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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatggttttgacttttgacaacattgattgtatgctagggcctaggggaaataaaagaagcaatttcattactgcttgattttctatttcttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGCAAATTGGGAGGTGCAAAGCCTGTTGTGAATGAAAATGCTGGTGGGATTATTACT

Basic information

species Glycine max
transcript GLYMA11G14960.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G14960.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g05800.1 (Oryza sativa), 3'ss of exon 8
---------------------------------------------------agatggttttgacttttgacaacattgattgtatgctagggcctaggggaaat---aaaagaagcaatttcattactgcttgattttctatttcttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGCAAATTGGGAGGTGCAAAGCCTGTTGTGAATGAAAATGCTGGTGGGATTATTACT
                                                   | |  | | || ||  |    |   ||    |   | |  ||  |            ||   | ||| | || ||    |      || || | |  ||  ||||| | ||| ||| |||| |||||||| || ||||| ||||| || ||| ||||||| |||||||||||||| ||| |    | | ||||||| ||||||
gtatgtgcatttgctattagttgtatgagtgtttcagtcatgttccatgctatagtgctatgcctcatagagattgtgggactcctccactgctcattaacttcttgcaattgatcaaatccaatatgtgtattgactccatgtttgctatcagGTTCACAAATAATATCCTCAGCACAGCCCAGCAAGTTTGGTTACGGAAACTGGGAGGAGCAAAGCCTGTTGTCAATCAGGGGGGTAGTGGGATAATTACT

upper sequence: GLYMA11G14960.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G839422_T01 (Zea mays), 3'ss of exon 8
---------------------------------------------------------------------------------------agatggttttgacttttgacaacattgattgtatgctagggcctaggggaaataaaagaagcaatttcattactgcttgattt---tctatttcttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGCAAATTGGGAGGTGCAAAGCCTGTTGTGAATGAAAATGCTGGTGGGATTATTACT
                                                                                       |   | |     |   |  |  | ||   |||   ||      ||     ||| |||      |||   ||     |||  ||   || || | ||  | |||||||| |||||||||||| |||||||| || || || ||||| || ||| ||||||| || |||||||| |||| |||    | | |||| || ||||| 
gtatgtgcatcagtctcttttgttctaatgggaaatatgttcagatatttgtttcacattatactgctagttgcttcatacaagatcacgagttcacagccccttgcccccttccctgttcactgaattttac----aatcaaattcatgattattttgtaatttgtattgactccatgttttccattagGTTTACAAACAATGTCCTCAGCACAGCCCAGCAGGTGTGGTTACGGAAAATGGGAGGAGCGAAGCCTGTAGTGACTGAGGGAGGTAGTGGAATAATTACC

upper sequence: GLYMA11G14960.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G110063_T01 (Zea mays), 3'ss of exon 9
------------------------------------------------------------------------------agatggttttgacttttgacaacattgattgtatgctagggcctaggggaaataaaagaagcaatttcattactgc-ttgattttctatttcttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGCAAATTGGGAGGTGCAAAGCCTGTTGTGAATGAAAATGCTGGTGGGATTATTACT
                                                                              | | | |  || |   |  |    || | | |   ||      || |   ||| |||   |||| ||  ||  ||  |||| |  | || | ||  | |||||| | |||||||||||| |||||||| || || || |||||||| ||| ||||||| || |||||||| |||| |||    | | |  |||| ||||| 
gtatgttcatgtcttttttttctaactacaaatatgttcatatattcttgttgcatattatgtcgctagttgcttcaaacaagatcatggccccttccc-tgttcagttttcactgaattttacgattaatcaaatccgcaagtttttttttgtattgact--ccatgttttccattagGTTCACAAACAATGTCCTCAGCACAGCACAGCAGGTTTGGTTGCGGAAAATGGGAGGAGCCAAGCCTGTAGTGAGTGAGGGGGATAGGAGGATAATTACA

upper sequence: GLYMA11G14960.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0004g04460.t01 (Vitis vinifera), 3'ss of exon 8
agatggttttgacttttgacaacattgattgtatgctagggcctaggggaaat--aaaagaagcaatttcattactgcttgattttctatttctt----ttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGCAAATTGGGAGGTGCAAAGCCTGTTGTGAATGAAAATGCTGGTGGGATTATTACT
      |||  | |   |    || | |    |   ||      |    |  |  | |  |||   ||  |||  |  |  ||    |  ||        |  |||||| | ||||||||| ||||||||||| |||||||||||||| |||||||| || ||||| || ||||||||||||||  ||||  |||| || ||||||
------tttctagtgaagttttcaataaaataaaaataaaatgcaaaatattttcagagcaagttcttcgattgttaatccataagatgctttgcatggctgttagGTTCACAAACAATGTACTGAGCACAGCACAACAAGTATGGTTACGCAAATTAGGTGGTGCCAAACCTGTTGTGAATGAGGATGCAAGTGGAATCATTACT

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|193484846|gb|FK452084.1|FK452084
EST:     ATGATTGGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACTG                         GTTTATAGACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGAAAATT
genomic: ATGATTGGCTACTTCTCACTATCTGTCCCATCAGGACTAACAATTTACTGgttagttttt ... cttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGCAAATT
EST: gi|22526016|gb|BU084827.1|BU084827
EST:     ATGATTGGCTACTTCTCACTATCTGTCCCATCAGGACTAACAATTTACTG                         GTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGCAAATT
genomic: ATGATTGGCTACTTCTCACTATCTGTCCCATCAGGACTAACAATTTACTGgttagttttt ... cttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGCAAATT
EST: gi|16104820|gb|BI892560.1|BI892560
EST:     ATGATTGGCTACTTCTCACTATCTGTCCCATCAGGACTAACAATTTACTG                         GTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGCAAATT
genomic: ATGATTGGCTACTTCTCACTATCTGTCCCATCAGGACTAACAATTTACTGgttagttttt ... cttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGCAAATT
EST: gi|16105954|gb|BI893694.1|BI893694
EST:     GCTACTTCTCACTATCTGTCCCATCAGGACTAACAATTTACTG                         GTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGCAAATT
genomic: GCTACTTCTCACTATCTGTCCCATCAGGACTAACAATTTACTGgttagttttt ... cttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGCAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggggaaataaaagaagcaatttcattactgcttgattttctatttcttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGCAAATTGGGAGGTGCAAAGCCTGTTGTGAATGAAAATGCTGGTGGGATTATTACT
                             gcttgat  putative branch site (score: 5)
                                   ttttctatttctttta  CT-rich tract
                                  attttctatttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatggttttgacttttgacaacattgattgtatgctagggcctaggggaaataaaagaagcaatttcattactgcttgattttctatttcttttactagGTTTATAAACAATGTCCTGAGCACAGCTCAACAAGTATGGTTGCGCAAATTGGGAGGTGCAAAGCCTGTTGTGAATGAAAATGCTGGTGGGATTATTACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
-gatggtt
- - - - - - - - tgacaac
- - - - - - - - - - - - - - - gtatgct
- - - - - - - - - - - - - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgct