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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgttagtcttgtggatcaggtatcataaattgaacctttttaaatatattttttttgtagcttcagttgagctttgaccctatatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC

Basic information

species Glycine max
transcript GLYMA08G20830.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 7
-gctgttagtcttgtggatcaggtatcataaattgaacctttttaaatatattttttttgtagcttcagttgagctttgaccctatatattattat-tgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC
     | |    |||| |  | || | |    |            | |||  | | | ||     |   || | |  |     | |||  |||| | ||||||||| |||||||| || || || |||||||| || |||||||||||||| ||||| || |||||||| || ||||| ||||||||| || ||||||||||
aaaactcaaa--tgtgaaatatgtgtaacttttgtggatggagggagtatcatctatctgcccaatgtatttatcgatattattttattgtattgtgtgcagAGGTGATAACATCTGCTGAGTTCCACCCTACTCACTGTAATACATTGGCTTATAGTAGCTCAAAGGGCTCCATTCGACTTGTTGACCTGAGGCAGTCAGC

upper sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 7
---gctgttagtcttgtggatcaggtatcataaattgaacctttttaaatatattttttttgtagcttcagttgagctttgaccctatatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC
     || |  |   |  || | || |||  |  || |  |||  |  |  |  | |  | |||   |  |||| || | ||    || | ||  |||| ||||||| || ||||  || || || ||||| || |||||||||||| |||| |||||||||||||||||||| || || ||  ||||  |||| || |||||
attattgatgtttaagatgacctggaatctgatctttacacttactgtaattcatgtcctggtaatat--gttgtgcat-gatgtaatttgttgatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCTATAGCAGTTCAAAGGGTTCTATCCGACTCATTGATCTGCGACAATCAGC

upper sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 7
gctgttagtcttgtggatcaggtatcataaattgaacctttttaaatatattttttttgtagctt-cagttgagctttgaccctatatattattat-tgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC
||| |     || | | |    |  ||||      |  ||| ||    |    | | ||| | |  | | |||   ||   | |   |  ||| |  ||||||||| |||||||| || ||||| || ||||| ||||| ||||||||||| ||||| || || ||||| || ||||| ||||||||  ||||||| |||||
gctttc--ctttattgtttttatcacatatccgttaagtttctactggtggcatctctgttgttagctgctgatagttattctttggttctatgacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGTATAGTAGCTCTAAGGGCTCCATTCGACTTGTTGATCTGCGGCAATCAGC

upper sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 7
---gctgttagtcttgtggatcaggtatcataaattgaaccttt-ttaaatatattttttttgt-agcttcagttgagctttgaccctatatattattat-tgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC
       ||  |  | |  ||||  |||  |   ||||   | |  |      || ||| |||| |||| | | | |||| ||    | |    ||| |  ||||||||| |||||||| || ||||| || ||||| || || ||||| ||||||||||| || || ||||| || ||||| ||||||||  |||| || |||||
gctttcctttattgtttttatcacatattct---ttgagtttctactggtggcatctttgttgttagctactgat-agctatggttttgttc--tatcacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACCCACTGCAATACGTTGGCATATAGTAGCTCTAAGGGATCCATTCGACTTGTTGATCTGCGCCAATCAGC

upper sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 8
gctgttagtcttgtggatcaggtatcata-aattg----aacctttttaaatatattttttttgtagcttcagttgagctttgaccctatatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC
  | | | ||| || |      | || || ||||     ||   || |   |||  ||  ||||    | || ||     ||  | |   | |||  |||| ||||||| || ||||  || || || || ||  | |||||||||||| |||| ||||| |||||||||||||| || || ||| ||||  |||| || |||||
--tttgaatctggtaggctcattttcctataattattacaagtcttattgctattcttgctttgcgtatgcacttcctgatttgctc---acattcatatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGC

upper sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 7
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 9
--------------gctgttagtcttgtggatcaggta-tcataaattgaacctttttaa-atatattttttttgtagcttcagttgagctt-tgaccctatatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC
               ||||||     ||  |  | ||  || || |  | |||  ||||  ||  | ||   | |     ||  | ||  ||  |||| |||   |  ||  |||||||||||| ||||||||||||||||| ||||| ||||| ||||  || || ||||||||||| || ||||||||||| ||  ||||  |||| ||||||||
gtaagccttggtctactgttatctcagtctaatatgttctcttatacggtacccatttatcatgcaattggat-gcgatatccttcgaatttacgaccatat---tcgttcatgcagAGGTTATCACATCAGCAGAATTTCATCCTACCCATTGCAATATGTTAGCCTATAGCAGTTCGAAAGGTTCAATTCGCCTGATTGATCTGCGCCAGTCAGC

upper sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 7
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 7
---------------------------------gctgt-tagtcttg----tggatcaggtatcataaattgaacctttttaaatatattttttttgtagcttca------gttgagctttgacccta----tatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC
                                   ||| | |||||     ||  |||  | |||  ||         ||| | ||| | ||||||  |  || |      || |||| |    |  |    || ||  |   |||||||||||| |||||||| || ||||| ||||  ||||||||||   | |||||||| |||||||| || || |||||| |  ||||  |||| || |||||
gtatgctacttctcctattttgttagatgttactttgtatggtcttaccattgattcatatgtcaacaacctccttacttttattatctatttttttcacgtttactgcttgtcgagcatgcttctaaatgctacatggtctgtgcagAGGTTATTACATCAGCTGAGTTTCATCCTATCCATTGTAATATGCTCGCATATAGTAGTTCAAAAGGCTCCATTCGTTTGATTGATATGCGTCAATCAGC

upper sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 7
gctgttagtcttgtggatcaggtatcataaattgaacctttttaaatatattttttttgtagcttcagttgagctttgaccctatat----attattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC
  | ||  || |||  ||||   ||      | |   || ||  | | | |  |  |  |   |||  |||||| |||  | |||||    ||| || |||||||||| ||||||||||| || ||||||||||| |||||||| |  || |||||||| |||||||| || ||||| || |||  ||| ||||| ||||||||
aatatt--tcctgtctatcattcatttgttctgggtgctattctactgtttaatgatgctgcattc--ttgagcattggacttatattccaattcttcttgcagAGGTGATAACATCAGCGGAGTTTCACCCTACCCATTGTAACATGTTAGCATATAGTAGTTCAAAAGGCTCAATCCGCCTTAATGATTTGCGACAGTCAGC

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|193650550|gb|FK599845.1|FK599845
EST:     GCAAATATGGAGGATCTGACCG                         AGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCAT
genomic: GCAAATATGGAGGATCTGACCGgtaagttttc ... attattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCAT
EST: gi|193636366|gb|FK584039.1|FK584039
EST:     AAGTTTTAATATTGTTGATGTAAAGCCTGCAAATATGGAGGATCTGACCG                         AGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCAT
genomic: AAGTTTTAATATTGTTGATGTAAAGCCTGCAAATATGGAGGATCTGACCGgtaagttttc ... attattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCAT
EST: gi|14990248|gb|BI315921.1|BI315921
EST:     TTTTAATATTGTTGATGTAAAGCCTGCAAATATGGAGGATCTGACCG                         AGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCAT
genomic: TTTTAATATTGTTGATGTAAAGCCTGCAAATATGGAGGATCTGACCGgtaagttttc ... attattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCAT
EST: gi|208216614|gb|GE012546.1|GE012546
EST:     AGTTTTTAATATTGTTGATGTAAAGCCTGCAAATATGGAGGATCTGACCG                         AGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCAT
genomic: AG-TTTTAATATTGTTGATGTAAAGCCTGCAAATATGGAGGATCTGACCGgtaagttttc ... attattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCAT
EST: gi|7796415|gb|AW781812.1|AW781812
EST:     AAGTTTTAATATTGTTGATGTAAAGCCTGCAAATATGGAGGATCTGACCG                         AGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCAT
genomic: AAGTTTTAATATTGTTGATGTAAAGCCTGCAAATATGGAGGATCTGACCGgtaagttttc ... attattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCAT
EST: gi|193687174|gb|FK630415.1|FK630415
EST:     TAAAGCCAGCAAATATGGAGGATCTGACCG                         AGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCAT
genomic: TAAAGCCTGCAAATATGGAGGATCTGACCGgtaagttttc ... attattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatattttttttgtagcttcagttgagctttgaccctatatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC
                            ctttgac  putative branch site (score: 4)
                                     tatatattattattgc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgttagtcttgtggatcaggtatcataaattgaacctttttaaatatattttttttgtagcttcagttgagctttgaccctatatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC

gctgtta
- - - - tcttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgaccc