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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaggggtttttttggtttcaggcccgagggggttccttttttttttttttttggggggggggggggggcgggggggcttttttggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG

Basic information

species Glycine max
transcript GLYMA06G34850.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
--------------ggaggggt--ttttttggtttcaggcccgagggggttccttttttttttttttttggggggggggggggggcgggggggcttttttggtttgtgtttt---------------gaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
               ||  | |  |||   | |  |  |  | | |  |    | ||   |||   |  |  |   |   |  |   |  |     | |  | |||||||||               |||| || ||||| ||||||||||| || |||||||||||||||||||| || || || |  |||||||| ||
gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG

upper sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os09g21770.1 (Oryza sativa), 3'ss of exon 2
-------------------------------ggaggggtttt---tttggtttcaggcccg-agggggttccttttttttttttttttggggggggggggggggcgggggggcttttttggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
                                 |  | ||||   | || ||   |    | |  | |  | ||  || |  |  |   ||  || || ||    ||   || | | |  || ||||| | | ||||| ||||| || |||||||| ||||||||||||||||| ||||| || || || || |||||||| ||
gtatttgctccaaccccccctccttttttgatcattgattttgcatctgcttgttgttatgcaatgtgggctttggttgtactgataatggttggtggtggttttggtttgggtgtgtgtgtgtgtgtgt-gcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG

upper sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
------ggaggggtttttttggt------ttcaggcccgagggggtt------ccttttttttttttttttggggggggggggggggcgggggggcttttttggt-ttgtgttt---tgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
        ||   ||  |||  |      ||  | |  | || ||||        | | || |||||  ||  |  |    | |||      |  ||| | ||   |||| | |   ||||| |||||||| ||||||||||| || ||||||||||| |||||||| || |||||||| |||||||| ||
gtgtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttttgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG

upper sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G091265_T05 (Zea mays), 3'ss of exon 2
----ggaggggtttttttggt------ttcaggcccgagggggtt------ccttttttttttttttttggggggggggggggggcgggggggcttttttggt-ttgtgttt---tgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
      ||   ||  |||  |      ||  | |  | || ||||        | | || |||||  ||  |  |    | |||      |  ||| | ||   |||| | |   ||||| |||||||| ||||||||||| || ||||||||||| |||||||| || |||||||| |||||||| ||
gtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttttgatcttatgtgacattgtttgtatgtgaagATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG

upper sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G119357_T01 (Zea mays), 3'ss of exon 2
ggaggggtttttttggtttcaggcccgagggggttccttttttttttttttttggggggggggggggggcgggggggcttt----tttggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
| | ||   |  |   |        |   |  |    ||| || | | |   || |    | |   |   | |     ||     | ||  || |  | | |||||||||||||||||||||||| || ||||||||||| |||||||| || || ||||  |||||||| ||
gtacggagctcctcaatcct---ttcattgttgactttttcttctctgtgcatgcgttttgagcctgcttgtgataatttgggtgtgtgtatttttctctaaagGTATTGCAAATGTGAGATGCCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTG

upper sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 2
ggaggggtttttttggtttcaggcccgagggggttccttttttttttttttttggggggggggggggggcgggggggcttttttggtt-tgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
| | |    |  |          ||   |  || |     ||||  | |   ||        |   |   | |  |  |   |||  | | |  | | |||||||||||||||||||||||| || ||||| ||||| |||||||| || || || |  |||||| | ||
gtatgaagctcctcaaccctt--ccattgctggctgtcccttttactgtgcatgcatttttagcttgcttgtgatgattgggttgtctattttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG

upper sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
-ggaggggtttttttggtttcaggcccgagggggttccttttttttttttttttggggggggggggggggcgggggggcttttttggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
   ||  | |   | |   ||||  | ||       | | || ||   |    |      |         | |  | |  || |||  ||| ||| |||||||| ||||||||||| |||||||| || || || ||||||||||| || |||||||| ||||| || ||
gtaagtagataaatagtaatcagatcagaactacgccttcttattacctggaatttccatgattttttatctgttgtgggttgttg--ttg-gttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG

upper sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
ggaggggtttttttggtttcaggcccgagggggttccttttttttttttttttggggggggggggggggcgggggggcttttttggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
      ||   ||||  ||  |    |  ||  |     ||  |  ||   |     ||     | |||| |  |     |||||  || ||| |||||||||||||||||| ||||||||||||||||| |||||||| ||||| || || || ||||||||||| ||
------gtgagtttgagtt--gttttgctggattgatgattgatgattgaatgtactggtattcgtgggctgatgaatacttttgaattttgtattgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG

upper sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S307_14V6.1 (Physcomitrella patens), 3'ss of exon 2
ggaggggtttttttggtttcaggcccgagg--gggttccttttttttttttttttggggggggggggggggcgggggggcttttttggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
       |   |   || | |  |     |    ||    | | ||  ||| ||  |       ||  |  |     ||  || |  |  |||  | |  |||||||| |||||||||||||||||||| || |||||| | ||||| ||||||||    ||||| |||||
--tatcctaagtcgagtgtaaaacattgagttaagtaaggtgtattcctttcttgtgatataaaggctgacccatttggtgttctctgactgttctgtatagGTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATGTGAGACTTGCAAAGATTG

upper sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ05369 (Selaginella moellendorffii), 3'ss of exon 2
ggaggggtttttttggtttcaggcccgagggggttccttttttttttttttttggggggggggggggggcgggggggcttttttggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
                    | |   ||    | ||    |||   || | |                  |       ||||| |||||| |      ||||| ||||| || ||||||||||| |||||||||||||| ||||| || ||||| | |||||| || ||
------------------gtaagattgacaaagctctcactttggattctct-----------atcttatgctctctttttttgggtttgcggaa-acagGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTG

upper sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ16306 (Selaginella moellendorffii), 3'ss of exon 2
--------------ggaggggtttttttggtttcaggcccgagggggttccttttttttttttttttggggggggggggggggcgggggggcttttttggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
              | |    | |||    | |  | | ||  | | |     || | ||| || |   | |          |||      |||| ||           |||||||||||||||||||||||||| || || ||||| ||| | ||||| || || ||    |||||||||||
gtctcgttgtgttcgaacttctctttcctctcttggtctcgttgtgatcgaacttctctttcttctcttgtgttcttaccaagcg------ctttatta--------cgtgaagGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG

upper sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ26805 (Selaginella moellendorffii), 3'ss of exon 2
ggaggggtttttttggtttcaggcccgagggggttccttttttttttttttttggggggggggggggggcgggggggcttttttggtttgtgttttgaa--gGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
                    | |   ||    | ||    |||   || | |                 |    |  || ||||  |||| ||||  ||  |||| ||||| || ||||||||||| |||||||||||||| ||||| || ||||| | |||||| || ||
------------------gtaagattgacaaagctctcactttggattctct---------------atcttatgctctctttt--tttgggtttgaaacagGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTG

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|207806317|gb|GD778794.1|GD778794
EST:     TTCGAGTACAAGGCCGCTTCTGGGGCTTTTACCCCTGACCGTGTTGCTGT                         GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATG
genomic: TTCGAGTACAAGGCCGCTTCTGGGGCTTTTACCCCTGACCGTGTTGCTGTgtgagttgtt ... tgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATG
EST: gi|151393735|gb|EV263610.1|EV263610
EST:     TTCGAGTACAAGGCCGCTTCTGGGGCTTTTACCCCTGACCGTGTTGCTGT                         GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATG
genomic: TTCGAGTACAAGGCCGCTTCTGGGGCTTTTACCCCTGACCGTGTTGCTGTgtgagttgtt ... tgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATG
EST: gi|193691248|gb|FK628371.1|FK628371
EST:     TTCGAGTACAAGGCCGCTTCTGGGGCTTTTACCCCTGACCGTGTTGCTGT                         GTATTGCAAATGTGAG
genomic: TTCGAGTACAAGGCCGCTTCTGGGGCTTTTACCCCTGACCGTGTTGCTGTgtgagttgtt ... tgttttgaagGTATTGCAAATGTGAG
EST: gi|208341882|gb|GE135504.1|GE135504
EST:     TTCGAGTACAAGGCCGCTTCTGGGGCTTTTACCCCTGACCGTGTTGCTGT                         GTATTGCAAATGTGAGATG
genomic: TTCGAGTACAAGGCCGCTTCTGGGGCTTTTACCCCTGACCGTGTTGCTGTgtgagttgtt ... tgttttgaagGTATTGCAAATGTGAGATG
EST: gi|193636344|gb|FK580811.1|FK580811
EST:     TTCGAGTACAAGGCCGCTTCTGGGGCTTTTACCCCTGACCGTGTTGCTGT                         GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATG
genomic: TTCGAGTACAAGGCCGCTTCTGGGGCTTTTACCCCTGACCGTGTTGCTGTgtgagttgtt ... tgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttggggggggggggggggcgggggggcttttttggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
                                 tttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaggggtttttttggtttcaggcccgagggggttccttttttttttttttttggggggggggggggggcgggggggcttttttggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG

ggagggg
- - - - - - - - - -caggccc
- - - - - - - - - - - - - gaggggg
- - - - - - - - - - - - - - - - - - - - - - - - - - -ggggggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtttg