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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaacaatcttttgttgccttatctaattcaactactgcattgccagagttgatatggcacaattttaaactagagtttggctgttaattctatgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAGTATGG

Basic information

species Glycine max
transcript GLYMA16G06850.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 7
attaacaatcttttgttgc-cttatctaattcaactactgcattgccagagttgatatggcacaattttaaactagagtttggctgttaattctatg--acagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAGTATGG
|  || |    | | || |  || |   |||  |  | |  |||||||      ||||||||     |   |   |   ||     | ||| | ||    ||||| || ||||| ||||| ||||| ||||| || ||||||||||||||||| || |||||
aaaaatataggtatatttcatttgtactattttaacagtatattgccaa---caatatggcatgccatagtagctgcaatttataatcaatacaatcctgcagATTGTATTCAGGGAGGACTTTGGGACTGACGGGCGTGGTGGATATTTTGATCAATATGG

upper sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
attaacaatcttttgtt-gccttatctaattcaactactgcattgccagagttgatatggcacaattttaaactagagtttggctgttaattctatgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAGTATGG
              ||  |   |   ||  | |   |    || | |||| |   | |     |   | ||   | | |||  |   |  || | |  ||||| |||||||| || |||||||||||||| || ||||| |||||||||||| | |||||
--------------gtgagagctgcatagctaagacagaa-atagtcagactgtttgttatttagagtcaattcacatttt--caaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG

upper sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G27300.1 (Arabidopsis thaliana), 3'ss of exon 7
attaacaatcttttgttgccttatctaattcaactactgcattgccagagttgatatggcacaattttaaactagagtttggctgttaattctatgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAGTATGG
      |   |||  | || |     || |  | | ||  | |     |  |    | | |    |  | |  |   | |   |     |  | |  ||||| ||||||||||| |||||||||||||| || || ||||||||||||||  | || ||
---gtgagagtttgatcgcttagcacaaat--atttctaaacttttgta--tagagttgaatccatccacataaatctctaatt-----tctttttgcagATCGTTTTCAGAGAAGATTTTGGAACTGAAGGTCGCGGTGGATATTTTGATGAATACGG

upper sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 7
attaacaatcttttgttgccttatctaattcaactactgcattgccagagttgatatggcacaattttaaactagagtttggc-tgttaattctatgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAGTATGG
  | ||       |||||   | ||| || |   | ||   |    | |  | ||||| || ||  |||| |  | |  |    | ||  |||| || ||||| || ||||| ||||||||||||||||| || |||||||||||||||||  | |||||
ggttacctcaaaatgttgaagtctctgat-cgttttctatttcaaaataagtaatatgccataaacttaagcatgtggctattattttttttctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG

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|15815763|gb|BI788038.1|BI788038
EST:     TGACAACGTACAG                         ATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC
genomic: TGACAACGTACAGgtgaggattt ... tctatgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC
EST: gi|16278453|gb|BI942912.1|BI942912
EST:     ATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAACGTACAG                         ATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC
genomic: ATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAACGTACAGgtgaggattt ... tctatgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC
EST: gi|192310375|gb|FK002255.1|FK002255
EST:     ATCGGTTTTTCTTACCACTTTGGAACCGCGACAACATTGACAACGTACAG                         ATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC
genomic: ATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAACGTACAGgtgaggattt ... tctatgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC
EST: gi|254331186|gb|GR843305.1|GR843305
EST:     ATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAACGTACAG                         ATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC
genomic: ATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAACGTACAGgtgaggattt ... tctatgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC
EST: gi|37995859|gb|CF807448.1|CF807448
EST:     ATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAACGTACAG                         ATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC
genomic: ATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAACGTACAGgtgaggattt ... tctatgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC
EST: gi|16348742|gb|BI974337.1|BI974337
EST:     ATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAACGTACAG                         ATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC
genomic: ATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAACGTACAGgtgaggattt ... tctatgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC
EST: gi|17519559|gb|BM188601.1|BM188601
EST:     ATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAACGTACAG                         ATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC
genomic: ATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAACGTACAGgtgaggattt ... tctatgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagagttgatatggcacaattttaaactagagtttggctgttaattctatgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAGTATGG
                                      tgttaat  putative branch site (score: 3)
               acaattttaaacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaacaatcttttgttgccttatctaattcaactactgcattgccagagttgatatggcacaattttaaactagagtttggctgttaattctatgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAGTATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA