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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttatttctgttttttttagtgagataatgttgtaagtgtttgaaatggtgggttttgttttgttgatttggttcggttttgtggtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG

Basic information

species Glycine max
transcript GLYMA12G35680.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G35680.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g21770.1 (Oryza sativa), 3'ss of exon 2
----------------------------------gtaagtttatttctgttttttttagtgagat---aatgttgtaagtgtttgaaatggtgggttttgttttgttgatttggttcggttttgtg-gtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
                                   | | |||   |||| || || |  ||  ||       |||   ||  |   |||||| |||  || ||| | | || |||  |  | |||| || || ||||| ||||||||||||||||| |||||||| ||||| || ||||||||||| ||||| |||||||| ||
gtatttgctccaaccccccctccttttttgatcattgattttgcatctgcttgttgttatgcaatgtgggctttggttgtactgataatggttggtggtggttt-tggtttgggtgtgtgtgtgtgtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG

upper sequence: GLYMA12G35680.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
---------------gtaagtttatttctgttttttttagtgagataatg--------------ttgtaagtgtttgaaatggtgggttttgttttgt---tgatttggttcggttttgtggttt---gaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
               |   ||| |||||    ||    ||||  ||  ||                 |  |   ||  |||| ||  |  || || ||   || ||  |||   ||||  | |||   |||| || |||||||| |||||||| || ||||| ||||| |||||||||||||| || |  |||||||| ||
gtatgcttgaatgctgattgttcatttcc-cgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG

upper sequence: GLYMA12G35680.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
-----------------------gtaagtttatttc-tgttttttttagtgagataatgttgtaagtgtttgaaatggtgggttttgttttgttgatttggttcggttttgt---ggtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
                       ||||  || | || |||  |  ||| | || |  | || |   || ||   |||    ||    ||||  |||| |  |  |   ||||     | ||||| ||||||||||| |||||||| || ||||| ||||||||||||||||||||||| || |||||||| ||
gtgtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttt--tgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG

upper sequence: GLYMA12G35680.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G091265_T05 (Zea mays), 3'ss of exon 2
---------------------gtaagtttatttc-tgttttttttagtgagataatgttgtaagtgtttgaaatggtgggttttgttttgttgatttggttcggttttgt---ggtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
                     ||||  || | || |||  |  ||| | || |  | || |   || ||   |||    ||    ||||  |||| |  |  |   ||||     | ||||| ||||||||||| |||||||| || ||||| ||||||||||||||||||||||| || |||||||| ||
gtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttt--tgatcttatgtgacattgtttgtatgtgaagATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG

upper sequence: GLYMA12G35680.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 2
--gtaagtttatttctgttttttttagtgagataatgttgtaagtgtttgaa-atggtgggttttgttttgttgatttggttcggttttgtggtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
   | |   |  |      ||   | |   | |     | | | |||      ||  |  | ||  || || ||||| |||| |  | | |  | | |||||||||||| || |||||||| || ||||| |||||||||||||||||||| || |  |||||| | ||
gtatgaagctcctcaacccttccattgctggctgtcccttttactgtgcatgcatttttagcttgcttgtgatgattgggtt-gtctattttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG

upper sequence: GLYMA12G35680.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G119357_T01 (Zea mays), 3'ss of exon 2
---gtaagtttatttctgttttttttagtgagataatgttgtaagtgtttgaaatggtgggttttgttttgttgatttggttcggttt--tgtggtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
      || |  |   |  |||  ||  |||  |  | || |  |||  ||   |  || |  |  || || | |||||| |  || |  | |  | | |||||||||||| || |||||||| || ||||| |||||||||||||||||||| || |  |||||||| ||
gtacggagctcctcaatcctttcattgttgactttttcttctctgtgcatgcgttt-tgagcctgcttgtgataatttgggtgtgtgtatttttctctaaagGTATTGCAAATGTGAGATGCCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTG

upper sequence: GLYMA12G35680.2 (Glycine max), 3'ss of exon 2
lower sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagtttatttctgttttttttagtgagataatg--ttgtaagtgtttgaaatggtgggttttgttttgttgatttggttcggttttgtggtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
||||||  ||   |  |  |   |     |  | |  || | | |   || |||        || |||   || | ||| | | | ||| | | |||||||| ||||| || || |||||||| || ||||| || ||||||||||||||||| || ||||| || ||
gtaagtagataaatagtaatcagatcagaactacgccttcttattacctggaatttccatgattttttatctgttgtgggttgttgttg-gttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG

upper sequence: GLYMA12G35680.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtttatttctgttttttttagtgagataatgttgtaagtgtttgaaatggtgggttttgttttgttgatttggttcggttttgtggtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
|| |||||   | ||||||  |   |  ||| || |  | | ||  || | ||||     | |  |  |  ||    ||   ||||||   ||||||||||||||| |||||||||||||||||||||||||| || ||||| ||||| |||||||||||||| ||
gtgagtttgagt-tgttttgctggatt-gatgat-tgatgattgaatgtactggtattcgtgggctgatgaatacttttgaattttgta--ttgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG

upper sequence: GLYMA12G35680.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S298_65V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaagtttatttctgttttttttagtgagataatgttgtaa-gtgtttgaaatggtgggttttgttttgttga---tttggttcggttttgtggtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
 ||  | ||| | | | | | |   | | || || || | | |||| ||     ||  |||  |  ||  |||   |     |||  |  |  ||||| || ||||||||||||||||||||||| || || |||||| | ||||| || |||||    ||||| || ||
atatatatatatatatatatatatat-atatcatcttatcatgtgtgtgtttgtgtttgttccgcattactgaacatcaccatcgactccgctgtttgcagTTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG

upper sequence: GLYMA12G35680.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ05369 (Selaginella moellendorffii), 3'ss of exon 2
gtaagtttatttctgttttttttagtgagataatgttgtaagtgtttgaaatggtgggttttgttttgttgatttggttcggttttgtggtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
                        || ||||  ||    |  | |       | |    | | || || |   ||  || || |||| ||     ||||| |||||||||||||||||||| ||||| ||||| || |||||||||||||||| |||||| || ||
------------------------gtaagat--tgacaaagctctcactttggattctctatcttatgctctctttttttgggtttgcggaa-acagGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTG

upper sequence: GLYMA12G35680.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ26805 (Selaginella moellendorffii), 3'ss of exon 2
gtaagtttatttctgttttttttagtgagataatgttgtaagtgtttgaaatggtgggttttgttttgttgatttggttcggttttgtggtttgaa---gGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
                              |||  |||  |  | |   | |  ||| || | | |  |    |    ||  ||||  ||||||||   |||| |||||||||||||||||||| ||||| ||||| || |||||||||||||||| |||||| || ||
-----------------------------gtaagattgacaaagctctcactt-tggattctctatcttatgct---ctctttttttgggtttgaaacagGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTG

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|298165839|gb|HO008810.1|HO008810
EST:     TTTGAGTACAAGGCTGCTACTGGGGCTTTCACGCCTGACCGTGTTGCTGT                         GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
genomic: TTTGAGTACAAGGCTGCTACTGGGGCTTTCACGCCTGACCGTGTTGCTGTgtaagtttat ... tggtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
EST: gi|298165969|gb|HO008940.1|HO008940
EST:     TTTGAGTACAAGGCTGCTACTGGGGCTTTCACGCCTGACCGTGTTGCTGT                         GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
genomic: TTTGAGTACAAGGCTGCTACTGGGGCTTTCACGCCTGACCGTGTTGCTGTgtaagtttat ... tggtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG
EST: gi|151409769|gb|EV279577.1|EV279577
EST:     TTTGAGTACAAGGCTGCTACTGGGGCTTTCACGCCTGACCGTGTTGCTGT                         GTATTGCAAGTGCGAGATGCCATATAACCCAGATGACCTCATGGTGCAGTG
genomic: TTTGAGTACAAGGCTGCTACTGGGGCTTTCACGCCTGACCGTGTTGCTGTgtaagtttat ... tggtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgaaatggtgggttttgttttgttgatttggttcggttttgtggtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
                        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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttatttctgttttttttagtgagataatgttgtaagtgtttgaaatggtgggttttgttttgttgatttggttcggttttgtggtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG