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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcttggaccttgggcagctttacagaacttctgtcttggctgtgaaaagggaattaattctgcaaagaaatgtgctcataattttaaattccctgcagTGTGCTTTGTGAAGATGAGAAACAAGCTGTGGCTGTAAAAAGTCAGTTGCAGCTGATTGCTAGACCCATGTACAGTAACCCACCTCTCCATGGAGCACTT

Basic information

species Glycine max
transcript GLYMA06G42830.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G30970.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------------------------------------------------aatcttggaccttgggcagctttacagaacttctgtcttggctgtgaaaaggg---aattaattctg---caaaga---aatgtgctcat---aattttaaattcc-ctgcagTGTGCTTTGTGAAGATGAGAAACAAGCTGTGGCTGTAAAAAGTCAGTTGCAGCTGATTGCTAGACCCATGTACAGTAACCCACCTCTCCATGGAGCACTT
                                                                                        ||  |||||   | |||   |  ||| |   | ||   | ||  | | |  ||   | ||| |  ||    ||| |   ||| ||  |||   || |||   |||  ||||||||||||||||||||||  ||| ||||| |||||||| |||||||| ||||||| | | |||||||| |||||||| ||||||||| | ||||| || |  
gtattcatttttctcaacaaagaacatcgttttcttcctacacgaaggaaaatatggaaattagaaagtacagatatcagcattttaaaaatttggattgtaggcg--tcaacaaattgtatgaaatagccatcatacaggttcatttagtgatgaagtaaaaactgaatatgaacatgacaactttgtcttctactgcagTGTGCTTTGTGAAGATCCGAAGCAAGCCGTGGCTGTGAAAAGTCAATTGCAGCAGCTAGCTAGACCAATGTACAGCAACCCACCTTTGCATGGTGCTCAG

upper sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv12s0028g01820.t01 (Vitis vinifera), 3'ss of exon 6
aatcttggaccttgggcagctttacagaacttctgtcttggctgtgaaaagggaattaattctgcaaagaaatgtgctcataattttaaattcc-ctgcagTGTGCTTTGTGAAGATGAGAAACAAGCTGTGGCTGTAAAAAGTCAGTTGCAGCTGATTGCTAGACCCATGTACAGTAACCCACCTCTCCATGGAGCACTT
  | |||   |  |      ||| |    | | ||   |   |||||| ||  |||  | |||   |          | | |  |||   | |   | |||| |||| ||||||||||| || ||||| |||||||| || ||||||||||||| |||||||||||||||||||||||| |||||| | || || || || 
gctgttgctgcaagcttttttttccccttcatatggagtaaatgtgaacaga-aatagactctcttatattccaatgtgacacctttctctacaatttcagTCTGCTCTGTGAAGATGAAAAGCAAGCAGTGGCTGTCAAGAGTCAGTTGCAGCAGATTGCTAGACCCATGTACAGTAATCCACCTGTTCAAGGTGCTCTC
















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|19269530|gb|BM885786.1|BM885786
EST:     TCATATGCAAAAAATATGGGACTGTATGGCCAGCGAGCAGGAAGCCTGAG                         TGTGCTTTGTG
genomic: TCATATGCAAAAAATATGGGACTGTATGGCCAGCGAGCAGGAAGCCTGAGgtaagtagac ... ttccctgcagTGTGCTTTGTG
EST: gi|22523470|gb|BU082281.1|BU082281
EST:     GGGACTGTATGGCCAGCGAGCAGGAAGCCTGAG                         TGTGCTTTGTGAAGATGAGAAACAAGCTGTGGCTGTAAAAAGTCAGTTGCA
genomic: GGGACTGTATGGCCAGCGAGCAGGAAGCCTGAGgtaagtagac ... ttccctgcagTGTGCTTTGTGAAGATGAGAAACAAGCTGTGGCTGTAAAAAGTCAGTTGCA
EST: gi|57574406|gb|CX547381.1|CX547381
EST:     ATATGGGACTGTATGGCCAGCGAGCAGGAAGCCTGAG                         TGTGCTTTGTGAAGATGAGAAACAAGCTGTGGCTGTAAAAAGTCAGTTGCT
genomic: ATATGGGACTGTATGGCCAGCGAGCAGGAAGCCTGAGgtaagtagac ... ttccctgcagTGTGCTTTGTGAAGATGAGAAACAAGCTGTGGCTGTAAAAAGTCAGTTGCA
EST: gi|254320419|gb|GR826868.1|GR826868
EST:     TCATATGCAAAAAATATGGGACTGTATGGCCAGCGAGCAGGAAGCCTGAG                         TGTGCTTTGTGAAGATGAGAAACAAGCTGTGGCTGTAAAAAGTCAGTTGCA
genomic: TCATATGCAAAAAATATGGGACTGTATGGCCAGCGAGCAGGAAGCCTGAGgtaagtagac ... ttccctgcagTGTGCTTTGTGAAGATGAGAAACAAGCTGTGGCTGTAAAAAGTCAGTTGCA
EST: gi|57574152|gb|CX547127.1|CX547127
EST:     GGGACTGTATGNCCAGCGAGCAGGAAGCCTGAG                         TGTGCTTTGTGAAGATGAGAAACAAGCTGTGGCTGTAAAAAGTCAGTTGCT
genomic: GGGACTGTATGGCCAGCGAGCAGGAAGCCTGAGgtaagtagac ... ttccctgcagTGTGCTTTGTGAAGATGAGAAACAAGCTGTGGCTGTAAAAAGTCAGTTGCA
EST: gi|254340271|gb|GR858396.1|GR858396
EST:     TCATATGCAAAAAATATGGGACTGTATGGCCAGCGAGCAGGAAGCCTGAG                         TGTGCTTTGTGAAGATGAGAAACAAGCTGTGGCTGTAAAAAGTCAGTTGCA
genomic: TCATATGCAAAAAATATGGGACTGTATGGCCAGCGAGCAGGAAGCCTGAGgtaagtagac ... ttccctgcagTGTGCTTTGTGAAGATGAGAAACAAGCTGTGGCTGTAAAAAGTCAGTTGCA
EST: gi|22523639|gb|BU082450.1|BU082450
EST:     GGGACTGTATGGCCAGCGAGCAGGAAGCCTGAG                         TGTGCTTTGTGAAGATGAGAAACAAGCTGTGGCTGTAAAAAGTCAGTTGCA
genomic: GGGACTGTATGGCCAGCGAGCAGGAAGCCTGAGgtaagtagac ... ttccctgcagTGTGCTTTGTGAAGATGAGAAACAAGCTGTGGCTGTAAAAAGTCAGTTGCA
EST: gi|13479298|gb|BG508641.1|BG508641
EST:     TCATATGCAAAAAATATGGGACTGTATGGCCAGCGAGCAGGAAGCCTGAG                         TGTGCTTTGTGAAGATGAGAAACAAGCTGTGGCTGTAAAAAGTCAGTTGCA
genomic: TCATATGCAAAAAATATGGGACTGTATGGCCAGCGAGCAGGAAGCCTGAGgtaagtagac ... ttccctgcagTGTGCTTTGTGAAGATGAGAAACAAGCTGTGGCTGTAAAAAGTCAGTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaagggaattaattctgcaaagaaatgtgctcataattttaaattccctgcagTGTGCTTTGTGAAGATGAGAAACAAGCTGTGGCTGTAAAAAGTCAGTTGCAGCTGATTGCTAGACCCATGTACAGTAACCCACCTCTCCATGGAGCACTT
        aattaat  putative branch site (score: 3)
                                             ttccctgc  putative PPT
                                tcataattttaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcttggaccttgggcagctttacagaacttctgtcttggctgtgaaaagggaattaattctgcaaagaaatgtgctcataattttaaattccctgcagTGTGCTTTGTGAAGATGAGAAACAAGCTGTGGCTGTAAAAAGTCAGTTGCAGCTGATTGCTAGACCCATGTACAGTAACCCACCTCTCCATGGAGCACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- -cttggac
- - - - - - - -gcagctt
- - - - - - - - - - - - - - - ttctgtc
- - - - - - - - - - - - - - - - - - - tggctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgctc