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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gataaaaatggctttctcactaaatatatccatattttcattcatgtgacatgttacgagatattttaaatctaatctatcgtttgtttccaattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTATTTCATAAAAAGTGGGATTGTCACAGTAATCAAGGATGCTTTAATTCCTA

Basic information

species Glycine max
transcript GLYMA02G47460.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 8
gataaaaatggctttctcactaaatatatccatattttcattcatgtgacatgttacgagatattttaa-atctaatctatcgtttgtttccaattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTATTTCATAAAAAGTGGGATTGTCACAGTAATCAAGGATGCTTTAATTCCTA
 | || ||| || ||   |     |  |||  ||| ||| |  |   |  |   | |    |   | |   | |     | |  |||  ||       ||||| || ||   |||||||||||||||||||||||| || || ||||| || || || |||||||| ||||| || || ||||||||||||||  | ||||
-aaaataattgcattgcaaaatcttgcatctctatgttcttctaaacgtaaaactgctttctgcgtaactgtatgtaacaacaattgactcatggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATACTTTATCAAAAGTGGCATTGTTACCGTGATCAAGGATGCTTTGCTCCCTA

upper sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 8
--gataaaaatggct--ttctcactaaatatatccatattttcattcatgtgacatgttacgagatattttaaatctaatctatcgtttgtttccaattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTATTTCATAAAAAGTGGGATTGTCACAGTAATCAAGGATGCTTTAATTCCTA
     | | ||| |   ||   ||| ||   | | | ||  |     ||||    ||     |   ||  | ||||| ||  ||  | |||| |   | |  |||| || ||    |||||| ||||||||||| ||||||| || ||||| || ||||| |||||||| |||||||| || |||||||| || ||||| ||||
tttccagagatgaccagttgatactgaactgaacaaaatgatgtgcaatgtttattgcattaattaatgatcaatcttat--atgatctgttgcttgtac--agATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATACTTCATCAAAAGTGGCATTGTCACTGTGATCAAGGACGCCTTAATCCCTA

upper sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G163437_T01 (Zea mays), 3'ss of exon 8
gataaaaatggctttctcactaaatatatcca---tattttcattcatgtgacatgttacgagatattttaaatctaatctatcgtttgtttccaattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTATTTCATAAAAAGTGGGATTGTCACAGTAATCAAGGATGCTTTAATTCCTA
     |  | |   | | | |||| |    ||    ||| | |  | ||  |||  ||   | ||       || |     |         || |  |  |||||  | |||  ||||||||| ||||||||||||||||| ||||| ||||| ||||| ||| |||| ||||||||||| ||||||||||||||| | ||||
--cttagcttgtaatatgattaaacacgaacagttcattattagacttgccacacatttt-atatggccgtgatatttctcacgagactcgtcgatcttgcagATACTCAACGCTGACAATGTTCAAGAAGCTGCAAGGGAGACAGACGGGTACTTCATCAAAGGTGGAATTGTCACAGTGATCAAGGATGCTTTACTCCCTA

upper sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G068506_T02 (Zea mays), 3'ss of exon 8
gataaaaatggctttctcactaaatatatccatattttcattcatgtgacatgttacgagatatttta----aatctaatctatcgtttgtttccaattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTATTTCATAAAAAGTGGGATTGTCACAGTAATCAAGGATGCTTTAATTCCTA
        | |   |   | |||| |      | |  | |||    |  | ||  || | || || ||    |     || | || |  |  || |  |   ||||  | ||   ||||||||| ||||||||||||| ||| ||||| ||||| ||||| ||| |||| ||||||||||| ||||||||||||||| | ||||
---ttcgcttgtcataggattaaacaggaaactttcattattagactttcctgccacaa-attttctatggcagcggcatttctcatgagactcgatcttgtagATACTCAATGCTGACAATGTTCAAGAAGCTGCAATGGAGACAGACGGGTACTTCATCAAAGGTGGAATTGTCACAGTGATCAAGGATGCTTTACTCCCTA

upper sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G106213_T02 (Zea mays), 3'ss of exon 8
--------gataaaaatggctttctcactaaatatatccatattttcattcatgtgacatgttacgagatattttaaatctaatctatcgtttgtttccaattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTATTTCATAAAAAGTGGGATTGTCACAGTAATCAAGGATGCTTTAATTCCTA
          | | | | | |     || ||| |||| ||   |    ||  ||| |  | ||    | |   |     ||||   || |||| ||     ||  ||||| || ||   ||| |||||||||||||| | |||||| ||||| || ||||| || |||||||| |||||||| || || || ||||||||||||||||
ttgactgctcttagagttgataatggacaaaaaatatgcac--tgatgtttttgttatgtattcattggttcatccttcctaa---atagtttattgt---tttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATATTTTATCAAAAGTGGAATTGTCACGGTGATTAAAGATGCTTTAATTCCTA

upper sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 8
----------------gataaaaatggctttctcactaaatatatccatattttc-attcatgtgacatgttacga-gatattttaaatctaatctatcgtttgtttccaat-tctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTATTTCATAAAAAGTGGGATTGTCACAGTAATCAAGGATGCTTTAATTCCTA
                  | |  |||| ||  |    |   || ||  | | | |   | ||||  | | | | || ||  || | | | |||| || ||      |    | | |||||| || || ||||| ||||| |||||||| ||||||||||| ||||| |||||||| || || || || ||||| |||||||||||||| ||  ||||||
gttgtgattttaattaacttagcatggattatttttcatcaatttcgttttctactggtaatgttgc-tatgatgatgaggttgtgattttaatttagcgaagaaatttgttatttcagATCATCAATAGTGATAATGTGCAAGAAGCGGCAAGGGAAACGGATGGATATTTCATTAAGAGCGGAATAGTCACGGTAATCAAGGATGCCTTGCTTCCTA

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|31471544|gb|CD413572.1|CD413572
EST:     TCAAAAGGGCAATAATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAG                         ATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
genomic: TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAGgttataacat ... caattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
EST: gi|22929719|gb|BU546858.1|BU546858
EST:     TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAG                         ATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
genomic: TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAGgttataacat ... caattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
EST: gi|31465216|gb|CD407244.1|CD407244
EST:     TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAG                         ATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
genomic: TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAGgttataacat ... caattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
EST: gi|9902053|gb|BE611021.1|BE611021
EST:     TCAAAAGGGCAATTATTGACAAGAATGCTCGAATTGGGGAAAATGTCAAG                         ATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
genomic: TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAGgttataacat ... caattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
EST: gi|214004859|gb|DB988868.1|DB988868
EST:     TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAG                         ATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
genomic: TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAGgttataacat ... caattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
EST: gi|15288165|gb|BI472056.1|BI472056
EST:     TCAAAAGGGCAATAATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAG                         ATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
genomic: TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAGgttataacat ... caattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
EST: gi|12489873|gb|BG043394.1|BG043394
EST:     TCAAAAGGGCAATTATTGACAAGAATGCTCGAATTGGGGAAAATGTCAAG                         ATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
genomic: TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAGgttataacat ... caattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
EST: gi|51338121|gb|CO981987.1|CO981987
EST:     TCAAAAGGGCAATTATTGACAAGAATGCTCGAATTGGGGAAAATGTCAAG                         ATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
genomic: TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAGgttataacat ... caattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
EST: gi|27424381|gb|CA935901.1|CA935901
EST:     TCAAAAGGGCAATTATTGACAAGAATGCTCGAATTGGGGAAAATGTCAAG                         ATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
genomic: TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAGgttataacat ... caattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
EST: gi|31310766|gb|CD395969.1|CD395969
EST:     TCGACAAGAATGCTCGAATTGGGGAAAATGTCAAG                         ATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
genomic: TCGACAAGAATGCTCGAATTGGGGAAAATGTCAAGgttataacat ... caattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
EST: gi|209702859|gb|BW655981.1|BW655981
EST:     TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAG                         ATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
genomic: TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAGgttataacat ... caattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
EST: gi|20498182|gb|BQ273112.1|BQ273112
EST:     TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAG                         ATTATTAACAGTGACAATGTCCAA
genomic: TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAGgttataacat ... caattctcagATTATTAACAGTGACAATGTCCAA
EST: gi|192316610|gb|FK006817.1|FK006817
EST:     TCAAAAGGGCAATTATTGACAAGAATGCCCGAATTGGGGAAAATGTCAAG                         ATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
genomic: TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAGgttataacat ... caattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
EST: gi|31465073|gb|CD407101.1|CD407101
EST:     GGAAAATGTCAAG                         ATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
genomic: GGAAAATGTCAAGgttataacat ... caattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
EST: gi|6070729|gb|AW100116.1|AW100116
EST:     TCAAAAGGGCAATTATTGACAAGAATGCTCGAATTGGGGAAAATGTCAAG                         ATTATTAACAGTGACAATGTCCAAGACGCTGCAAGGGAAACAGATGGGTAT
genomic: TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAGgttataacat ... caattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
EST: gi|21637686|gb|BM107841.1|BM107841
EST:     TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAG                         ATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
genomic: TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAGgttataacat ... caattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
EST: gi|13266691|gb|BG370154.1|BG370154
EST:     TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAG                         AGTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
genomic: TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAGgttataacat ... caattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
EST: gi|23728098|gb|BU762095.1|BU762095
EST:     TCAAAAGGGCAATTATTGACAAGAATGCTCGAATTGGGGAAAATGTCAAG                         ATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
genomic: TCAAAAGGGCAATTATCGACAAGAATGCTCGAATTGGGGAAAATGTCAAGgttataacat ... caattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
EST: gi|7640083|gb|AW734392.1|AW734392
EST:     GGGAAAATGTCAAG                         ATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT
genomic: GGGAAAATGTCAAGgttataacat ... caattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgacatgttacgagatattttaaatctaatctatcgtttgtttccaattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTATTTCATAAAAAGTGGGATTGTCACAGTAATCAAGGATGCTTTAATTCCTA
                        atctaat  putative branch site (score: 3)
                                     tttgtttcc  putative PPT
             agatattttaaatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gataaaaatggctttctcactaaatatatccatattttcattcatgtgacatgttacgagatattttaaatctaatctatcgtttgtttccaattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTATTTCATAAAAAGTGGGATTGTCACAGTAATCAAGGATGCTTTAATTCCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
-ataaaaa
- - - - - - - - - - - - - - - - - - - cattcat
- - - - - - - - - - - - - - - - - - - - - - - tgacatg