttttgatctttgctcttaatgactttctccttttttactgtggcaaaaactggagtaattggttcttgcactttcattgagagtcgcaatactctttcataattgtatcatctctacttgatcaacttgtcaaacctttccacttaaaacattgagcagGTGAGGATGATCCTGAGACAAGGAGCAAACTGGTTCAGGACTTGAATGATCTAACTGGAGATGGAAACATTGAGAGTATGCTTTCAGTTGAAATGGGTTT

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|57573966|gb|CX546941.1|CX546941
EST:     GGTCGTTGTTTCTGCTGGACAAAAGGCTAAGGAGGAATGCTGGGAAAAAG                         GTGATGATGCAATAGAGAAGAGGAGCAAACTTGTTCCTGACTTAAATGATC
genomic: GGTCGTTGTTTCTGCTGGACAAAAGGCTAAGGAGGAATGCTGGGAAAAAGgcatgaaata ... ttttaagcagGTGATGATGCAATAGAGAAGAGGAGCAAACTTGTTCCTGACTTAAATGATC
EST: gi|58015739|gb|CX702481.1|CX702481
EST:     GGTCGTTGTTTCTGCTGGACAAAAGGCTAAGGAGGAATGCTGGGAAAAAG                         GTGATGATGCAATAGAGAAGAGGAGCAAACTTGTTCCTGACTTAAATGATC
genomic: GGTCGTTGTTTCTGCTGGACAAAAGGCTAAGGAGGAATGCTGGGAAAAAGgcatgaaata ... ttttaagcagGTGATGATGCAATAGAGAAGAGGAGCAAACTTGTTCCTGACTTAAATGATC
EST: gi|58018947|gb|CX705689.1|CX705689
EST:     GGTCGTTGTTTCTGCTGGACAAAAGGCTAAGGAGGAATGCTGGGAAAAAG                         GTGATGATGCAATAGAGAAGAGGAGCAAACTTGTTCCTGACTTAAATGATC
genomic: GGTCGTTGTTTCTGCTGGACAAAAGGCTAAGGAGGAATGCTGGGAAAAAGgcatgaaata ... ttttaagcagGTGATGATGCAATAGAGAAGAGGAGCAAACTTGTTCCTGACTTAAATGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatttcatggacatgtgaattttctagagataattgttgtgatttttaagcagGTGATGATGCAATAGAGAAGAGGAGCAAACTTGTTCCTGACTTAAATGATCTTACTGGAGAAGGAAATATTGAAAGTATGCTTTCAGTTGAAATGGGACT
                                            ttttt  CT-rich tract
                                         tgatttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgaaataaagatctggactctacagttcatattagtttggctgcatagtagcgcaaatctttgctgttatattttttcttatagtgatgattttcattattctatttcatggacatgtgaattttctagagataattgttgtgatttttaagcagGTGATGATGCAATAGAGAAGAGGAGCAAACTTGTTCCTGACTTAAATGATCTTACTGGAGAAGGAAATATTGAAAGTATGCTTTCAGTTGAAATGGGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA