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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctgattgtctgttgttctcatcctctatattttgattctgagcttctgcttttctcaatattatgactaaatgtatggttggtaattttacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATACATGTCTCTGGATCAGATCTCTCCTTTGACGTTTAGCATTGGAAACACC

Basic information

species Glycine max
transcript GLYMA02G25290.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G25290.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g08840.2 (Oryza sativa), 3'ss of exon 4
-ttctgattgtctgttgttctcatcct-ctatattttgattctgagcttctgcttttctcaatattatgactaaatgtatggttggtaattttacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATACATGTCTCTGGATCAGATCTCTCCTTTGACGTTTAGCATTGGAAACACC
  | |  |  |   |  ||  || | | ||| |   |       | |   ||  | | | | |  ||| ||| ||  | |||  ||   ||  | |    |||||| | ||||| || || || ||||| ||  ||||||| || ||||| ||||||||||||||| |||| ||||| ||||| ||||||||||| || || 
tatattgtatttgatgatttacaacatactacagcgtatgcagcaacacttgagtattttattgatattacttaaattttgg--ggatgttgaatattgtagGTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTACATGTCTCTGGATGAGATTTCTCCATTGACATTTAGCATTGGCAATACG

upper sequence: GLYMA02G25290.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G431314_T01 (Zea mays), 3'ss of exon 4
---ttctgattgtctgttgttctcatcctctatatt---ttgattctgagcttctgcttttctcaatattatgactaaatgtatggttggtaattttacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATACATGTCTCTGGATCAGATCTCTCCTTTGACGTTTAGCATTGGAAACACC
   | |||    | |   |  || ||    ||| ||   || ||| |  | ||     | | |  ||||| |  ||||  || |   ||   | |||| |     ||||| | ||||| || || || ||||||||  |||| || || ||||| ||||||||||| |||||||||||||| ||||||||||||||||| || || 
tagtgctgcccttattgaggacttatatattatgttggattaattttatgattgcatgtatattgatattttccctaa-cgtgttactgtcgaatttata-----gGTGGATCGCTGCACAGAGCGTGTTCTATCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATCTCTCCATTGACGTTTAGCATTGGCAATACA

upper sequence: GLYMA02G25290.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 4
------ttctgattgtctgttgttctcatcctctatattttgattctgagcttctgcttttctcaatattatgactaaatgtatggttggtaattttacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATACATGTCTCTGGATCAGATCTCTCCTTTGACGTTTAGCATTGGAAACACC
      ||  |||||    | |     |       |  | | ||     |  | |   | |    ||||| |  |||| ||| |   || | | |||| |     ||||| | ||||| || || || ||||| ||  |||| || || ||||| ||||||||||| |||||||| ||||| ||||| || |||||||| || || 
tattattttggattgatgttaggatctaatgatagtgatattatatcacgactgtatgtatactgatattttccctaa-tgtgttactgttgaatttata-----gGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATTTCTCCATTGACATTCAGCATTGGCAATACA

upper sequence: GLYMA02G25290.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 3
ttctgattgtctgttgttctcatcctctatattttgattctgagcttctgcttttctcaatattatgactaaat--gtatggttggtaattttacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATACATGTCTCTGGATCAGATCTCTCCTTTGACGTTTAGCATTGGAAACACC
  || |  || |     ||      ||| | |  |||||  |    |       || || |    |  |  | |    ||  ||  | | |  |     ||||||| | | ||| || ||||| |||||||| || ||||| |||||||| ||||||||| | || || |||||||| |||||||||||  |||| ||||||
--ctaaacgtttaagaatccttgagtctttttagtgattagggcaatgaatccatcccattcacttatccgattccacatttttctttaatcaaatttgcagGTGGGTGGTTGCGCAGAGTGTGTTCTATCACCTCTACAACCAAGTGTCTTACATGTCTTTAGACCAAATCTCTCCCTTGACGTTTAGTGTTGGTAACACC

upper sequence: GLYMA02G25290.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 3
ttctgattgtctgttgttctcatcc---tctatattttgattctgagcttctgcttttctcaatattatg--actaaatgtatggttggtaattttacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATACATGTCTCTGGATCAGATCTCTCCTTTGACGTTTAGCATTGGAAACACC
     |||  ||||  ||| ||  |   | ||  |  |  || |   ||| |   ||      |  || |  | |   ||| ||| || || || ||||    |||||| | || || || |||||||||||||| || |||||||| |||||||||||||| |||||| |||||||||| ||||||||||||||||||||||||
-----attccctgtgtttcccactcagttgtaagtggtagttgttttctttttgcttggcttttgctaaggaaatgtttgtgtggctgttatttgtacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATACATGTCGCTGGATGAGATCTCTCCCTTGACGTTTAGCATTGGAAACACC

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|26058858|gb|CA801772.1|CA801772
EST:     GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATG                         GTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
genomic: GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATGgtaatttcaa ... tacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
EST: gi|22933643|gb|BU550782.1|BU550782
EST:     GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATG                         GTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
genomic: GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATGgtaatttcaa ... tacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
EST: gi|21285521|gb|BQ473392.1|BQ473392
EST:     GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATG                         GTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
genomic: GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATGgtaatttcaa ... tacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
EST: gi|5678151|gb|AI939281.1|AI939281
EST:     GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATG                         GTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
genomic: GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATGgtaatttcaa ... tacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
EST: gi|5770799|gb|AI973973.1|AI973973
EST:     GCTGCTGGATGGCAAACAGCCATGTCTCANATTGGACCCCAATTCATATG                         N
genomic: GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATGgtaatttcaa ... tacacaacag-
EST: gi|5770799|gb|AI973973.1|AI973973
EST:     GCTGCTGGATGGCAAACAGCCATGTCTCANATTGGACCCCAATTCATATG                         N
genomic: GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATGgtaatttcaa ... tacacaacag-
EST: gi|38191725|gb|CF920931.1|CF920931
EST:     GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATG                         GTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
genomic: GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATGgtaatttcaa ... tacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
EST: gi|18734052|gb|BM527958.1|BM527958
EST:     GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATG                         GTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
genomic: GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATGgtaatttcaa ... tacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
EST: gi|6567001|gb|AW234628.1|AW234628
EST:     GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATG                         GTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
genomic: GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATGgtaatttcaa ... tacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
EST: gi|208193486|gb|GD992903.1|GD992903
EST:     GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATG                         GTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
genomic: GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATGgtaatttcaa ... tacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
EST: gi|298191223|gb|HO038702.1|HO038702
EST:     GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATG                         GTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
genomic: GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATGgtaatttcaa ... tacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
EST: gi|15664125|gb|BI701496.1|BI701496
EST:     GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATG                         GTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
genomic: GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATGgtaatttcaa ... tacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
EST: gi|10236345|gb|BE805233.1|BE805233
EST:     GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATG                         GTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
genomic: GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATGgtaatttcaa ... tacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
EST: gi|23729684|gb|BU762944.1|BU762944
EST:     GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATG                         GTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA
genomic: GCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATGgtaatttcaa ... tacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgcttttctcaatattatgactaaatgtatggttggtaattttacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATACATGTCTCTGGATCAGATCTCTCCTTTGACGTTTAGCATTGGAAACACC
                     gactaaa  putative branch site (score: 2)
             aatattatgactaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctgattgtctgttgttctcatcctctatattttgattctgagcttctgcttttctcaatattatgactaaatgtatggttggtaattttacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATACATGTCTCTGGATCAGATCTCTCCTTTGACGTTTAGCATTGGAAACACC

- ctgattg
- - - - -tctgttg
- - - - - - - - - - catcctc
- - - - - - - - - - - - - - - - - -gattctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttgg