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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaagagtgttgctagcatttctcaataatgatgtggctcttgtcaagaaaagataataatataaactaatttccatgcgttattttattttctctatagGTACTGGCAAAGAAGTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTACTATGGAAAGAGTTCCCCATTTAATTCTTTGGAGACAGAAAATTTGAAAT

Basic information

species Glycine max
transcript GLYMA16G24270.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G24270.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G031572_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------taaagagtgt-tgctagcatttctcaataatgatgtggctcttgtcaagaaa------agataataatataaactaattt---ccatgcgttattttattttctcta------tagGTACTGGCAAAGAAGTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTACTATGGAAAGAGTTCCCCATTTAATTCTTTGGAGACAGAAAATTTGAAAT
                                                    |  | |   | | ||      ||| | |   ||  ||  || | |  | ||       |   | |  | |  |  || ||   |  |  | ||   |||              |||||  |||||||||| ||||| || ||  ||||| ||| ||| ||||| ||||||||||||||||| || |||||   ||||   ||||||||| |  | |
gtaagtttaatgagtatatagacatgcagtcacatatttttagttaaatgattggacatcttatactgcttactctaactctagacatgattcatattcataatttactcaaccatttgtgtgcaacaactttggctgttagataacatatacatatggatggattagGTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATACTATGGAAAGAGTTCTCCTTTTAACAGTTTGACAACAGAAAATCTACAGT

upper sequence: GLYMA16G24270.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G18080.1 (Arabidopsis thaliana), 3'ss of exon 2
taaagagtgttgctagcatttctcaataatgatgtggctcttgtcaagaaaagataataatataaactaatttccatgcgttattttattttctctatagGTACTGGCAAAGAAGTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTACTATGGAAAGAGTTCCCCATTTAATTCTTTGGAGACAGAAAATTTGAAAT
             ||  ||||  |||     || ||  | |||| || ||||  ||| || ||  | |  |||  |  | |              |||||||| | ||||||||||||  ||||| | ||||| | || |||||| | ||||||||||| || ||||| ||||| || || |  ||||||||||||||||
------------gtaagattttacaa-----atttgattattgtaaaaaaaatctaaaaagattga-tgttttataaacata-------------tatagGTATTAGCAAAGAAGTTTCAAGCAGGTGTGGTTTCACTAGAACATAGGTACTATGGAAAAAGCTCCCCCTTTAACTCATTAGCTACAGAAAATTTGAAAT

upper sequence: GLYMA16G24270.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0023g03020.t01 (Vitis vinifera), 3'ss of exon 2
--------taaagagtgttgctagcatttctcaataatgatgtggctcttgtcaagaaaagataataatataaactaatttccatgcgttattttattttctctatagGTACTGGCAAAGAAGTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTACTATGGAAAGAGTTCCCCATTTAATTCTTTGGAGACAGAAAATTTGAAAT
        ||||     |    ||  | |   |  || || | |  | ||      | || | | |     |||  || |||    | || |  | |    |  | ||||  |||||||||| |||||||||||| ||||| ||||||| |||||||||||||||||||||||||| |||   ||| ||   ||||||||| ||||||
ctcaaaactaaaatccatcctcagattgtaggagcaaggaggag--ttttacttgtataacaaacttgctgaaa--aaattctgaaccttgtaatgt----tggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTACTATGGAAAGAGTTCCCCCTTTCGGTCTCTGAGAACAGAAAATCTGAAAT

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|298172950|gb|HO019934.1|HO019934
EST:     TAATCGGTGGTGAAGGTCCATGTAATGGGATAACAAATGACTATATTGGT                         GTACTGGCAAAGAAGTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTAC
genomic: TAATCGGTGGTGAAGGTCCATGTAATGGGATAACAAATGACTATATTGGTgtaagttgca ... ttctctatagGTACTGGCAAAGAAGTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTAC
EST: gi|13252300|gb|BG363203.1|BG363203
EST:     TAATCGGTGGTGAAGGTCCATGTAATGGGATAACAAATGACTATATTGGT                         GTACTGGCAAAGAAGTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTAC
genomic: TAATCGGTGGTGAAGGTCCATGTAATGGGATAACAAATGACTATATTGGTgtaagttgca ... ttctctatagGTACTGGCAAAGAAGTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTAC
EST: gi|192307849|gb|FG999328.1|FG999328
EST:     TAATCGGTGGTGAAGGTCCATGTAATGGGATAACAAATGACTATATTGGT                         GTACTGGCAAAGAAGTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTAC
genomic: TAATCGGTGGTGAAGGTCCATGTAATGGGATAACAAATGACTATATTGGTgtaagttgca ... ttctctatagGTACTGGCAAAGAAGTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTAC
EST: gi|192303244|gb|FG995580.1|FG995580
EST:     TAATCGGTGGTGAAGGTCCATGTAATGGGATAACAAATGACTATATTGGT                         GTACTGGCAAAGAAGTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTAC
genomic: TAATCGGTGGTGAAGGTCCATGTAATGGGATAACAAATGACTATATTGGTgtaagttgca ... ttctctatagGTACTGGCAAAGAAGTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTAC
EST: gi|151399803|gb|EV269674.1|EV269674
EST:     TAATCGGTGGTGAAGGTCCATGTAATGGGATAACAAATGACTATATTGGT                         GTACTGGCAAAGAATTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTAC
genomic: TAATCGGTGGTGAAGGTCCATGTAATGGGATAACAAATGACTATATTGGTgtaagttgca ... ttctctatagGTACTGGCAAAGAAGTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTAC
EST: gi|7232689|gb|AW568043.1|AW568043
EST:     TAATCGGTGGTGAAGGTCCATGTAATGGGATAACAAATGACTATATTGGT                         GTACTGGCAAAGAAGTNTGGAGCAGCTATGGTTACTCTTGAACATCGCTAC
genomic: TAATCGGTGGTGAAGGTCCATGTAATGGGATAACAAATGACTATATTGGTgtaagttgca ... ttctctatagGTACTGGCAAAGAAGTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaaaagataataatataaactaatttccatgcgttattttattttctctatagGTACTGGCAAAGAAGTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTACTATGGAAAGAGTTCCCCATTTAATTCTTTGGAGACAGAAAATTTGAAAT
                   aactaat  putative branch site (score: 2)
                                   ttattttattttctct  putative PPT
     aagataataatataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaagagtgttgctagcatttctcaataatgatgtggctcttgtcaagaaaagataataatataaactaatttccatgcgttattttattttctctatagGTACTGGCAAAGAAGTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTACTATGGAAAGAGTTCCCCATTTAATTCTTTGGAGACAGAAAATTTGAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - -tgttgct
- - - - - - - -gcatttc
- - - - - - - - - - - - - - - gatgtgg
- - - - - - - - - - - - - - - - - - - - - - -aagaaaa