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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgctggctccaaagaattcattggcatagtttctgacaaaattttccgtaccttctgttcaacagtaagtgacttactttaattcttaatttagGTTCTAAGGTATCTACTCTCGAATTCAAGATGGTGGCTGGATGAATACAAGTTTGATGGATTTCGATTTGATGGTGTTACATCAATGATGTACACTCATC

Basic information

species Glycine max
transcript GLYMA03G35020.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 12
gtaagtgctggctccaaagaattcattggcatagtttctgacaaaattttccgtaccttctgttcaacagtaagtgact-tactttaattcttaatttagGTTCTAAGGTATCTACTCTCGAATTCAAGATGGTGGCTGGATGAATACAAGTTTGATGGATTTCGATTTGATGGTGTTACATCAATGATGTACACTCATC
|||||      |   ||    | | |     ||     |  ||  |||     | | ||    || |  ||   || |   | ||| || |||| |  |||||||||| | |||||| || ||| ||||||||||||| || || || ||||||||||| ||  ||||||| ||||| || |||||||||||||||||||
gtaaggaaca-cgttaatcgctacttccctttacaaagtatcattattcat-atgcattaatctctattgtgtttgccaacatttttatcctta-tacagGTTCTAAGATTTCTACTATCCAATGCAAGATGGTGGCTCGAGGAGTATAAGTTTGATGGTTTCAGATTTGACGGTGTAACCTCAATGATGTACACTCATC

upper sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G032628_T01 (Zea mays), 3'ss of exon 12
gtaagtgctggctccaaagaattcattggcatagtttctgacaaaattttccgtaccttctgttcaacagtaagtgacttactttaattcttaatttagGTTCTAAGGTATCTACTCTCGAATTCAAGATGGTGGCTGGATGAATACAAGTTTGATGGATTTCGATTTGATGGTGTTACATCAATGATGTACACTCATC
    || | |     |||   |  ||   |||   || |      ||| |||     |||||      |       |   | ||||  ||   ||  ||||| |||| | ||| ||||| ||| | ||||||||||| || ||||| ||||||||||| || || ||||||||||| || || ||||||||||||||||
----gtacggaacaaaaatgctctatctccattaatttt------attctcctatttttctgcctg-tatcgttccaacaatttta--tccgtatgcagGTTTTAAGATTTCTTCTCTCCAATGCTAGATGGTGGCTCGAGGAATATAAGTTTGATGGTTTCCGTTTTGATGGTGTGACCTCCATGATGTACACTCATC

upper sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 12
gtaagtgctggctccaaagaattcattggcatagtttctgacaaaattttccgtaccttctgttcaacagtaagtgacttactttaattcttaatttagGTTCTAAGGTATCTACTCTCGAATTCAAGATGGTGGCTGGATGAATACAAGTTTGATGGATTTCGATTTGATGGTGTTACATCAATGATGTACACTCATC
                   |  ||||  ||| | | | | |   |||  | | ||  |  | |  |     |  | ||  | || | ||  |     ||||| | || | |||| | || ||| | ||||||||||| || ||||| || |||||||| |||||||||||||| || || || |||||||| ||||| |
-----------------gtatgtcatgtgcagaatgtattagctaatagttcatatttattttctatacacacataac--aattcattttgtg---cagGTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAATTTGATGGGTTTCGATTTGATGGGGTGACCTCCATGATGTATACTCACC

upper sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 12
lower sequence: AT2G36390.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaagtgctggctccaaagaattcat-tggcatagtttctgacaaaattttccgta---ccttctgttcaacagtaagtg------------acttac-tttaattctta---atttagGTTCTAAGGTATCTACTCTCGAATTCAAGATGGTGGCTGGATGAATACAAGTTTGATGGATTTCGATTTGATGGTGTTACATCAATGATGTACACTCATC
||| || ||   |||  ||| || || | |||   ||| ||  |||   ||  ||    ||   || |      || ||             | | || |||  | |||    |||||||| || |||||||| || || ||  | |||||||||||||| ||||||||||||||||| ||  ||||||||||||| || || ||||||||||||||||
gtatgt-ctctttccgtagagttgatattgcaatatttatgggaaagcctttagtgtagccccatgctggtggttatgtctggtccttgtgtattgacgtttggtccttgtgtatttagGTGCTTAGGTATCTTCTTTCCAACGCGAGATGGTGGCTGGAAGAATACAAGTTTGATGGGTTCAGATTTGATGGTGTGACTTCCATGATGTACACTCATC

upper sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaagtgctggctccaaagaattcattggcatagtttctgacaaaat--tttccgtaccttctgttcaacagtaagtgacttactttaattcttaatttagGTTCTAAGGTATCTACTCTCGAATTCAAGATGGTGGCTGGATGAATACAAGTTTGATGGATTTCGATTTGATGGTGTTACATCAATGATGTACACTCATC
||| ||      | |    | || | | | | |  |  |||  | |    |||| ||    || | ||     ||  | ||   || |  | ||     ||||  || | ||||| || || ||| || | |||||||| || ||||||||||||||||||||| ||||||||||||| || ||||||||||| |||||||
gtatgtaactttttcgtgaattttaatcgaaaatgtagtgaacatacaacttccttaagcactat-cagttccaacagtctcttttgatcttttctaacagGTATTACGATATCTCCTTTCAAATGCACGGTGGTGGCTAGAAGAATACAAGTTTGATGGATTTAGATTTGATGGTGTAACCTCAATGATGTATACTCATC

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|207810208|gb|GD781066.1|GD781066
EST:     GTTATCATTGGATGTGGGATTCTCGCCTTTTTAACTACGGAAGCTGGGAA                         GTTCTAAGGTATCTACTCTCGAATTCAAGATGGTGGCTGGATGAATACAAG
genomic: GTTATCATTGGATGTGGGATTCTCGCCTTTTTAACTACGGAAGCTGGGAAgtaagtgctg ... cttaatttagGTTCTAAGGTATCTACTCTCGAATTCAAGATGGTGGCTGGATGAATACAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattttccgtaccttctgttcaacagtaagtgacttactttaattcttaatttagGTTCTAAGGTATCTACTCTCGAATTCAAGATGGTGGCTGGATGAATACAAGTTTGATGGATTTCGATTTGATGGTGTTACATCAATGATGTACACTCATC
                                           ttctt  CT-rich tract
                                acttactttaattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgctggctccaaagaattcattggcatagtttctgacaaaattttccgtaccttctgttcaacagtaagtgacttactttaattcttaatttagGTTCTAAGGTATCTACTCTCGAATTCAAGATGGTGGCTGGATGAATACAAGTTTGATGGATTTCGATTTGATGGTGTTACATCAATGATGTACACTCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA