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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatgccattcaatgtaaaaactggtcttttttttcttatgttttgtttttattttgtttgattcaaaatttctatatgaaaattcttaattttatccataccattgtgtaacctgtttctcctgttttttgtttttttttaaattcttcttacctttgtgcag

Basic information

species Glycine max
transcript GLYMA11G34980.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G34980.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G061745_T03 (Zea mays), 5'ss of exon 5
AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatgccattcaatgtaaaaactggtcttttttttcttatgttttgtttttattttgtttgattcaaaatttctatatgaaaattcttaattttatccataccattgtgtaacctgtttctcctgttttttgtttttttttaaattcttcttacctttgtgcag
||||| ||||| |||||||| || || ||||| ||||| || ||||| ||||| |||||||||||||||||||| ||||   | ||    ||    | || |     |           |    || | |  |||||  |    || | ||     | | |||||| ||  ||  |  |  || | |   |                                                      
AATGCAACTCAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgcatgaacaacaacca----------aaaagttatatggattttacta---tcgagatggtattgttaaaattgtt--ttcaagtcggacgacttgct------------------------------------------------------

upper sequence: GLYMA11G34980.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 5
AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatgccattc----aatgtaaaaactggtcttttttttcttatgttttgtt-tttattttgtttgattcaaaatttctatatgaaaattcttaattttatccataccattgtgtaacctgtttctcctgttttttgtttttttttaaattcttcttacctttgtgcag
||||| || || |||||||| || || ||||| ||||| || ||||| |||||||||||||||||||||||||| ||||   | ||    ||    | || |  |||           |   |   ||||  | | ||  | || |  |  ||  |    || |  |   || |                                                                            
AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgatactgcatgaacaacaaaaaggatatgtggattttactatctagatggtgttgtcaaatgtcatcatttataggctccttc--------------------------------------------------------------------------

upper sequence: GLYMA11G34980.1 (Glycine max), 5'ss of exon 5
lower sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 5
AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatgccattcaatgtaaaaactggtcttttttttcttatgttttgtttttattttgtttgattcaaaatttctatatgaaaattcttaattttatccataccattgtgtaacctgtttctcctgttttttgtttttttttaaattcttcttacctttgtgcag
||||| ||||| ||||| || ||||| || || |||||| |  |||| |||||||||||||||||||||||||| ||||| ||         || |  ||||| | ||||||  |  ||   |    | |   ||  |||| |   |||  |  | | |||   |||| |     ||        || ||  || |   |      || || ||| || |  |                      
AATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATTGCTGCTCATGAAGTTGAGGAAATCGgtatgtc-------caaaagggaaaacagttcttttgatgatttcat--catctcggttgagttttaaagaaatgtgttttgtgattgttctgaggaagatt-------ttctgacacttacctgcgtcattctt-gttcttgtacag---------------------

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|254323156|gb|GR835764.1|GR835764
EST:     GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAG                         GAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
genomic: GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatg ... ctttgtgcagGAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
EST: gi|208217759|gb|GE016057.1|GE016057
EST:     GCTCATGAAGTTGAGGAAATAG                         GAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
genomic: GCTCATGAAGTTGAGGAAATAGgtatttcatg ... ctttgtgcagGAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
EST: gi|6071648|gb|AW101035.1|AW101035
EST:     GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAG                         GAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTT
genomic: GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatg ... ctttgtgcagGAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTT-
EST: gi|193562849|gb|FK518652.1|FK518652
EST:     GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAG                         GAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
genomic: GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatg ... ctttgtgcagGAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
EST: gi|58016090|gb|CX702832.1|CX702832
EST:     GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAG                         GAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
genomic: GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatg ... ctttgtgcagGAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
EST: gi|15662128|gb|BI699499.1|BI699499
EST:     GCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAG                         GAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
genomic: GCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatg ... ctttgtgcagGAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
EST: gi|12774685|gb|BG239612.1|BG239612
EST:     GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAG                         GAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
genomic: GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatg ... ctttgtgcagGAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
EST: gi|193630911|gb|FK585066.1|FK585066
EST:     GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAG                         GAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
genomic: GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatg ... ctttgtgcagGAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
EST: gi|207802987|gb|GD773500.1|GD773500
EST:     CATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAG                         GAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
genomic: CATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatg ... ctttgtgcagGAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
EST: gi|254323157|gb|GR835765.1|GR835765
EST:     GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAG                         GAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
genomic: GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatg ... ctttgtgcagGAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
EST: gi|58017218|gb|CX703960.1|CX703960
EST:     GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAG                         GAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
genomic: GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatg ... ctttgtgcagGAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
EST: gi|5058103|gb|AI736579.1|AI736579
EST:     GCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAG                         GAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
genomic: GCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatg ... ctttgtgcagGAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
EST: gi|58017413|gb|CX704155.1|CX704155
EST:     GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAG                         GAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
genomic: GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatg ... ctttgtgcagGAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
EST: gi|58023179|gb|CX709920.1|CX709920
EST:     GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAG                         GAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
genomic: GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatg ... ctttgtgcagGAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
EST: gi|208056626|gb|GD850343.1|GD850343
EST:     GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAG                         GAGTGGAACACTTGCTTAGAGATGTGAAGGA
genomic: GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatg ... ctttgtgcagGAGTGGAACACTTGCTTAGAGATGTGAAGGA
EST: gi|151411180|gb|EV280991.1|EV280991
EST:     GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTCGAGGAAATAG                         GAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG
genomic: GTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatg ... ctttgtgcagGAGTGGAACACTTGCTTAGAGATGTGAAGGATACAACCATTAGCACCCTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatgccattcaatgtaaaaactggtcttttttttcttatgttttgtttttattttgtttgattcaaaatttctatatgaaaattcttaattttatccataccattgtgtaacctgtttctcctgttttttgtttttttttaaattcttcttacctttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT