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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttttttatttctgtttttactgagataatggtgttgtttgtgttttaagtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG

Basic information

species Glycine max
transcript GLYMA13G34740.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G34740.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g21770.1 (Oryza sativa), 3'ss of exon 2
------------------gtaagtttttttatttctgttttta---ctgag-ataatggtgttgtttgtgttttaagtgt-ttga-aatggtgggttttgttttgttgatttagtttggttttgtgt-tttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
                       |||||| ||   || ||||    |||    |  |  ||   | || | |||   |||  ||| |||||| |||  || ||| | | ||  || ||  | ||||| | || ||||| ||||||||||||||||| |||||||| ||||| || ||||||||||| ||||| |||||||| ||
gtatttgctccaaccccccctccttttttgatcattgattttgcatctgcttgttgttatgcaatgtgggctttggttgtactgataatggttggtggtggttt-tggtttgggtgtgtgtgtgtgtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG

upper sequence: GLYMA13G34740.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
------------gtaagtttttttatttctgttttt-actgagataatggtgttgtttgtgttttaagtgt--ttgaaatggtgggttttgttttgt---tgatttagtttggttttgtgtttt---gaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
            |    || ||   || | |||    | ||  ||  |||  |||||    ||  | | |   ||  |||| ||  |  || || ||   || ||  ||||  ||||  |||||   |||| || |||||||| |||||||| || ||||| ||||| |||||||||||||| || |  |||||||| ||
gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG

upper sequence: GLYMA13G34740.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
-----gtaagtttttttatttctgt---ttttactgagataatggtg---ttgtttgtgttttaagtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttt---tgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
       ||| | ||   |||||||    |||  | |  |  ||||      |||||| || |   || ||   |||    ||    ||||  |||| |  | ||   |||| | |   ||||| ||||||||||| |||||||| || ||||| ||||||||||||||||||||||| || |||||||| ||
gtgtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttt--tgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG

upper sequence: GLYMA13G34740.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G091265_T05 (Zea mays), 3'ss of exon 2
---gtaagtttttttatttctgt----ttttac--tgagataatggtgttgtttgtgttttaagtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttt---tgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
     ||| | ||   |||||||    ||||    || | |  |      |||||| || |   || ||   |||    ||    ||||  |||| |  | ||   |||| | |   ||||| ||||||||||| |||||||| || ||||| ||||||||||||||||||||||| || |||||||| ||
gtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttt--tgatcttatgtgacattgtttgtatgtgaagATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG

upper sequence: GLYMA13G34740.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 2
--gtaagtttttttatttctgtttttactgagataatggtgttgtttgtgttttaagtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
   | |   |  | |   ||    || |||       | |||   || |  | |   ||      ||  |  | ||  || || |||||  ||| |  | | |  | | |||||||||||| || |||||||| || ||||| |||||||||||||||||||| || |  |||||| | ||
gtatgaagctcctcaacccttccattgctg-------gctgtcccttttactgtgcatgc-----atttttagcttgcttgtgatgattgggtt-gtctattttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG

upper sequence: GLYMA13G34740.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G119357_T01 (Zea mays), 3'ss of exon 2
--gtaagtttttttatttctgtttttactgagataatggtgttgtttgtgttttaagtgtttgaaatggtgggttttgttttgttgatttag-tttg-gttttgtgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
         |  | | | || |  ||  |||  |  |    || | ||||  |   | ||||       || |  |  || || | |||| | | || || || |  | | |||||||||||| || |||||||| || ||||| |||||||||||||||||||| || |  |||||||| ||
gtacggagctcctcaatcctttcattgttgactttttc---ttctctgtgcat---gcgttt-------tgagcctgcttgtgataatttgggtgtgtgtatttttctctaaagGTATTGCAAATGTGAGATGCCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTG

upper sequence: GLYMA13G34740.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagtttttttatttctgtttttactgagataatggtgttgtttgtgttttaagtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
||||||   |  ||         || | |||| |        |  |  || | | |   || |||        || |||   || | | | ||| | ||| ||| |||||||| ||||| || || |||||||| || ||||| || ||||||||||||||||| || ||||| || ||
gtaagtagataaata-------gtaatcagatcagaac----tacgccttcttattacctggaatttccatgattttttatctgttgtgggttgttgttg-gttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG

upper sequence: GLYMA13G34740.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtttttttatttctgtttttactgagataatggtgttgtttgtgttttaa-gtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
|| |||||   |     ||||||  |||   | ||| |     |  || || || ||  | | | | ||||| |       | ||| |   ||||  ||| ||| ||||||||||||||| |||||||||||||||||||||||||| || ||||| ||||| |||||||||||||| ||
gtgagtttgagt-----tgtttt-gctggattgatgat-----tgatgattgaatgtactggtattcgtgggct-------gatgaatacttttgaattt-tgtattgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG

upper sequence: GLYMA13G34740.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S298_65V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaagtttttttatttctgtttttactgagataatggtgttgtttgtgttttaagtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
  |  | | | ||| | | | | ||   | || ||  | |  | ||||| ||  |||||||      |  |  ||  |  |   ||     | |  |  |   |||| || ||||||||||||||||||||||| || || |||||| | ||||| || |||||    ||||| || ||
--atatatatatatatatatatatatatatatcatcttatcatgtgtgtgttt-gtgtttg-----ttccgcattact--gaacatcaccatcgactccgctgtttgcagTTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG

upper sequence: GLYMA13G34740.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ05369 (Selaginella moellendorffii), 3'ss of exon 2
gtaagtttttttatttctgtttttactgagataatggtgttgtttgtgttttaagtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
                                  |    |||     | | | |   |||| | |       | | || || |   ||  ||||| |||| |      ||||| |||||||||||||||||||| ||||| ||||| || |||||||||||||||| |||||| || ||
---------------------------------gtaagattgacaaagctctcac--tttggattct----ctatcttatgctctctttttttgggtttgcggaa-acagGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTG

upper sequence: GLYMA13G34740.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ26805 (Selaginella moellendorffii), 3'ss of exon 2
gtaagtttttttatttctgtttttactgagataatggtgttgtttgtgttttaagtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttttgaa--gGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
                                            |  | || |      |   |   ||| || | | |  |    |   |||  ||||| ||||  ||  |||| |||||||||||||||||||| ||||| ||||| || |||||||||||||||| |||||| || ||
-------------------------------------------gtaagattgacaaagctctcactttggattctctatcttatgctctcttt--ttttgggtttgaaacagGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTG

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|193300267|gb|FK267210.1|FK267210
EST:     GACCGTGTTGCTGT                         GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
genomic: GACCGTGTTGCTGTgtaagttttt ... tgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
EST: gi|193368742|gb|FK335710.1|FK335710
EST:     GACCGTGTTGCTGT                         GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
genomic: GACCGTGTTGCTGTgtaagttttt ... tgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
EST: gi|209709125|gb|BW658841.1|BW658841
EST:     TTTGAGTACAAAGCTGCCACTGGGGCTTTCACGCCTGACCGTGTTGCTGT                         GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
genomic: TTTGAGTACAAAGCTGCCACTGGGGCTTTCACGCCTGACCGTGTTGCTGTgtaagttttt ... tgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
EST: gi|193375728|gb|FK339153.1|FK339153
EST:     GACCGTGTTGCTGT                         GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
genomic: GACCGTGTTGCTGTgtaagttttt ... tgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
EST: gi|7029681|gb|AW459464.1|AW459464
EST:     TTTGAGTACAAAGCTGCCACTGGGGCTTTCACGCCTGACCGTGTTGCTGT                         GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGAG
genomic: TTTGAGTACAAAGCTGCCACTGGGGCTTTCACGCCTGACCGTGTTGCTGTgtaagttttt ... tgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
EST: gi|9258286|gb|BE346433.1|BE346433
EST:     TTTGAGTACAAAGCTGCCACTGGGGCTTTCACGCCTGACCGTGTTGCTGT                         GTATTGCAAGTGCGAGATGCCTTATGACCCATATGACCTCATGGTGCAGTG
genomic: TTTGAGTACAAAGCTGCCACTGGGGCTTTCACGCCTGACCGTGTTGCTGTgtaagttttt ... tgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
EST: gi|193379467|gb|FK343569.1|FK343569
EST:     GACCGTGTTGCTGTT                         GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGT
genomic: GACCGTGTTGCTG-Tgtaagttttt ... tgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGT
EST: gi|207771270|gb|GD746385.1|GD746385
EST:     TTTGAGTACAAAGCTGCCACTGGGGCTCTCACGCCTGACCGTGTTGCTGT                         GTATTGCAAGT
genomic: TTTGAGTACAAAGCTGCCACTGGGGCTTTCACGCCTGACCGTGTTGCTGTgtaagttttt ... tgttttgaagGTATTGCAAGT
EST: gi|209701039|gb|BW652617.1|BW652617
EST:     TTTGAGTACAAAGCTGCCACTGGGGCTTTCACGCCTGACCGTGTTGCTGT                         GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
genomic: TTTGAGTACAAAGCTGCCACTGGGGCTTTCACGCCTGACCGTGTTGCTGTgtaagttttt ... tgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
EST: gi|208024940|gb|GD822386.1|GD822386
EST:     CACTGGGGCTTTCACGCCTGACCGTGTTGCTGT                         GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
genomic: CACTGGGGCTTTCACGCCTGACCGTGTTGCTGTgtaagttttt ... tgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
EST: gi|151394164|gb|EV264035.1|EV264035
EST:     TTTGAGTACAAAGCTGCCACTGGGGCTTTCACGCCTGACCGTGTTGCTGT                         GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
genomic: TTTGAGTACAAAGCTGCCACTGGGGCTTTCACGCCTGACCGTGTTGCTGTgtaagttttt ... tgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
EST: gi|193370284|gb|FK338134.1|FK338134
EST:     GACCGTGTTGCTGT                         GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
genomic: GACCGTGTTGCTGTgtaagttttt ... tgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
                        tgttgat  putative branch site (score: 4)
                ttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttttttatttctgtttttactgagataatggtgttgtttgtgttttaagtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG

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