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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttttttattcttacctttgctagatacgagagtatgacacatatcttcttagtttctaaagtagatatcattttactccttttcagGCAATGGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGGATTGGTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATG

Basic information

species Glycine max
transcript GLYMA06G44340.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM5G816609_T01 (Zea mays), 3'ss of exon 1
gtgagtttttttattcttacctttgctagatacgagagtatgacacatatcttcttagtttctaaagtagatatcattttactccttttcagGCAATGGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGGATTGGTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATG
    || | |       |   || ||| |    ||     || |||    | ||||  ||||   | ||    ||| ||| || |    |||||  | ||  ||||    || ||||| |  ||||| ||| |    ||  | ||||| |||||  ||||| | |||||||||||||||||||||||||| |
----gtatgtgctccactttgttagcttgtcttgaccccttg-caccctgcatctttttttccctaataccc-tcacttttctac----cagGCGTTTGCTATTCTCATGGAGTATATTGGCAAAGATGACTCAAACATTCGTATTGGAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAG

upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G155384_T03 (Zea mays), 3'ss of exon 15
gtgagtttttttattc-ttacctttgctagatacgagagtatgacacatatcttcttagtttctaaagtagatatcattttactccttttcagGCAATGGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGGATTGGTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATG
|| |||  |    ||  ||| ||   ||     ||    |    |    ||||||||  |  |  ||     || | |    ||   |  |||||  | ||  ||||    || ||||| |  || || ||| |    ||  | ||||| |||||  ||||| | |||||||||||||||||||||||||| |
gtaagtggtccactttgttagctactctccccccg----tcccccctgcatcttctttttcccctaa-----taccctaac-ctttctgccagGCGTTTGCTATTCTTATGGAGTATATTGGCAAGGATGACTCAAACATTCGTATTGGAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAG

upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 15
lower sequence: AT4G28470.1 (Arabidopsis thaliana), 3'ss of exon 13
gtgagtttttttattcttacctttgctagatacgagagtatgacacatatcttcttagtttctaaagtagatatcattttactccttttcagGCAATGGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGGATTGGTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATG
|||||||||||| ||      |||   | ||  ||   | ||   || |  || |     |  |   |   |  ||  |  ||| || ||||||| | || |||||    |  ||||| || || || ||  | ||  || | |||||||| ||||||||| | || ||||||||||| |||||||| ||||
gtgagtttttttttt------tttttaatatgggaacctctgtgtcacaatttttcgccattcattctcact--cagct--ctctttctcagGCATTTGCCCTTCTTTCAGGTTATATTGACAATGAGGATTCATCTGTCCGAATTGGTGCTATTATGGGTCTCGGGATTGCATATGCGGGTTCCCAAAATG

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|193522231|gb|FK482104.1|FK482104
EST:     TACTGGGAGTTGGAATTGTGAATTGTAGTATCAAGAATGACTGTGATCCT                         GCAATGGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGG
genomic: TACTGGGAGTTGGAATTGTGAATTGTAGTATCAAGAATGACTGTGATCCTgtgagttttt ... tccttttcagGCAATGGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGG
EST: gi|208223861|gb|GE020962.1|GE020962
EST:     TACTGGGAGTTGGAATTGTGAATTGTAGTATCAAGAATGACTGTGATCCT                         GCAATGGCACTTCTAGGTGACTATATAGATAAAGTAAGACACTTCAATCAG
genomic: TACTGGGAGTTGGAATTGTGAATTGTAGTATCAAGAATGACTGTGATCCTgtgagttttt ... tccttttcagGCAATGGCACTTCTAGGTGACTATATAGATAAAG-AAGACACTTCAATCAG
EST: gi|193493116|gb|FK460902.1|FK460902
EST:     TACTGGGAGTTGGAATTGTGAATTGTAGTATCAAGAATGACTGTGATCCT                         GCAATGGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGG
genomic: TACTGGGAGTTGGAATTGTGAATTGTAGTATCAAGAATGACTGTGATCCTgtgagttttt ... tccttttcagGCAATGGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGG
EST: gi|193481819|gb|FK446938.1|FK446938
EST:     TACTGGGAGTTGGAATTGTGAATTGTAGTATCAAGAATGACTGTGATCCT                         GCAATGGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGG
genomic: TACTGGGAGTTGGAATTGTGAATTGTAGTATCAAGAATGACTGTGATCCTgtgagttttt ... tccttttcagGCAATGGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGG
EST: gi|208067895|gb|GD861405.1|GD861405
EST:     TACTGGGAGTTGGAATTGTGAATTGTAGTATCAAGAATGACTGTGATCCT                         GCAATGGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGG
genomic: TACTGGGAGTTGGAATTGTGAATTGTAGTATCAAGAATGACTGTGATCCTgtgagttttt ... tccttttcagGCAATGGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgacacatatcttcttagtttctaaagtagatatcattttactccttttcagGCAATGGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGGATTGGTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATG
                      ttctaaa  putative branch site (score: 2)
                                    tcattttactcctttt  putative PPT
                              tagatatcatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttttttattcttacctttgctagatacgagagtatgacacatatcttcttagtttctaaagtagatatcattttactccttttcagGCAATGGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGGATTGGTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG