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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgattatttttatgattgattactttgattcgtatctttgatgattaatgatagtttgtttgtgctaaatgggttatggctttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACCCTCTCAAGGTCTCTCTGGAGGACCTTTATCTCGGGACTTCTAAGAAGCT

Basic information

species Glycine max
transcript GLYMA11G17930.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G17930.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g57340.1 (Oryza sativa), 3'ss of exon 2
gttgattatttttatgattgattactttgattcgtatctttgatgattaatgatagtttgtttg--tgctaaatgggttatggctttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACCCTCTCAAGGTCTCTCTGGAGGACCTTTATCTCGGGACTTCTAAGAAGCT
     |       ||||   |  |  |  ||||       || |||||     | ||||| ||   |  | | ||| |       | ||   ||||||| || ||| | || ||||| ||| |  | ||||| ||||||||||||||||| ||||| |||||||||||  | ||    || || || ||||||||
----gtacgagacatgag-aagcagctcaattcaacctcctggtgattg----tggtttgcttagattttgactggctctcattgtggtctgcagGTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACCCTCTGAAGGTTTCTCTGGAGGAATTGTACAATGGCACATCAAAGAAGCT

upper sequence: GLYMA11G17930.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G134917_T01 (Zea mays), 3'ss of exon 2
gttgattatttttatgattgattactttgattcg-tatctttgatgattaatgatagtttgtttgtgctaaatgggttatggctttgt---gaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACCCTCTCAAGGTCTCTCTGGAGGACCTTTATCTCGGGACTTCTAAGAAGCT
     |   ||  || |   |   ||  ||| |  |  | ||||  ||| |  |     | | |       |||   ||||   ||||    |   ||||| || ||| | || || |||||| |  | ||||| ||||||||||| ||||| ||||| |||||||||||  | ||    || || || |||||   
----gtatgttacataacaaaaagct--gatgcaatgacattgac-attgagaagcacatatgtagttctcatgctgtatgtacttgtccgaagGTGGTGGCAGCAGTAGGGGCAGAAGGCAGCGAAGGGGAGAGGATGTGGTTCATCCTCTAAAGGTTTCTCTGGAGGATTTGTACAATGGCACATCAAAGAA---

upper sequence: GLYMA11G17930.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G028218_T02 (Zea mays), 3'ss of exon 2
gttgattatttttatgattgattact-ttgattcgtatctttgatgattaatgatagtttgttt-gtgctaaatgggttatggctttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACCCTCTCAAGGTCTCTCTGGAGGACCTTTATCTCGGGACTTCTAAGAAGCT----------
|||    |     | ||   |  |    |||| |  ||      |||| ||  || |  |   | |||    |     | ||   ||||| | |||||| || ||| | || || |||||  | || ||||| ||||||||||| ||||| ||||| |||||||||||  | ||    || || || ||||||||          
gttacaaaagaaaaagaaaaaaaagaactgatgca-atgccatttgatcaagaattgcctacatagtggctcaccctgtttgttcttgtgcaaaggtggcagcagTAGGGGCAGAAGGCAACGACGGGGAGATGATGTGGTTCATCCTCTGAAGGTTTCTCTGGAGGATTTGTACAATGGCACATCAAAGAAGCTCTCTCTGTCC

upper sequence: GLYMA11G17930.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G028218_T01 (Zea mays), 3'ss of exon 2
gttgattatttttatgattgattactttgattcgtatctttgatgattaatgatagtttgtttgt------gctaaatgggttatggctttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACCCTCTCAAGGTCTCTCTGGAGGACCTTTATCTCGGGACTTCTAAGAAGCT
||   |||        |  ||  |    ||   |   |  ||    || || |    |||  |        ||| |    ||| ||   ||||| | |||||| || ||| | || || |||||  | || ||||| ||||||||||| ||||| ||||| |||||||||||  | ||    || || || ||||||||
gtatgttacaaaagaaaaagaaaaaaaagaactgatgcaatgccatttgatcaagaattgcctacatagtggctcaccctgtt-tgttcttgtgcaaagGTGGCAGCAGTAGGGGCAGAAGGCAACGACGGGGAGATGATGTGGTTCATCCTCTGAAGGTTTCTCTGGAGGATTTGTACAATGGCACATCAAAGAAGCT

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|207842272|gb|GD817628.1|GD817628
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
EST: gi|38192432|gb|CF921638.1|CF921638
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
EST: gi|254346520|gb|GR856242.1|GR856242
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
EST: gi|208277788|gb|GE075313.1|GE075313
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAG
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAG
EST: gi|193315020|gb|FK282192.1|FK282192
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGA
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGA
EST: gi|193400501|gb|FK369654.1|FK369654
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAGG
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGG
EST: gi|209696486|gb|BW672828.1|BW672828
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
EST: gi|213590203|gb|DB963808.1|DB963808
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
EST: gi|298184711|gb|HO029924.1|HO029924
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
EST: gi|209718480|gb|BW666264.1|BW666264
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
EST: gi|193312126|gb|FK277730.1|FK277730
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGA
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGA
EST: gi|207764357|gb|GD736730.1|GD736730
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
EST: gi|213600517|gb|DB960065.1|DB960065
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
EST: gi|213611999|gb|DB958953.1|DB958953
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGT
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGT
EST: gi|209714486|gb|BW684862.1|BW684862
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
EST: gi|209723723|gb|BW662591.1|BW662591
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGCATCAG                         GTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
EST: gi|11412476|gb|BF424487.1|BF424487
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
EST: gi|23732018|gb|BU764162.1|BU764162
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAAGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
EST: gi|213619545|gb|DB957246.1|DB957246
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
EST: gi|254324916|gb|GR834341.1|GR834341
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
EST: gi|193312142|gb|FK275618.1|FK275618
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGT
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGT
EST: gi|193397689|gb|FK365151.1|FK365151
EST:     TTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTAGGATCAG                         GTGGAA-TAGTC-AGGTAGGAGG
genomic: TTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTT-GGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGG
EST: gi|193406228|gb|FK370581.1|FK370581
EST:     TTTGAATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAGG
genomic: TTTGA-TATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGG
EST: gi|298171609|gb|HO021201.1|HO021201
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGCGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
EST: gi|17963719|gb|BM270465.1|BM270465
EST:     GTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
genomic: GTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
EST: gi|19452816|gb|BM954226.1|BM954226
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
EST: gi|207832094|gb|GD805144.1|GD805144
EST:     GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAG                         GTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC
genomic: GTTTGATATCTTTTCATCTTTCTTTGGAGGTGGGAGTCCCTTTGGATCAGgttgattatt ... ttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgatgattaatgatagtttgtttgtgctaaatgggttatggctttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACCCTCTCAAGGTCTCTCTGGAGGACCTTTATCTCGGGACTTCTAAGAAGCT
                          tgctaaa  putative branch site (score: 2)
       attaatgatagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgattatttttatgattgattactttgattcgtatctttgatgattaatgatagtttgtttgtgctaaatgggttatggctttgtgaacagGTGGAAGTAGTCGAGGTAGGAGGCAGAGGCGCGGAGAAGATGTGGTTCACCCTCTCAAGGTCTCTCTGGAGGACCTTTATCTCGGGACTTCTAAGAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC