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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagaactttgtcgtttggcttctgcatgttgaaattcttaaaatattattttcatttcttctaattttatggtgtacatgtcttttgatgctgatgcagAAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGGAAAGGGACACTCGACCGAATGAAAGAGTCTCTTTGAACAGAATTGGATA

Basic information

species Glycine max
transcript GLYMA04G39490.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39490.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 5
-----------------------------------------------------------------------------------ttagaactttgtcgtttggcttctgcatgttgaaa--ttcttaaaat--attattttcatttcttctaattttatggt---gtacatgtcttttgatgctg----atgcagAAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGGAAAGGGACACTCGACCGAATGAAAGAGTCTCTTTGAACAGAATTG-GATA
                                                                                   |||     |    |  | |  |  | ||| | |||  ||| | || |  ||         |  |||||| ||| |  |   ||   | ||||||  | |||    || ||||||| |||||||| ||||||||||||||||||||| ||||  |  |  | |||     | |  |   ||   | |   ||  | | || |||||   ||  
gttggttctcctatcttgcttatgtactatctcctactgcaatattgcatgatcatgtgctattttactggtttctcctgtgcttaatttctctctgcatagagt--ggatgataaaaccttcctgaagtcaatcgacccatgtaattctaaatttctaatacagtgtttttcttttctttctgcatcattcagAAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTGAACCCACCCCAAGGAAGAGCCAGAATATCCGTCTAAATAGAATAATGAC-

upper sequence: GLYMA04G39490.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g36110.2 (Oryza sativa), 3'ss of exon 6
------------------ttagaactttgtcgtttggcttctgcatgtt----gaaattc---ttaaaatattatttt----catttcttctaattttatggtgtacatgtcttttgatgctgatgcagAAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGGAAAGGGACACTCGACCGAATGAAAGAGTCTCTTTGAACAGAATTGGATA
                  ||   |  ||  ||||||  | ||   | ||       || |   | |   | ||||  |    |||||||  || |  | |  | |  |||   ||||    |  | |||||||||||||||| ||||||||||| ||||| ||| ||||  |  ||   | |       | |    |  | | ||   |  ||| ||||||||      
gttggttccttttccaaattttgaagttaccgtttgtgtgctaggtcttttctcctatccaattcagtgttttatcctagtacatttctcttattcatctaatct-tatgctctttgtactttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAGGACAAACACCCCATAAGGGTCAGAGCACCCGTTTAAACAGAATGATGAG

upper sequence: GLYMA04G39490.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G073415_T03 (Zea mays), 3'ss of exon 7
--ttagaactttgtcgtttggcttctgcatgttgaaattcttaaaatattattttcatttcttctaattttatggtgtacatgtcttttgatgctgatgcagAAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGGAAAGGGACACTCGACCGAATGAAAGAGTCTCTTTGAACAGAATTGGATA---
     ||| | ||     ||  ||||       |||  |   | ||  | |   ||   || ||  |     |  | ||  | ||| |||    || | ||||||| |||||||| ||||||||||||||||||||| ||||  |  || |||||       ||||   ||   |    |||  |||  ||||| |  |      
caactgaattatgctcagtgttttcttggc-ccgaagctaaaacaaattcaccgtcgactcatcataacacttaatatattt-tctgttgtgcatgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCACAGGTGATCACGTCACTGGAACCAACACCTCGGAAGAGCCAC---GTCCGTTTAGACAGAGTGAGGACTGT

upper sequence: GLYMA04G39490.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G052855_T01 (Zea mays), 3'ss of exon 6
----ttagaactttgtcgtttggcttctgcatgttgaaattcttaaaatattattttcatttcttctaattttatggtgtacatgtcttttgatgctgatgcagAAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGGAAAGGGACACTCGACCGAATGAAAGAGTCTCTTTGAACAGAATTGGATA
    |   ||  |     ||     |       |   ||  ||| | |||||  |     || ||||||| | ||| | |   ||   | ||    || | ||||||| |||||||| ||||||||||||||||| ||| ||||     || |||||       ||||   ||   | |  |||  |||| ||||| |  |   
ttggtccaaagctacaaattcattgttgattcatcataacacttcatatatt--tgctggttattctaatctgatgatttttctgctgtgtgcg--tgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGGAACCAACACCTCGGAAGAGCCAGAACGTCCGTTTGGACAGAGTGAGGAC

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|193639094|gb|FK585559.1|FK585559
EST:     AGAAGGCATTG                         AAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGG
genomic: AGAAGGCATTGgtaggttctc ... gctgatgcagAAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGG
EST: gi|254349027|gb|GR860299.1|GR860299
EST:     TAATTCCAAAGATATTATAAGACCAAATCTTTCCATTCGAGAAGGCATTG                         AAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGG
genomic: TAATTCCAAAGATATTATAAGACCAAATCTTTCCATTCGAGAAGGCATTGgtaggttctc ... gctgatgcagAAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGG
EST: gi|151407101|gb|EV276916.1|EV276916
EST:     TAATTCCAAAGATATTATAAGACCAAATCTTTCCATTCGAGAAGGCATTG                         AAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGG
genomic: TAATTCCAAAGATATTATAAGACCAAATCTTTCCATTCGAGAAGGCATTGgtaggttctc ... gctgatgcagAAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGG
EST: gi|151397141|gb|EV267014.1|EV267014
EST:     TAATTCCAAAGATATTATAAGACCAAATCTTTCCATTCGAGAAGGCATTG                         AAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGG
genomic: TAATTCCAAAGATATTATAAGACCAAATCTTTCCATTCGAGAAGGCATTGgtaggttctc ... gctgatgcagAAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGG
EST: gi|254330500|gb|GR841765.1|GR841765
EST:     TAATTCCAAAGATATTATAAGACCAAATCTTTCCATTCGAGAAGGCATTG                         AAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGG
genomic: TAATTCCAAAGATATTATAAGACCAAATCTTTCCATTCGAGAAGGCATTGgtaggttctc ... gctgatgcagAAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGG
EST: gi|31466200|gb|CD408228.1|CD408228
EST:     TAATTCCAAAGATATTATAAGACCAAATCTTTCCATTCGAGAAGGCATTG                         AAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGG
genomic: TAATTCCAAAGATATTATAAGACCAAATCTTTCCATTCGAGAAGGCATTGgtaggttctc ... gctgatgcagAAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGG
EST: gi|31459279|gb|CD401307.1|CD401307
EST:     TAATTCCAAAGATATTATAAGACCAAATCTTTCCATTCGAGAAGGCATTG                         AAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGG
genomic: TAATTCCAAAGATATTATAAGACCAAATCTTTCCATTCGAGAAGGCATTGgtaggttctc ... gctgatgcagAAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGG
EST: gi|193608000|gb|FK557025.1|FK557025
EST:     ATTCGAGAAGGCATTG                         AAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGG
genomic: ATTCGAGAAGGCATTGgtaggttctc ... gctgatgcagAAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGG
EST: gi|51342654|gb|CO983619.1|CO983619
EST:     CAAATCTTTCCATTCGAGAAGGCATTG                         AAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGG
genomic: CAAATCTTTCCATTCGAGAAGGCATTGgtaggttctc ... gctgatgcagAAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attattttcatttcttctaattttatggtgtacatgtcttttgatgctgatgcagAAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGGAAAGGGACACTCGACCGAATGAAAGAGTCTCTTTGAACAGAATTGGATA
     tttcatttcttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagaactttgtcgtttggcttctgcatgttgaaattcttaaaatattattttcatttcttctaattttatggtgtacatgtcttttgatgctgatgcagAAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGGAAAGGGACACTCGACCGAATGAAAGAGTCTCTTTGAACAGAATTGGATA

- - - - - - - - tggcttc
- - - - - - - - - - - - gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgtc