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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagttgaatttaacagccaagtttacacttgtttctttgaggtgattttctttctttggtgaaagtcctaataatctagttgctttaattatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTACAGCGTAAAGAGGATACGAATGACCGCTATGTTGCTGCTCTAAGAGGAG

Basic information

species Glycine max
transcript GLYMA11G02900.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G02900.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g29320.1 (Oryza sativa), 3'ss of exon 1
taagttgaatttaacagccaagtttacacttgtttctttgaggtgattttctttctt-tggtgaaagtcctaataatctagttgcttta-attatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTACAGCGTAAAGAGGATACGAATGACCGCTATGTTGCTGCTCTAAGAGGAG
  | | |   || || |  |  |||    |   || |||  | |  |  | | |||     || |  |  |  |  |  | || | ||  || |   | ||||||||||||||||| ||    ||||||||||||||||  || |||||||| ||  | |||||||| || |||||| | ||||||||||| || | ||| |
ccattggttcttcactgttagttttgt--tgacttgtttatgctactactttgtctaacattgcacatgttgtttttgcaattccattgtatgacaaaacagATGATGGGGCAAGTGAACCGGGAGAGACTGGCAGAGTTTCTTGGAGAGCTGCAAAGGAAAGAGGACACAAATGACAGATATGTTGCTGCCCTCAAAGGGG

upper sequence: GLYMA11G02900.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv19s0085g00990.t01 (Vitis vinifera), 3'ss of exon 1
-------taagttgaatttaacagccaagtttacacttgtttctttgaggtgattttctttctttggtgaaagtcctaataatctagttgctttaattatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTACAGCGTAAAGAGGATACGAATGACCGCTATGTTGCTGCTCTAAGAGGAG
       ||   |||| |       | | |||    | |||   |||| |   |||| |||        | | |  | | | | |   ||||| |||    |  |||||||||||| |||| ||| ||||||| |||||||| |  || || || || ||||||||||||||||| |||||||| ||||||||||||||  ||||||
aactgtctactatgaaatgggtt-tcgattttgtgatggttctcttgaag---ttttgttttcccacaaacatttttgacagttt---tgcttgaatcgaatggcagATGATGGGGAAAGTAAATCAAGAGAGGCTGGCAGAATTTCTTGGGGAACTGCAGCGTAAAGAGGATACAAATGACCGGTATGTTGCTGCTCTGCGAGGAG
















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|9983184|gb|BE657292.1|BE657292
EST:     ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTG                         ATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
genomic: ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTGgtattccttc ... tatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
EST: gi|193426424|gb|FK386147.1|FK386147
EST:     ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTG                         ATGATGGGGCAAGTCAATAGAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
genomic: ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTGgtattccttc ... tatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
EST: gi|254333436|gb|GR848354.1|GR848354
EST:     ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTG                         ATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
genomic: ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTGgtattccttc ... tatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
EST: gi|12774006|gb|BG238933.1|BG238933
EST:     ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCC--AATCATTG                         ATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
genomic: ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTGgtattccttc ... tatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
EST: gi|7640674|gb|AW734971.1|AW734971
EST:     ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTG                         ATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
genomic: ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTGgtattccttc ... tatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
EST: gi|51336352|gb|CO980218.1|CO980218
EST:     ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCC--AATCATTG                         ATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
genomic: ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTGgtattccttc ... tatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
EST: gi|213599301|gb|DB960041.1|DB960041
EST:     ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTG                         ATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
genomic: ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTGgtattccttc ... tatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
EST: gi|6747246|gb|AW317702.1|AW317702
EST:     ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTG                         ATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
genomic: ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTGgtattccttc ... tatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
EST: gi|254333435|gb|GR848353.1|GR848353
EST:     ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTG                         ATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
genomic: ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTGgtattccttc ... tatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
EST: gi|192305440|gb|FG998280.1|FG998280
EST:     ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTG                         ATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
genomic: ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTGgtattccttc ... tatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
EST: gi|57575350|gb|CX548325.1|CX548325
EST:     ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTG                         ATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
genomic: ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTGgtattccttc ... tatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
EST: gi|31470885|gb|CD412913.1|CD412913
EST:     ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTG                         ATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
genomic: ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTGgtattccttc ... tatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
EST: gi|192319616|gb|FK011810.1|FK011810
EST:     ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTG                         ATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
genomic: ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTGgtattccttc ... tatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
EST: gi|213602569|gb|DB978068.1|DB978068
EST:     ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTG                         ATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
genomic: ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTGgtattccttc ... tatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
EST: gi|192319617|gb|FK011811.1|FK011811
EST:     ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTG                         ATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA
genomic: ACGAGAAGCTTGAGTCCCATCTTCGCACAAATGCCCGTCCCGAATCATTGgtattccttc ... tatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttctttctttggtgaaagtcctaataatctagttgctttaattatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTACAGCGTAAAGAGGATACGAATGACCGCTATGTTGCTGCTCTAAGAGGAG
                                       tttaattatgtatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taagttgaatttaacagccaagtttacacttgtttctttgaggtgattttctttctttggtgaaagtcctaataatctagttgctttaattatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTACAGCGTAAAGAGGATACGAATGACCGCTATGTTGCTGCTCTAAGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - cagccaa
- - - - - - - - - - - - - cacttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgctt