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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttaatcatcaccaataggtactctaatgctaaagcatacttgttaaattagcagtttttgtggtttccttaattctgatctcttgcattgtgtatagCGAGAAAATGCTGTTGATAACTTCAGAGCTGGAAAAACATGGGTTTTGATTGCTACTGATGTAGTTGCCCGGGGCATGGATTTCAAAGGTGTGAACTGTG

Basic information

species Glycine max
transcript GLYMA03G33590.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33590.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os07g45360.1 (Oryza sativa), 3'ss of exon 9
cttttaatcatcaccaataggtactctaa--tgctaaagcatacttgttaaattagcagtttttgtggtttccttaattctgatctcttgcattgtgtatagCGAGAAAATGCTGTTGATAACTTCAGAGCTGGAAAAACATGGGTTTTGATTGCTACTGATGTAGTTGCCCGGGGCATGGATTTCAAAGGTGTGAACTGTG
         |||||  |     | | | |  ||||||   ||  ||||   | |     |||   || |   |||   ||   |    |    |   |  ||||  || |||||||||| ||||| ||||| ||||| || |||||  |||| ||||| || ||  |||||||||| ||||||||||||||||| ||||| |
-------gtatcacttaatatcatttttagttgctaataaatgtttgtggtagttttgttttcactgctacacttggctcaatttctatctcctcactgaagCGTCAAGATGCTGTTGACAACTTGAGAGCCGGAAAGACTTGGGTACTGATAGCTACCGAAGTCATTGCCCGGGGAATGGATTTCAAAGGTGTTAACTGCG

upper sequence: GLYMA03G33590.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G083580_T01 (Zea mays), 3'ss of exon 9
-----------cttttaatcatcaccaataggtactctaatgctaaagcatactt-gttaaattagcagtttttgt------ggtttccttaattctga--tctcttgcattgtgtatagCGAGAAAATGCTGTTGATAACTTCAGAGCTGGAAAAACATGGGTTTTGATTGCTACTGATGTAGTTGCCCGGGGCATGGATTTCAAAGGTGTGAACTGTG
           | | | ||  ||||   ||  |     |    |    |||  || |||| | | ||  |  ||||      ||||| | |  |    |  | | || | ||   |  ||||  || |||||||||| || || ||||||||||| || |||||  |||| || || || ||  |||||||||| ||||| |||||||||||   || ||
gtatagctttgcatattattgtcactgctatatttcagagacatctttcatgttttgttagagttgcgctacttgtgtatgaggtttacatgttgtcaacatatgtttcctttactgcagCGTCAAGATGCTGTTGACAATTTGAGAGCTGGAAAGACCTGGGTACTGATAGCAACGGAAGTCATTGCCCGGGGAATGGACTTCAAAGGTGTCGCCTCTG

upper sequence: GLYMA03G33590.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G09720.1 (Arabidopsis thaliana), 3'ss of exon 11
cttttaatcatcaccaataggtactctaatgctaaagcatacttgtt-----aaattagcagtttttgtggtttccttaattctgatctcttgcattgtg-tatagCGAGAAAATGCTGTTGATAACTTCAGAGCTGGAAAAACATGGGTTTTGATTGCTACTGATGTAGTTGCCCGGGGCATGGATTTCAAAGGTGTGAACTGTG
  |  |||||||    ||  ||| ||      |||||  | ||  |      ||| ||      | | |   ||  |        || |         || |  |||| |||||||| |||||| | |||||||| ||| ||| |||||||||||| || ||||||||  ||||| | || ||||||||||||||  | ||||| |
-gtaaaatcatctttcat--gtagtcatcaaataaagtttgctcctctatggaaagtatagagatatataaattgatatgaaacaatttaccattggatgctgcagCGGGAAAATGCAGTTGATCAATTCAGAGCGGGAGAAAAATGGGTTTTGATAGCCACTGATGTGATTGCCAGAGGTATGGATTTCAAAGGCATCAACTGCG

upper sequence: GLYMA03G33590.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv08s0040g02300.t01 (Vitis vinifera), 3'ss of exon 10
cttttaatcatc-accaataggtactc-taatgctaaagcatacttgttaaattagcagtttttgtggtttccttaattctgatctcttgca-ttgtgtatagCGAGAAAATGCTGTTGATAACTTCAGAGCTGGAAAAACATGGGTTTTGATTGCTACTGATGTAGTTGCCCGGGGCATGGATTTCAAAGGTGTGAACTGTG
  | || ||| |  || || | ||    | ||| |     || | |   |  ||        |  || |||  || || |  ||   ||  | ||   || |||||||||||||||| ||| |||||||||| || ||||| |||||||||||||| ||||||||  |||| || || ||||||||||||||  | |||||||
-ctctactcagctgcctattgatataaatcatgatttt-tatgcctccaagtttctttaccctcatg-tttaatttatgccaattgattttacttaaatacagCGAGAAAATGCTGTGGATGACTTCAGAGCCGGGAAAACTTGGGTTTTGATTGCAACTGATGTTATTGCTCGTGGTATGGATTTCAAAGGCATTAACTGTG

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|19269760|gb|BM886016.1|BM886016
EST:     TTGACAGCATTAGAGTTGATGTTATCCATTCTGATTTGTCTCAAGCAGAG                         CGAGAAAATGCTGTTGATAACTTCAGAGCTGGAAAAACATGGGTTTTGATT
genomic: TTGACAGCATTAGAGTTGATGTTATCCATTCTGATTTGTCTCAAGCAGAGgtagttctca ... ttgtgtatagCGAGAAAATGCTGTTGATAACTTCAGAGCTGGAAAAACATGGGTTTTGATT
EST: gi|37996746|gb|CF808335.1|CF808335
EST:     TTGACAGCATTAGAGTTGATGTTATCCATTCTGATTTGTCTCAAGCAGAG                         CGAGAAAATGCTGTTGATAACTTCAGAGCTGGAAAAACATGGGTTTTGATT
genomic: TTGACAGCATTAGAGTTGATGTTATCCATTCTGATTTGTCTCAAGCAGAGgtagttctca ... ttgtgtatagCGAGAAAATGCTGTTGATAACTTCAGAGCTGGAAAAACATGGGTTTTGATT
EST: gi|21600899|gb|BQ611230.1|BQ611230
EST:     TTGACAGCATTAGAGTTGATGTTATCCATTCTGATTTGTCTCAAGCAGAG                         CGAGAAAATGCTGTTGATAACTTCAGAGCTGGAAAAACATGGGTTTTGATT
genomic: TTGACAGCATTAGAGTTGATGTTATCCATTCTGATTTGTCTCAAGCAGAGgtagttctca ... ttgtgtatagCGAGAAAATGCTGTTGATAACTTCAGAGCTGGAAAAACATGGGTTTTGATT
EST: gi|209698970|gb|BW656111.1|BW656111
EST:     TTGACAGCATTAGAGTTGATGTTATCCATTCTGATTTGTCTCAAGCAGAG                         CGAGAAAATGCTGTTGATAACTTCAGAGCTGGAAAAACATGGGTTTTGATT
genomic: TTGACAGCATTAGAGTTGATGTTATCCATTCTGATTTGTCTCAAGCAGAGgtagttctca ... ttgtgtatagCGAGAAAATGCTGTTGATAACTTCAGAGCTGGAAAAACATGGGTTTTGATT
EST: gi|14989998|gb|BI315671.1|BI315671
EST:     TTGACAGCATTAGAGTTGATGTTATCCATTCTGATTTGTCTCAAGCAGAG                         CGAGAAAATGCTGTTGATAACTTCAGAGCTGGAAAAACATGGGTTTTGATT
genomic: TTGACAGCATTAGAGTTGATGTTATCCATTCTGATTTGTCTCAAGCAGAGgtagttctca ... ttgtgtatagCGAGAAAATGCTGTTGATAACTTCAGAGCTGGAAAAACATGGGTTTTGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaattagcagtttttgtggtttccttaattctgatctcttgcattgtgtatagCGAGAAAATGCTGTTGATAACTTCAGAGCTGGAAAAACATGGGTTTTGATTGCTACTGATGTAGTTGCCCGGGGCATGGATTTCAAAGGTGTGAACTGTG
                              ttctgat  putative branch site (score: 3)
                          ttaattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttaatcatcaccaataggtactctaatgctaaagcatacttgttaaattagcagtttttgtggtttccttaattctgatctcttgcattgtgtatagCGAGAAAATGCTGTTGATAACTTCAGAGCTGGAAAAACATGGGTTTTGATTGCTACTGATGTAGTTGCCCGGGGCATGGATTTCAAAGGTGTGAACTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - tcaccaa
- - - - - - - - - - - - -ctaatgc
- - - - - - - - - - - - - - - - - - gcatact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcttgc