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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcctggttttctagcggagatattagtcattggaaaacagtgatacttggtaccaatttgatttatatatgaaaaaaaaaatgatttttgttgtggcagTTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG

Basic information

species Glycine max
transcript GLYMA16G25220.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G25220.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G054247_T04 (Zea mays), 3'ss of exon 2
-agcctggttttctagcggagatattagtcattggaaaacagtgatacttggtaccaatttgatttatatatgaaaaaaaaaatgatttttgttgtggcagTTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG-------
  ||||| ||    ||  |||||  || || ||            | | | ||    ||| |||   | |  ||  ||     |   | |||| | || || |  ||||||| ||||||||||||||||| |||||||||||||||||||||||  | |||||||| ||||| ||||| || |||||| | |||       
gtgcctgcttc---agtagagatgctactcctt------------tgccttgtg---attcgatggttttgagactaattggttctatgttgt-gcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGGTACGCT

upper sequence: GLYMA16G25220.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G054247_T03 (Zea mays), 3'ss of exon 2
-agcctggttttctagcggagatattagtcattggaaaacagtgatacttggtaccaatttgatttatatatgaaaaaaaaaatgatttttgttgtggcagTTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG
  ||||| ||    ||  |||||  || || ||            | | | ||    ||| |||   | |  ||  ||     |   | |||| | || || |  ||||||| ||||||||||||||||| |||||||||||||||||||||||  | |||||||| ||||| ||||| || |||||| | |||
gtgcctgcttc---agtagagatgctactcctt------------tgccttgtg---attcgatggttttgagactaattggttctatgttgt-gcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG

upper sequence: GLYMA16G25220.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G174971_T01 (Zea mays), 3'ss of exon 2
-agcctggttttctagcggagatattagtcattggaaaacagtgatacttggtaccaatttgatttatatatgaaaaaaaaaatgatttttgttgtggcagTTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG
  ||||| ||   ||| |  | ||||     ||||            ||||      ||| |||   | |  ||  ||     |   | |||  ||||||| |  |||  || ||||||||||||||||| |||||||| |||||||| |||||  | |||||||| ||||| ||||| || |||||| | |||
gtgcctgcttcagtagagatgctattctctcttgg------------cttg----tgattcgatggttttgagattaatcggttctatgttgc-gtggcagCTTGTTGCTCTCTACGTGGATTTCAAGCTCGACGAGAGCTACACGCCCAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTCAAG

upper sequence: GLYMA16G25220.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g01940.t01 (Vitis vinifera), 3'ss of exon 2
agcctggttttctagcggagatattagtcattggaaaacagtgatacttggtaccaatttgatttatata--tgaaaaaaaaaatgatttttgttgtggcagTTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG
          | |    |  || || |   |  ||      |  | |    |     |||| |||   |   ||||     ||  ||||| | ||     || |  ||||  | || |||||||||||||| |||||||| ||||||||||| ||  | || || || ||||| ||||| || ||||||||||||
---------gtgtgtatgcaattttgggtttctgatttttttctttcccccttatcgtttggttttggtgactgaatggtgaatagatttctctt---aaagCTGGTTGTAATTTATGTGGATTTCAAGCTGGACGAGAGCTACACGCCGAGTAAGATCTCTATTCGAGCCGGAGATGGCTTCCACAACTTGAAG

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|298183131|gb|HO028394.1|HO028394
EST:     GGCAACCCCATTTAGTTAACATTCAGTTTCAGAAGAAAGTTAGACTTCAA                         TTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGC
genomic: GGCAACCCCATTTAGTTAACATTCAGTTTCAGAAGAAAGTTAGACTTCAAgtacgtacac ... gttgtggcagTTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGC
EST: gi|298190530|gb|HO032651.1|HO032651
EST:     GGCAACCCCATTTAGTTAACATTCAGTTTCAGAAGAAAGTTAGACTTCAA                         TTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGC
genomic: GGCAACCCCATTTAGTTAACATTCAGTTTCAGAAGAAAGTTAGACTTCAAgtacgtacac ... gttgtggcagTTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGC
EST: gi|22540274|gb|BU090117.1|BU090117
EST:     GGCAACCCCATTTAGTTAACATTCAGTTTCAGAAGAAAGTTAGACTTCAA                         TTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGC
genomic: GGCAACCCCATTTAGTTAACATTCAGTTTCAGAAGAAAGTTAGACTTCAAgtacgtacac ... gttgtggcagTTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGC
EST: gi|15286034|gb|BI469925.1|BI469925
EST:     GGCAACCCCATTTAGTTAACATTCAGTTTCAGAAGAAAGTTAGACTTCAA                         TTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGC
genomic: GGCAACCCCATTTAGTTAACATTCAGTTTCAGAAGAAAGTTAGACTTCAAgtacgtacac ... gttgtggcagTTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGC
EST: gi|207814375|gb|GD786898.1|GD786898
EST:     GGCAACCCCATTTAGTTAACATTCAGTTTCAGAAGAAAGTTAGACTTCAA                         TTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGC
genomic: GGCAACCCCATTTAGTTAACATTCAGTTTCAGAAGAAAGTTAGACTTCAAgtacgtacac ... gttgtggcagTTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGC
EST: gi|207814375|gb|GD786898.1|GD786898
EST:     GGCAACCCCATTTAGTTAACATTCAGTTTCAGAAGAAAGTTAGACTTCAA                         TTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGC
genomic: GGCAACCCCATTTAGTTAACATTCAGTTTCAGAAGAAAGTTAGACTTCAAgtacgtacac ... gttgtggcagTTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGC
EST: gi|298186464|gb|HO037097.1|HO037097
EST:     GGCAACCCCATTTAGTTAACATTCAGTTTCAGAAGAAAGTTAGACTTCAA                         TTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGC
genomic: GGCAACCCCATTTAGTTAACATTCAGTTTCAGAAGAAAGTTAGACTTCAAgtacgtacac ... gttgtggcagTTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGC
EST: gi|208266419|gb|GE065538.1|GE065538
EST:     ATTCTAGTTTCAAGAAGAAAGTTAGACTTCAA                         TTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGC
genomic: ATTC-AGTTTC-AGAAGAAAGTTAGACTTCAAgtacgtacac ... gttgtggcagTTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttggtaccaatttgatttatatatgaaaaaaaaaatgatttttgttgtggcagTTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG
           atttgat  putative branch site (score: 5)
                                        tttttgtt  putative PPT
          aatttgatttatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcctggttttctagcggagatattagtcattggaaaacagtgatacttggtaccaatttgatttatatatgaaaaaaaaaatgatttttgttgtggcagTTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - ggaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa