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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacataacatgaatgattctatcaggtgcagagtttctctgcgtttttagatgtgttttaatttaattaaaatgcatgtacttttcttttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG

Basic information

species Glycine max
transcript GLYMA11G15010.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 4
aacataacatgaatgattctatcaggtgcagagtttctctgcgtttttagatgtgttttaattta----attaaaatgcatgtacttttcttttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG
  | ||| |  | | |   | |   | |   ||||     |  | || | | || | ||| | |     ||||||||   ||  ||||| |||   |    ||||||||||  |||   || |  | |||||||| ||||||||||| ||||| ||||||||||| ||||||||||||||  |||||||||| |||
--cttaagac-actaaactttttttgcgatcagttctatcgtatcttcaaaagtatattattgtgagatattaaaattt-tgaccttttttttattcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTCAAG

upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G157772_T02 (Zea mays), 3'ss of exon 1
aacataacatgaatg-attctatcaggtgcagagtttctctgcgtttttagatgtgttttaatttaatta--aaatgcatgtacttttcttttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG
| ||||   | ||||  ||   | || ||     |   |     || ||   | || | | | || |  |   | || |  | ||||   |||   |    ||||||||  ||||   |  |  | || ||||| ||||||||||| ||||| ||||||||||| ||||||||||||||  |||||||||| |||
atcatatagtcaatgtgtttcctgagttgtctgttgaatgaattttctttcttctgctcttaattgaccatttactgtaaattctttctatttgttt---tagATGTCATCGAGCCGCTTCTTGTAGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG

upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 3
-aacataacatgaatgattctatcaggtgcagagtttctctgcgtttttagatgtgttttaatttaattaaaatgcatgtacttttcttttccctgaac-agATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG
 |   ||||| ||    |  | |||| ||     ||| |      | |  |     |  | | |||   |       ||||  ||  || |   ||    ||||||||| ||||   |  |  | || ||||| ||||||||||| ||||| ||||||||||| ||||||||||||||  |||||||||| |||
cagtctaaca-gatcactcttctcagttgtttc-tttttaaataatatgtgcctcctcatgagttaggcacttattctgtaaattctttctatttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG

upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 5
----aacataa-catgaatgattctatcaggtgcagagtttctctgcgtttttagatgtgttttaatttaattaaaatgcatgtacttttcttttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG
       | ||  ||   |||||   |  |   ||||     |  | |||||      ||  |||    | | |   || |  | ||||   |||   |    ||||||||| ||||   |  |  | || ||||| ||||||||||| ||||| ||||||||||| ||||||||||||||  ||||| |||| |||
ttttggtacaagtattgttgatttctttggaatcagaaccaattag-gttttagttcatgagttaggc-actgattctgtaaattctttctgtttgttt---tagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACTCTGTTAAG

upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 4
--------aacataacatgaatgattctatcaggtgcagagtttctctgcgtttttagatgtgttttaatttaattaaaatgcatgtacttttcttttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG
        |||| | ||    || | || |      ||| || | | ||| |  | |  || |||   |   | |||   || |  | ||||   | |   |    ||||||||| |||| | |  |  | |||||||| || |||||||| ||||| ||||||||||| ||||||||||||||  |||| ||||| |||
aagagtctaacagatcactgctgctccttttttaatcagtgtatgtgtgcttcctca--tgagtt---aagcacttatcttgtaaatcctttctatctgttt---tagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG

upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 10
----aacataa-catgaatgattctatcaggtgcagagtttctctgcgtttttagatgtgttttaatttaattaaaatgcatgtacttttcttttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG
       | ||  ||   |||||   |  |   ||||     |  | |||||      ||  |||    | | |   || |  | ||||   |||   |    ||||||||| ||||   |  |  | || ||||| ||||||||||| ||||| ||||||||||| ||||| ||||||||  ||||| |||| |||
ttttggtacaagtattgttgatttctttggaatcagaaccaattag-gttttagttcatgagttaggc-actgattctgtaaattctttctatttgttt---tagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATATTCTACAAGCACAACTCTGTTAAG

upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 4
----aacataa-catgaatgattctatcaggtgcagagtttctctgcgtttttagatgtgttttaatttaattaaaatgcatgtacttttcttttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG
       | ||  ||   |||||   |  |   ||||     |  |   |||||| |   |  | |   | | |   || |  | ||||   |||   |    ||||||||| ||||   |  |  | || ||||| ||||||| ||| ||||| ||||||||||| ||||||||||||||  ||||| |||| |||
ttttggtacaagtattgttgatttctttggaatcagaaccaattagg--ttttagttcattagttaggcactgattctgtaaattctttctatttgttt---tagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTGTCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACTCTGTTAAG

upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 3
aacataacatgaatgattctatcaggtgcagagtttctctgcgtttttagatgtgttttaatttaattaaaatgcatgtacttttcttttc--cctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG
                 | ||  |  | |  | ||  ||    ||  |  ||     ||||   ||  ||        ||||  |  ||      |   ||||||| || || |   | ||  | ||||||||||||||||| ||| | ||||| || ||||||||||| ||||||||||||||||| || |||
----------------gtatagtatcttcttaattaatcaaacttacttaatactcattaaccaaaacaatgcattaatactcattcttgtgattttttcagATGTGACTGAACCTCTTTTCGTCGAGGTTGATCAAATCTACCATTTAGCATGTCCCGCTTCTCCAATTTTCTACAAATACAACCCCGTTAAG

upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 3
aacataacatgaatgattcta-tcaggtgcagagtttctctgcgtttttagatgtgttttaatttaattaaaatg-catgtacttttctttt---ccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG
   ||    |  |   |   | |  | ||   ||  |||    |||     ||||     |  |  || |   ||   | || ||    |||   |  | ||||||||| || ||||  |||||||| ||||||||||  || || |||||||| || ||||| ||||| ||||||||||||||||||||||| |||
-gtatggtctcgagactctcagtttgttgttaagcgtcttcttgttc----atgtcaacaagatccatcatcgtgatctctatttggaatttgggctttaaacagATGTTACCGAGCCTTTGTTGATCGAGGTTGATCGGATTTACCATCTTGCTTGTCCTGCCTCTCCTATCTTCTACAAATACAACCCTGTTAAG

upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 4
aacataacatgaatgattctatcaggtgcagagtttctctgcgtttttagatgtgttt-taatttaattaaaatgcatgtacttttcttttcc-ctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG--------
   ||    |   |||   | || ||      | | || |      |   || |   | |  |||  |  |      | || |||  ||||    | |||||||||||| |||| | | ||||| ||||||||||| || || ||||||||||| ||||||||||| ||||||||||| ||||||||||| |||        
-gtatggttt---tgaaattctctggcttgttgctgctattgagaatggaatattcctgtcttttgttctatccatttatattttggttttgggtttaacagATGTCACGGAGCCACTTTTGATCGAGGTTGATCAGATTTACCATCTTGCATGTCCTGCTTCTCCTATCTTCTACAAGTACAACCCTGTGAAGACAATCAA

upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 4
-aacataacatgaatgattctatcaggtgcagagtttctctgcgtttttagatgtgttttaatttaattaaaatgcatgtacttt---tcttttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG
  |  ||| || |   | |  | ||  ||   | | | |    | |  |  |   |||| | ||  | | |   || | || |     | ||||| ||  ||||||||||| |||| ||||||||||||||||||| | || || || |||||||| || |||||||| || || || ||| |||| |||||||||
tcagttaagatcac--aatgaaccacttgtt-aatcttttaatgataattcaca-gtttcatttctaatgattagcttttattccatattttttctcttcacagATGTCACTGAGCCATTGTTGATTGAGGTTGATAAGATATACCACCTTGCATGTCCCGCTTCTCCTATTTTTTATAAACACAATCCTGTAAAG

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|22525432|gb|BU084243.1|BU084243
EST:     CAACCTTAAAAGATGGATTGGCCATCCAAGATTTGAGCTAATTCGTCATG                         ATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCAT
genomic: CAACCTTAAAAGATGGATTGGCCATCCAAGATTTGAGCTAATTCGTCATGgtataatttt ... ccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCAT
EST: gi|18040716|gb|BM309010.1|BM309010
EST:     CAACCTTAAAAGATGGATTGGCCATCCAAGATTTGAGCTAATTCGTCATG                         ATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCAT
genomic: CAACCTTAAAAGATGGATTGGCCATCCAAGATTTGAGCTAATTCGTCATGgtataatttt ... ccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagatgtgttttaatttaattaaaatgcatgtacttttcttttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG
                               tgtacttttcttttcc  CT-rich tract
          ttttaatttaattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacataacatgaatgattctatcaggtgcagagtttctctgcgtttttagatgtgttttaatttaattaaaatgcatgtacttttcttttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG

- - - -catgaat
- - - - - - - - - - - caggtgc
- - - - - - - - - - - - - - - - - -tctctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatgca