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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaatttggcaattccaaatgagtagtttggattcgtctatccgcttttcttgttctgagttttatgagactgaaagaacttttaatcatatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTCGGGGATCCAACCA

Basic information

species Glycine max
transcript GLYMA18G01590.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g18770.1 (Oryza sativa), 3'ss of exon 6
agaaatttggcaattccaaatgagtagtttgg-attcgtctatccgcttttcttgttctgagttttatgagactga----aagaacttttaatcatatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTCGGGGATCCAACCA
       |  ||||  | | |     |||| |   |  | ||  |   ||  |||  |   |||    |   |  |    ||  | ||| |||      |  ||||| ||||| ||||| ||||| || ||||| ||  |||| || || |||||||| || || ||||||||||| ||||| ||||| || ||||||||||   
----gcatatcaatatctagtagtctgttttgtggttttataaacatattaattggacactgttcccagcctcccacattaaatagtttgaattgctcgtg-cagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAGAAAGTTGCTATGTTAATCGGAAAATGGGATGAAGCTATGTATTATGTTCTTGGGGATCCAAGTG

upper sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G156608_T03 (Zea mays), 3'ss of exon 1
-agaaatttggcaat--tccaaatg-agtagttt--ggattcgtctatccgcttttcttgttctgagttttatgagactgaaagaacttttaatcatatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTCGGGGATCCAACCA
    || || |||    || |  || |   ||    | | |    ||||   ||        ||  |||||  || ||  |  |   || ||||||| | |  ||||| ||||| ||||| ||||| || ||||| ||  | || ||||| ||||||||||| || ||||||||||| ||||| ||||| || ||||||||||   
ggttaagttagcagcagtctacttgcaactgtacaagcacttaaatatctatttgatcgagcctaggtttt--gacacaaattg---ttctaatcatttgtg-cagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAAAAAGTAGCTATGTTAATTGGAAAATGGGATGAAGCTATGTATTATGTGCTTGGGGATCCAAGTG

upper sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 6
agaaatttggcaattccaaatgagtagtttggattcgtctatccgcttttcttgttctgagttttatgagactgaaagaacttttaatcatatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTCGGGGATCCAACCA
                      |||||  || |||  | | || |  ||||| | ||   || | |  || |    | |   |  |||    ||   ||||| ||||||||||| |||||||||||||| || ||||| ||||| ||  | || || || |||||||||||||||||||||||| | || ||||| || |
--------------------gtagtagaatg-atttttatttctgtctttct-gctc---gtatgaacaggcctttaaa---tggaatttggtaatgcagGTTCATGGGTTTGTGCAAGACAACAGAACCGGGGAGAAAGTAGCTATACTGATAGGCAAATGGGATGAAGCAATGTACTATGTATTGGGAGATCCGACAA

upper sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 6
--agaaatttggcaattccaaatgagtagtttggattcgtctatccgcttttcttgttctgagttttatgagac-tgaaagaacttttaatcatata-taacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTCGGGGATCCAACCA
  |    |      | ||  |||   |  |||    | |  |||           ||    |   | |  | |  | ||   || |||    ||||| |  ||||| ||||| ||||| ||||| ||  ||||||||||||||||||| |||||  | ||||| |||||||| |||||||| |||||  | || |||||||| |
caaacggtgctatcactctgaatcgatgcttt----ttgaatattaatggcctgggtaagaaaactgaatatatataaatttacattttggtatataattgcagGTTCATGGATTTGTGCAAGATAATCGAACTGGAGAGAAGGTAGCTATGTTGGTGGGGAAATGGGATGAGGCAATGTATTATGTGTTGGGAGATCCAACAA

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|208112006|gb|GD911082.1|GD911082
EST:     GCAAACTGAAATTCAAGGAGCAATCCATTATTGACAGAAATCCACATCAG                         GTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
genomic: GCAAACTGAAATTCAAGGAGCAGTCTATTATAGACAGAAATCCACATCAGgtaggattgt ... tatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
EST: gi|208067824|gb|GD864946.1|GD864946
EST:     GCAAACTGAAATTCAAGGAGCAATCCATTATTGACAGAAATCCACATCAG                         GTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
genomic: GCAAACTGAAATTCAAGGAGCAGTCTATTATAGACAGAAATCCACATCAGgtaggattgt ... tatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
EST: gi|8286012|gb|BE023500.1|BE023500
EST:     GCAAACTGAAATTCAAGGAGCAATCCATTATTGACAGAAATCCACATCAG                         GTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAACGATGTTA
genomic: GCAAACTGAAATTCAAGGAGCAGTCTATTATAGACAGAAATCCACATCAGgtaggattgt ... tatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
EST: gi|208082346|gb|GD883880.1|GD883880
EST:     GCAAACTGAAATTCAAGGAGCAATCCATTATTGACAGAAATCCACATCAG                         GTCCATGGGTTTGTTCAAGACAA
genomic: GCAAACTGAAATTCAAGGAGCAGTCTATTATAGACAGAAATCCACATCAGgtaggattgt ... tatataacagGTCCATGGGTTTGTTCAAGACAA
EST: gi|23729543|gb|BU762863.1|BU762863
EST:     GCAAACTGAAATTCAAGGAGCAATCCATTATTGACAGAAATCCACATCAG                         GTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
genomic: GCAAACTGAAATTCAAGGAGCAGTCTATTATAGACAGAAATCCACATCAGgtaggattgt ... tatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
EST: gi|12773259|gb|BG238186.1|BG238186
EST:     GCAAACTGAAATTCAAGGAGCAGTCTATTATAGACAGAAATCCACATCAG                         GTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
genomic: GCAAACTGAAATTCAAGGAGCAGTCTATTATAGACAGAAATCCACATCAGgtaggattgt ... tatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
EST: gi|209724148|gb|BW659682.1|BW659682
EST:     GCAAACTGAAATTCAAGGAGCAATCTATTATAGACAGAAATCCACATCAG                         GTCCATGGG-TTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
genomic: GCAAACTGAAATTCAAGGAGCAGTCTATTATAGACAGAAATCCACATCAGgtaggattgt ... tatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
EST: gi|58015839|gb|CX702581.1|CX702581
EST:     GCAAACTGAAATTCAAGGAGCAGTCTATTATAGACAGAAATCCACATCAG                         GTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
genomic: GCAAACTGAAATTCAAGGAGCAGTCTATTATAGACAGAAATCCACATCAGgtaggattgt ... tatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
EST: gi|298199576|gb|HO043453.1|HO043453
EST:     GCAAACAGAAATTCAAGGAGCAATCCATTATTGACAGAAATCCACATCAG                         GTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
genomic: GCAAACTGAAATTCAAGGAGCAGTCTATTATAGACAGAAATCCACATCAGgtaggattgt ... tatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
EST: gi|14205607|gb|BG839285.1|BG839285
EST:     GCAAACTGAAATTCAAGGAGCAGTCTATTATAGACAGAAATCCACATCAG                         GTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
genomic: GCAAACTGAAATTCAAGGAGCAGTCTATTATAGACAGAAATCCACATCAGgtaggattgt ... tatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
EST: gi|207781423|gb|GD752784.1|GD752784
EST:     GCAAACTGAAATTCAAGGAGCAGTCTATTATAGACAGAAATCCACATCAG                         GTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
genomic: GCAAACTGAAATTCAAGGAGCAGTCTATTATAGACAGAAATCCACATCAGgtaggattgt ... tatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
EST: gi|58016257|gb|CX702999.1|CX702999
EST:     GCAAACTGAAATTCAAGGAGCAGTCTATTATAGACAGAAATCCACATCAG                         GTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA
genomic: GCAAACTGAAATTCAAGGAGCAGTCTATTATAGACAGAAATCCACATCAGgtaggattgt ... tatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttcttgttctgagttttatgagactgaaagaacttttaatcatatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTCGGGGATCCAACCA
                                    ttttaat  putative branch site (score: 3)
                             aaagaacttttaatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaatttggcaattccaaatgagtagtttggattcgtctatccgcttttcttgttctgagttttatgagactgaaagaacttttaatcatatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTCGGGGATCCAACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - caattcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaaag