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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtgatcatctacatttctttttcatcttatgattatttatataacaattttccttcaaaatggtggcagctttattttgtagaatctattctag...

Basic information

species Glycine max
transcript GLYMA08G03630.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G03630.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os05g09550.3 (Oryza sativa), 5'ss of exon 3
AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtgatcatctacatttctttttcatcttatgattatttatataacaattttccttcaaaatggtggcagctttattttgtagaatctattctag----------
|| ||| || || || ||  | || || ||  |||||||    || || ||||||||||||||||||||||||||||||||| |  ||||  ||||  |||  | | | ||| | | |||||       | || |   |  | | || ||   ||||      |  ||    || |   || ||    |||| |          
AGCAAGATACGGCGTGCAGTTAGAAAAGGGTGCATTTGAAAAGCGCACAGCTGATTTCTTGTGGATGATGATATTTGGTGCCATATCACTGCTGgtcagtgctagcttgtac-tgtatttttagcagcttaatcag--accttaaaaattcaattcattggactcaca----tactacatataaatctttcttgcttggatcag

upper sequence: GLYMA08G03630.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G143817_T01 (Zea mays), 5'ss of exon 4
AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga---tcatctaca-tttctttttcatcttatgattatttatataacaattttc--cttcaaaatggtggcagctttattttgtagaatctattctag
|| |||||||||||||    | || || ||| ||||||||  ||||||||| |||||||||||||||||||||||||||||| |  ||||||||||  |||  |      |||||| |     |||||  ||| |   |   |    ||| | ||   |||| |  |       |  | | | ||||     |     ||
AGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGCAGATTTCTTGTGGATGATGATATTTGGTGCCATCTCACTATTGgtcagtggtagttctttctacaatcagaatttcagattaggcgaaaccaagagacattcttgaacttctacttaacttgcgtatgactctgtattgcttgaatcag

upper sequence: GLYMA08G03630.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G117388_T04 (Zea mays), 5'ss of exon 4
------AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgt-----atgtgtgat-----catctacatttctt--tttcatcttatgattatttatataacaattttccttcaaaatggtggcagctttattttg-tagaatctattctag
      || |||||||||||||    | || || ||  ||||||||   |||||||| |||||||| ||||||||||||||||||||| |  ||||||||||     || | |  |     ||| |||| ||     ||| | |  |  |      ||   | || |||   | ||  ||    || || | | ||| | |||||        
ATGCAGAGCAAGGTATGGTGTCATGTTGGAAAAGGGTGCATTTGATAAGCGGACTGCAGATTTCTTATGGATGATGATATTTGGTGCCATCTCACTATTGgtcagttatttttactttttgcatttacaatttcaaatttgaccaaaccaagggacattctagaacttttactaaacttgtatacaactctgtattgcttgaatcag------

upper sequence: GLYMA08G03630.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G117388_T01 (Zea mays), 5'ss of exon 4
AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGg-----tatgtgtgat-----catctacatttctt--tttcatcttatgattatttatataacaattttccttcaaaatggtggcagctttattttg-tagaatctattctag
|| |||||||||||||    | || || ||  ||||||||   |||||||| |||||||| ||||||||||||||||||||| |  |||||||||     ||| | |  |     ||| |||| ||     ||| | |  |  |      ||   | || |||   | ||  ||    || || | | ||| | |||||        
AGCAAGGTATGGTGTCATGTTGGAAAAGGGTGCATTTGATAAGCGGACTGCAGATTTCTTATGGATGATGATATTTGGTGCCATCTCACTATTGgtcagttatttttactttttgcatttacaatttcaaatttgaccaaaccaagggacattctagaacttttactaaacttgtatacaactctgtattgcttgaatcag------

upper sequence: GLYMA08G03630.1 (Glycine max), 5'ss of exon 4
lower sequence: AT4G29330.1 (Arabidopsis thaliana), 5'ss of exon 4
AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtgatcatctacatttctttttcatcttatgattatttatataacaattttccttcaaaatggtggcagctttattttgtagaatctattctag------
|| ||| ||||| || ||||| |||||||| ||||||||  | ||||| || || || |||||||||||||| |||||  ||||  | ||||||||||||     |  |    | |  | ||| |  |  ||| |||  |||       ||| || | ||     | |    ||| | |||      |   |||      
AGCAAGATATGGAGTTCAACTCGAGAAAGGGCCATTTGAAAGGCGGACAGCAGACTTTTTGTGGATGATGATCTTTGGATCCTTCACTCTATTGgtatgtaaagcctcccctgtattctattcttact--gatcattgttattgg----ttctttgagaaccccagtactagtatgtggtatgccacaaagtagataatc

upper sequence: GLYMA08G03630.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv04s0008g00510.t01 (Vitis vinifera), 5'ss of exon 4
AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtgatcatctacatttcttttt-catcttat--gattattt-atataacaattttccttcaa--aatg-gtggcagctttattttgtagaatctattctag------------------------------------------------------------
||  || ||||| ||||| || ||||| |||  ||||||  | || || || |||||||||||||||||||||||||| ||  |  || |  |||||||| |||  | |||  ||||| ||   || ||||  | | |||| | |     |||||   |     ||||  |   ||  || || |||   || | |  |                                                              
AGCCAGATATGGGGTCCAGCTGGAGAAGGGAGTATTTGAAAGGCGCACGGCAGATTTCTTGTGGATGATGATATTTGGAGCTCTGACATTGCTGgtatgtctgaa-acctatttttctcttaatattttatctggtcattttagactgtcattttaagttggctaatgcatcagagagttcttctgttagat-tgtcatgtgcattaaaatacattagaatactatctttattcttgtcttgttggactttggatgcttag

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|192308725|gb|FG999764.1|FG999764
EST:     GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG                         GTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
genomic: GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga ... tcaattatagGTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
EST: gi|213599245|gb|DB960013.1|DB960013
EST:     GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG                         GTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
genomic: GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga ... tcaattatagGTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
EST: gi|151406483|gb|EV276298.1|EV276298
EST:     GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG                         GTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
genomic: GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga ... tcaattatagGTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
EST: gi|4305349|gb|AI443749.1|AI443749
EST:     GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG                         GTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
genomic: GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga ... tcaattatagGTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
EST: gi|192332520|gb|FK025625.1|FK025625
EST:     GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG                         GTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
genomic: GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga ... tcaattatagGTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
EST: gi|42723245|gb|CK769144.1|CK769144
EST:     GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG                         GTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
genomic: GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga ... tcaattatagGTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
EST: gi|8827592|gb|BE211322.1|BE211322
EST:     GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG                         GTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
genomic: GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga ... tcaattatagGTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
EST: gi|19452471|gb|BM953881.1|BM953881
EST:     GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG                         GTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
genomic: GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga ... tcaattatagGTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
EST: gi|298172446|gb|HO019486.1|HO019486
EST:     GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG                         GTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
genomic: GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga ... tcaattatagGTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
EST: gi|298183475|gb|HO028688.1|HO028688
EST:     GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG                         GTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
genomic: GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga ... tcaattatagGTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
EST: gi|22524785|gb|BU083596.1|BU083596
EST:     GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG                         GTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
genomic: GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga ... tcaattatagGTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
EST: gi|298169339|gb|HO020699.1|HO020699
EST:     GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG                         GTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
genomic: GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga ... tcaattatagGTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
EST: gi|21887095|gb|BQ740308.1|BQ740308
EST:     GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG                         GTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
genomic: GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga ... tcaattatagGTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
EST: gi|192332519|gb|FK025624.1|FK025624
EST:     GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG                         GTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
genomic: GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga ... tcaattatagGTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
EST: gi|298171588|gb|HO021180.1|HO021180
EST:     GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG                         GTTTTGTCTGCTATCCCCATATTTTGGTCCTCATTTTTGGCAGTACCACTT
genomic: GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga ... tcaattatagGTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
EST: gi|193672594|gb|FK615912.1|FK615912
EST:     GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG                         GTTTTGTCTGCTATCCCCATACTTTGGTCCCCATTTTTGGCAGTACCGCTT
genomic: GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga ... tcaattatagGTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
EST: gi|192308389|gb|FK001347.1|FK001347
EST:     TGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG                         GTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
genomic: TGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga ... tcaattatagGTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
EST: gi|192308360|gb|FK001346.1|FK001346
EST:     GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG                         GTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
genomic: GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga ... tcaattatagGTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
EST: gi|22522837|gb|BU081648.1|BU081648
EST:     GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG                         GTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT
genomic: GGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtga ... tcaattatagGTTTTGTCTGCTATCCCCATATTTTGGTCCCCATTTTTGGCAGTACCACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtgatcatctacatttctttttcatcttatgattatttatataacaattttccttcaaaatggtggcagctttattttgtagaatctattctag

- - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT