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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagaaaaaagttgagtaaaaaaatctcacccctcggtcctccataaaaaatgtttttctttcctgacattcatttaattcacatttaccgaatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAG

Basic information

species Glycine max
transcript GLYMA04G39690.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G158021_T01 (Zea mays), 3'ss of exon 8
-------------------------gagaaaaaagttgagtaaaaaaatctcaccc-ctcggtcctccataaaaaatgtttttctttcctgacattcatttaattcacatttaccgaatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAG
                                 | |||| |  ||   | | | |  ||  || |   ||||    |   ||  |||  || |  || | |     |  |   || ||   ||||| ||| |||| |||||||| ||||  ||||| |||||||| ||||||||||||
gtgagtgccatataattatgttattattgtctcacttgaatggaatcttttgatcggctatgtaccagataattttttacttgtttttttggccctcgtct---ctaactgctccaaaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG

upper sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 8
gagaaaaaagttgagtaaaaaaatctcacccctcggtcctccataaaaaatgtttttctttcctgacattcattta---attcacatttaccgaa----tgatgcagTGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAG
       ||||  | | ||||    | ||   |   |  ||  |   | ||| || |   ||   |   ||  | |   || |  |  ||  ||     |||| ||| ||| |||| |||||||||||||| ||||||||||| ||||||||||| |||
-----gtaagt--aattaaaatccttaacatttttcttttctctgttatatggttcttgctcaaaagcatcgctcatgaatacttaactaatgatctcctgatacagCGCTCTGGTTTGGGGTTCAAGTGCCAAACACAAGCCACAAAGAGTTGGAAAG

upper sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv07s0031g01620.t01 (Vitis vinifera), 3'ss of exon 8
----gagaaaaaagttgagtaaaaaaatctcacccctcggtcctccataaaaaatgtttttctttcctgacattcatttaattcacatttaccgaatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAG
    |   || |   |   |         | |    | |      ||| |  |   |||| | || ||||     | |  |||  |  |     |||| |||||||| || |||||||| ||||| |  ||||||||||| ||||||||||||| |
cctagctgaatatcctctttgggtttgaataaatatttg--tagacatcatcacgattttaccttgctgaatcctaatgcattttc--tgggtaaatgttgcagTGCATTAGTCTGGGGATCAAGCGTGAAACACAAGCCCCAAAGAGTTGGCAGG

upper sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S26_115V6.1 (Physcomitrella patens), 3'ss of exon 8
----------gagaaaaaagttgagtaaaaaaatctcacccctcggtcctccataaaaa--atgtttttctttcctgac----------attcatttaattcacatt-----taccgaatg-atg-cagTGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAG
           ||   | | |||  | |    ||||      ||  |  || ||||  |  || ||||| | |||| |           ||||| | ||||||  |      || |  ||| ||| |||||||||||| ||||||||||| |||||||||||||| || ||||| || |||
gtaagtcctgaagttgacatttggtttatgttatcttgattgtccattttctataactaccatatttttatatccttattttgatagtgattcactgaattcaactcatgagtatcatatggatgacagTGCTTTGGTGTGGGGTTCAAGCGCAAAACACAAGCCACAGAGAGTGGGAAAG

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|192305461|gb|FG994283.1|FG994283
EST:     AAACAGTTTAAGTA                         TGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAA
genomic: AAACAGTTTAAGTAgtgagcactt ... aatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAA
EST: gi|14991431|gb|BI317104.1|BI317104
EST:     GAGGACTTCTGCGATCGCATTCACAAGGACATGCTTAAACAGTTTAAGTA                         TGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAA
genomic: GAGGACTTCTGCGATCGCATTCACAAGGACATGCTTAAACAGTTTAAGTAgtgagcactt ... aatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAA
EST: gi|58024862|gb|CX711603.1|CX711603
EST:     GAGGACTTCTGCGATCGCATTCACAAGGACATGCTTAAACAGTTTAAGTA                         TGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAA
genomic: GAGGACTTCTGCGATCGCATTCACAAGGACATGCTTAAACAGTTTAAGTAgtgagcactt ... aatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAA
EST: gi|58023958|gb|CX710699.1|CX710699
EST:     GAGGACTTCTGCGATCGCATTCACAAGGACATGCTTAAACAGTTTAAGTA                         TGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAA
genomic: GAGGACTTCTGCGATCGCATTCACAAGGACATGCTTAAACAGTTTAAGTAgtgagcactt ... aatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAA
EST: gi|22933763|gb|BU550902.1|BU550902
EST:     GAGGACTTCTGCGATCGCATTCACAAGGACATGCTTAAACAGTTTAAGTA                         TGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAA
genomic: GAGGACTTCTGCGATCGCATTCACAAGGACATGCTTAAACAGTTTAAGTAgtgagcactt ... aatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAA
EST: gi|15816018|gb|BI788293.1|BI788293
EST:     GAGGACTTCTGCGATCGCATTCACAAGGACATGCTTAAACAGTTTAAGTA                         TGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAA
genomic: GAGGACTTCTGCGATCGCATTCACAAGGACATGCTTAAACAGTTTAAGTAgtgagcactt ... aatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAA
EST: gi|151407189|gb|EV277004.1|EV277004
EST:     GAGGACTTCTGCGATCGCATTCACAAGGACATGCTTAAACAGTTTAAGTA                         TGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAA
genomic: GAGGACTTCTGCGATCGCATTCACAAGGACATGCTTAAACAGTTTAAGTAgtgagcactt ... aatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAA
EST: gi|14008785|gb|BG725389.1|BG725389
EST:     GAGGACTTCTGCGATCGCATTCACAAGGACATGCTTAAACAGTTTAAGTA                         TGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAA
genomic: GAGGACTTCTGCGATCGCATTCACAAGGACATGCTTAAACAGTTTAAGTAgtgagcactt ... aatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAA
EST: gi|57575753|gb|CX548728.1|CX548728
EST:     GAGGACTTCTGCGATCGCATTCACAAGGACATGCTTAAACAGTTTAAGTA                         TGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAA
genomic: GAGGACTTCTGCGATCGCATTCACAAGGACATGCTTAAACAGTTTAAGTAgtgagcactt ... aatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaatgtttttctttcctgacattcatttaattcacatttaccgaatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAG
                          atttaattcacattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagaaaaaagttgagtaaaaaaatctcacccctcggtcctccataaaaaatgtttttctttcctgacattcatttaattcacatttaccgaatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAG

- gaaaaaa
- - - - - - - -taaaaaa
- - - - - - - - aaaaaaa
- - - - - - - - - - - - ctcaccc
- - - - - - - - - - - - - - - - - - tcctcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attcaca