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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaatagctgtaacaatgatatctgtgcatatagttcagaaggttttttccaacccaaagtccaaagctaacagtctttgtggttgcccctgtccacagCTTTGCAGTGGAGTGGATGAGCATGCGGTTGGCACCAGTGCAGAACTTGTTTTTGCTCCAATTGACGCATCTTTCTCTGATGATGCACCCATTTTACCTT

Basic information

species Glycine max
transcript GLYMA06G09100.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G09100.2 (Glycine max), 3'ss of exon 4
lower sequence: AT4G32880.1 (Arabidopsis thaliana), 3'ss of exon 14
----ttgaatagctgtaacaatgatat-ctgtgcatatagttcagaaggttttttccaacccaaagtccaaagctaacagtctttgtggttgcccctgtccacagCTTTGCAGTGGAGTGGATGAGCATGCGGTTGGCACCAGTGCAGAACTTGTTTTTGCTCCAATTGACGCATCTTTCTCTGATGATGCACCCATTTTACCTT
     |  ||||     | |  || |   | |   | | |||   |     |  || |    |   | | ||  ||      |||||   ||         | || | |||||||| ||||||||| | || ||||   |  | ||||| ||| | ||||| ||||| |||||||||||||||||||||||||| ||  | ||||
gctcattgatagactctatagcgagacgttattagtcttgttgcaa----ctactcaattttatgattctaatatatataattttgta-ctgtttgatgatatagATGTGCAGTGGGGTGGATGAGAACGCAGTTGAATCATGCGCAGAGCTTATATTTGCACCAATCGACGCATCTTTCTCTGATGATGCACCAATCATTCCTT

upper sequence: GLYMA06G09100.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g03250.t01 (Vitis vinifera), 3'ss of exon 13
--ttgaatagctgtaacaatgatatctgtgcatatagttcagaaggttttttccaaccca-aagtccaaagctaacagtc---tttgtggttgcccctgt-ccacagCTTTGCAGTGGAGTGGATGAGCATGCGGTTGGCACCAGTGCAGAACTTGTTTTTGCTCCAATTGACGCATCTTTCTCTGATGATGCACCCATTTTACCTT
  |  | |  || |||  | ||| | |   | || | |      |||  || | ||| || ||   || |   | || |    ||  |  || |     | || |||||||| ||||||||||| ||  |||| || |||||| || | |||||  | |||||||||||||| || ||||||||||||||||||||  || | ||||
attctagtttctttaa-gacgat-tttaatcttaaatt-----gggtcattgcaaactcacaaaatcatattcagcattactgttcctaattactttgattccccagCTTTGTAGTGGAGTGGACGATAATGCTGTGGGCACCTGTTCTGAACTCATCTTTGCTCCAATTGATGCCTCTTTCTCTGATGATGCACCTCTTCTTCCTT
















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|22541805|gb|BU091648.1|BU091648
EST:     GCTACTATAGGGACGACATGAGTATACCTGGTGATGTTTTCCTCTTGCAA                         CTTTGCAGTGGAGTGGATGAGCATGCGGTTGGCACCAGTGCAGAACTTGTT
genomic: GCTACTATAGGGACGACATGAGTATACCTGGTGATGTTTTCCTCTTGCAAgtaagtaatt ... ctgtccacagCTTTGCAGTGGAGTGGATGAGCATGCGGTTGGCACCAGTGCAGAACTTGTT
EST: gi|151395024|gb|EV264895.1|EV264895
EST:     GCTACTATAGGGACGACATGAGTATACCTGGTGATGTTTTCCTCTTGCAA                         CTTTGCAGTGGAGTGGATGAGCATGCGGTTGGCACCAGTGCAGAACTTGTT
genomic: GCTACTATAGGGACGACATGAGTATACCTGGTGATGTTTTCCTCTTGCAAgtaagtaatt ... ctgtccacagCTTTGCAGTGGAGTGGATGAGCATGCGGTTGGCACCAGTGCAGAACTTGTT
EST: gi|15286780|gb|BI470671.1|BI470671
EST:     GCTACTATAGGGACGACATGAGTATACCTGGTGATGTTTTCCTCTTGCAA                         CTTTGCAGTGGAGTGGATGAGCATGCGGTTGGCACCAGTGCAGAACTTGTT
genomic: GCTACTATAGGGACGACATGAGTATACCTGGTGATGTTTTCCTCTTGCAAgtaagtaatt ... ctgtccacagCTTTGCAGTGGAGTGGATGAGCATGCGGTTGGCACCAGTGCAGAACTTGTT
EST: gi|9819663|gb|BE555176.1|BE555176
EST:     GCTACTATAGGGACGACATGAGTATACCTGGTGATGTTTTCCTCTTGCAA                         CTTTGCAGTGGAGTGGATGAGCATGCGGTTGGCACCAGTGCAGAACTTGTT
genomic: GCTACTATAGGGACGACATGAGTATACCTGGTGATGTTTTCCTCTTGCAAgtaagtaatt ... ctgtccacagCTTTGCAGTGGAGTGGATGAGCATGCGGTTGGCACCAGTGCAGAACTTGTT
EST: gi|4396314|gb|AI495311.1|AI495311
EST:     GCTACTATAGGGACGACATGAGTATACCTGGTGATGTTTTCCTCTTGCAA                         CTTTGCAGTGGAGTGGATGAGCATGCGGTTGGCACCAGTGCAGAACTTGTT
genomic: GCTACTATAGGGACGACATGAGTATACCTGGTGATGTTTTCCTCTTGCAAgtaagtaatt ... ctgtccacagCTTTGCAGTGGAGTGGATGAGCATGCGGTTGGCACCAGTGCAGAACTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttccaacccaaagtccaaagctaacagtctttgtggttgcccctgtccacagCTTTGCAGTGGAGTGGATGAGCATGCGGTTGGCACCAGTGCAGAACTTGTTTTTGCTCCAATTGACGCATCTTTCTCTGATGATGCACCCATTTTACCTT
                     agctaac  putative branch site (score: 2)
                                          cccctgtcc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaatagctgtaacaatgatatctgtgcatatagttcagaaggttttttccaacccaaagtccaaagctaacagtctttgtggttgcccctgtccacagCTTTGCAGTGGAGTGGATGAGCATGCGGTTGGCACCAGTGCAGAACTTGTTTTTGCTCCAATTGACGCATCTTTCTCTGATGATGCACCCATTTTACCTT

- - - agctgta
- - - - - - - - - - - - - tgcatat
- - - - - - - - - - - - - - - - - - - - - - - - - - -acccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggttg