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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcagactagcttgatctgttttatagatcatctttcttctcgttcttgtctttcaattcagaaatcctgatttatatttgaatgattgtatgctgaagGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACTGATGCATTCATGGTGGCACGAGGTGATCTTGGAATGGAGATCCCAGTTG

Basic information

species Glycine max
transcript GLYMA19G00870.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G00870.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g58110.1 (Oryza sativa), 3'ss of exon 2
tagcagactagcttgatctgttttatagatcatctttcttctcgttcttgtctttcaattcagaaatcctgatttatatttgaatgattgtatgctga-agGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACTGATGCATTCATGGTGGCACGAGGTGATCTTGGAATGGAGATCCCAGTTG
|    ||  |   | ||   | | |     |   |   ||  | | || ||  |     |  |   ||    ||  |  || | |  ||   || |   ||||||| || || || || ||  | || || || || ||| || | || || |||||||| ||||| ||  |||||||||||||||||||||| |||||||
ttcgtgatgatgataatacatatgaggtgcctggtaatttaccatgctggttatgttgctgtgcg-tctaatttctttcttaactttttccttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACGGATGCATTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCAGTTG

upper sequence: GLYMA19G00870.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G008714_T01 (Zea mays), 3'ss of exon 2
tagcagactagcttgatctgttttatagatcatctttcttctcgttcttgtctttcaattcagaaatcctgatttatatttga-atgattgt-atgctgaagGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACTGATGCATTCATGGTGGCACGAGGTGATCTTGGAATGGAGATCCCAGTTG
   || | ||  |     |  | || | ||     || |  ||||  | ||  | |  | ||   |||    |   |   ||| ||| ||       || ||||||| || || || || ||  | || ||||| || ||| || | ||||||||||| || ||||| ||  |||||||||||||||||||||| || ||||
-ttcatattacatcatgataatgtacatatagaacttatgatcgtgttggttatgctgt-catggatctgattcctttcatgatatggtttccgctatgcagGTTGAAAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCTGTTG

upper sequence: GLYMA19G00870.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G150098_T01 (Zea mays), 3'ss of exon 2
tagcagactagcttgatctgttttatagatcatctttcttctcgttcttgtctttcaa-ttcaga-aatcctgattt--atatttgaatgattgtatgctgaagGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACTGATGCATTCATGGTGGCACGAGGTGATCTTGGAATGGAGATCCCAGTTG
    |  |||  ||  ||    |  |||    | || || ||        ||| | || |||| |     |||||||   || |   ||| || |    || |||||||||| || || || ||  | || ||||| || ||| || | ||||||||||| || ||||| ||  |||||||||| ||||||||||| ||||| |
--tgacgctacatt--tccacctggtaggctgttttactcctaaccgaattctgttaacttcacatggatctgatttccttaatgatatggttctgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG

upper sequence: GLYMA19G00870.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G63680.1 (Arabidopsis thaliana), 3'ss of exon 3
tagcagactagcttgatctgttttatagatcatctttcttctcgttcttgtctttcaattcagaaatcctgatttatatttgaatgattgtatgctgaagGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACTGATGCATTCATGGTGGCACGAGGTGATCTTGGAATGGAGATCCCAGTTG
              |  |    ||| |  | || |  ||| | | |   ||       ||   ||     ||||   ||| ||||  || | |  | ||||||||||| || ||||||||||||||||| || || ||  |||| || ||||||||||||||||| || || ||||||||||| |||||||| ||  | |
--------------gtacaaagttacaccttatttcacttgtggctaaagtt----ggttttaaaggtaggattgtgattagaatttttatcttattaagGTTGAGAACCAAGAAGGAGTCCTGAATTTCGATGAGATTTTGCGTGAAACTGATGCATTCATGGTTGCTCGTGGTGATCTTGGGATGGAGATTCCGATAG

upper sequence: GLYMA19G00870.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0071g01060.t01 (Vitis vinifera), 3'ss of exon 2
----tagcagactagcttgatctgttttatagatcatctttcttctcgttcttgtctttcaattcagaaatcctgatttatatttgaatgattgtatgctgaagGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACTGATGCATTCATGGTGGCACGAGGTGATCTTGGAATGGAGATCCCAGTTG
     |    |||   ||  | || ||  |  |  |   || | |   ||||||       | | | |  |  |  | | | ||    |||   | | |   |||||||||| || || || ||  | || || || |||||  | || ||||||||  | |||||||| || ||||||||||| ||||||||||||||||| |
atgagaaattactgagtttctgtggttcttcaaggagtgttttgcat-ttcttggtcactgaatgatatgtttttttctttgttgagctgaaaattttc---agGTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACTGACTCCTTCATGGTTGCCCGAGGTGATCTCGGAATGGAGATCCCAGTGG

upper sequence: GLYMA19G00870.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0056g00190.t01 (Vitis vinifera), 3'ss of exon 2
tagcagactagcttgatctgttttatagatcatctttcttctcgttcttgtctttcaattcagaaatcctg--atttatatttgaatgattgta--tgctgaagGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACTGATGCATTCATGGTGGCACGAGGTGATCTTGGAATGGAGATCCCAGTTG
  ||  | |  | || |  ||| |  | ||   ||| | | |   | |  |   |   |       || ||  || |   |||   ||  ||||  | |||||||| ||||| ||||| || ||  | || ||||| ||||| ||||| ||||| ||| |||| ||||| || || |||||||||||||||||||||||||| |
--gcttattt-catggttggttgtgca-atttgcttacatgtttctttgataaatatgtcatagcctcatggcatcttcctttctgtggctgtaattcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACCGATTCATTTATGGTTGCCCGTGGTGATCTTGGAATGGAGATCCCAGTGG

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|254316243|gb|GR827780.1|GR827780
EST:     GTTCTGGGGCCACATGCAAAGACTATTCAGTTGATGTCTAAG                         GTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACT
genomic: GTTCTGGGGCCACATGCAAAGACTATTCAGTTGATGTCTAAGgtattttttt ... tatgctgaagGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACT
EST: gi|254329673|gb|GR839226.1|GR839226
EST:     TCCGCAAGGTTCTGGGGCCACATGCAAAGACTATTCAGTTGATGTCTAAG                         GTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACT
genomic: TCCGCAAGGTTCTGGGGCCACATGCAAAGACTATTCAGTTGATGTCTAAGgtattttttt ... tatgctgaagGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACT
EST: gi|193454775|gb|FK417394.1|FK417394
EST:     TCCGCAAGGTTCTGGGGCCACATGCAAAGACTATTCAGTTGATGTCTAAG                         GTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACT
genomic: TCCGCAAGGTTCTGGGGCCACATGCAAAGACTATTCAGTTGATGTCTAAGgtattttttt ... tatgctgaagGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACT
EST: gi|208178908|gb|GD979659.1|GD979659
EST:     TCCGCAAGGTTCTGGGGCCACATGCAAAGACTATTCAGTTGATGTCTAAG                         GTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACT
genomic: TCCGCAAGGTTCTGGGGCCACATGCAAAGACTATTCAGTTGATGTCTAAGgtattttttt ... tatgctgaagGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACT
EST: gi|18040013|gb|BM308307.1|BM308307
EST:     TCCGCAAGGTTCTGGGGCCACATGCAAAGACTATTCAGTTGATGTCTAAG                         GTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACT
genomic: TCCGCAAGGTTCTGGGGCCACATGCAAAGACTATTCAGTTGATGTCTAAGgtattttttt ... tatgctgaagGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACT
EST: gi|207826461|gb|GD800720.1|GD800720
EST:     AAAGACTATTCAGTTGATGTCTAAG                         GTTGAGAATACAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGAC
genomic: AAAGACTATTCAGTTGATGTCTAAGgtattttttt ... tatgctgaagGTTGAGAAT-CAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGAC
EST: gi|7685758|gb|AW756406.1|AW756406
EST:     TCCGCAAAGTTATGGGGCCACATGCAAAGACTATTCAGTTGATGTCTAAG                         GTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACT
genomic: TCCGCAAGGTTCTGGGGCCACATGCAAAGACTATTCAGTTGATGTCTAAGgtattttttt ... tatgctgaagGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgtctttcaattcagaaatcctgatttatatttgaatgattgtatgctgaagGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACTGATGCATTCATGGTGGCACGAGGTGATCTTGGAATGGAGATCCCAGTTG
                     tcctgat  putative branch site (score: 3)
                          atttatatttgaatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagcagactagcttgatctgttttatagatcatctttcttctcgttcttgtctttcaattcagaaatcctgatttatatttgaatgattgtatgctgaagGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACTGATGCATTCATGGTGGCACGAGGTGATCTTGGAATGGAGATCCCAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC