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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagcacaactgtgatagggattcttgagtcaggcaatacatttctgcattaactggctgatatctctgattcgtttattaaaatgatttttatgttttagGTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATTATCAAGTCTACAAATATGAAGTGCCTGACTCCACC

Basic information

species Glycine max
transcript GLYMA07G00610.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00610.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G011101_T01 (Zea mays), 3'ss of exon 2
aagcacaactgtgatagggattcttgagtcaggcaatacatttctgcattaactg--gctgatatctctgattc-gtttattaaaatgatttttatgttttagGTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATTATCAAGTCTACAAATATGAAGTGCCTGACTCCACC
   | ||  | |  |  |   |  |   |   |   |   |    ||||| | ||    || | || ||  ||  | | | |   ||  ||| |   | | |||| || || ||||| ||  | ||||| |||| ||| ||| |||| |||||||||||||| ||||| |||||||| ||||| |||||
---ctcattttttttctgccatgctcctttctgtgttgtctgaaagcattcattgtgattggtttcacttcttttgctaagttttattgtttcttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACC
















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|298177195|gb|HO023442.1|HO023442
EST:     CCGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAG                         GTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
genomic: CCGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatgtctct ... tatgttttagGTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
EST: gi|10233968|gb|BE802856.1|BE802856
EST:     CCGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAG                         GTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
genomic: CCGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatgtctct ... tatgttttagGTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
EST: gi|22523781|gb|BU082592.1|BU082592
EST:     CCGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAG                         GTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
genomic: CCGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatgtctct ... tatgttttagGTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
EST: gi|21676110|gb|BQ628461.1|BQ628461
EST:     CCGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAG                         GTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
genomic: CCGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatgtctct ... tatgttttagGTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
EST: gi|209718244|gb|BW657849.1|BW657849
EST:     CCGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAG                         GTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
genomic: CCGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatgtctct ... tatgttttagGTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
EST: gi|14011032|gb|BG725954.1|BG725954
EST:     CCGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAG                         GTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
genomic: CCGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatgtctct ... tatgttttagGTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
EST: gi|193385928|gb|FK352354.1|FK352354
EST:     TGGGAAAACAAG                         GTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
genomic: TGGGAAAACAAGgtatgtctct ... tatgttttagGTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
EST: gi|151408238|gb|EV278046.1|EV278046
EST:     CTGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAG                         GTTGCTGTAAATACAGTATTACAAGATGGGAGGGACTTCCTGAACCACATT
genomic: CCGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatgtctct ... tatgttttagGTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
EST: gi|6455211|gb|AW185894.1|AW185894
EST:     TGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAATTACA-G                         GTTGCTGTAAAT
genomic: CGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAA-ACAAGgtatgtctct ... tatgttttagGTTGCCGTAAAT
EST: gi|22525741|gb|BU084552.1|BU084552
EST:     CCGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAG                         GTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
genomic: CCGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatgtctct ... tatgttttagGTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
EST: gi|207691805|gb|GD674808.1|GD674808
EST:     AGTGGGAAAACAAG                         GTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
genomic: AGTGGGAAAACAAGgtatgtctct ... tatgttttagGTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
EST: gi|6070472|gb|AW099859.1|AW099859
EST:     CTGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAG                         GTTGCTGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT
genomic: CCGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatgtctct ... tatgttttagGTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattaactggctgatatctctgattcgtttattaaaatgatttttatgttttagGTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATTATCAAGTCTACAAATATGAAGTGCCTGACTCCACC
                                         tttttat  CT-rich tract
                       attcgtttattaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagcacaactgtgatagggattcttgagtcaggcaatacatttctgcattaactggctgatatctctgattcgtttattaaaatgatttttatgttttagGTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATTATCAAGTCTACAAATATGAAGTGCCTGACTCCACC

- - - aactgtg
- - - - - - - - - - - - - - tcaggca
- - - - - - - - - - - - - - - - - - - - - - - - - - -tggctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattc