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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acattgtattatcttaaattttcccttggttgtgaataaacattgtttattagcttcagtaaaacttctcccttctaaaaattatcactctttctcttagGAACTGTTCGTTTCAATCTTGATCCATTTAATGAACACAATGATGCTGACCTATGGCAAGCTTTAGAAAGGGCGCATTTGAAGGATGTAATAAGAAGAAA

Basic information

species Glycine max
transcript GLYMA06G46940.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 23
acattgtattatcttaaattttcccttggttg-tgaataaacattgtttattagcttcagtaaaacttctcccttctaaaaattatcactctttctcttagGAACTGTTCGTTTCAATCTTGATCCATTTAATGAACACAATGATGCTGACCTATGGCAAGCTTTAGAAAGGGCGCATTTGAAGGATGTAATAAGAAGAAA
    | |  ||    ||| |     || | || || |    | || |||   | |||  ||  |          |  || | |||| | |    || | |||  ||||||| || ||||| ||||| |||||||| ||||||||||| ||||| ||| | ||| | |||||||| ||| | || ||||| ||||| || ||
---gtatgctagtgaaaaatacatgttagctgctggagcttctttttttggcaacttgggtttag---------tgaaatatttattaatgcc-ctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA

upper sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 25
lower sequence: AT1G30420.1 (Arabidopsis thaliana), 3'ss of exon 23
acattgtattatcttaaattttcccttggttgtgaataaacattgtttattagcttcagtaaaacttctcccttctaaaaattatcactctttctcttagGAACTGTTCGTTTCAATCTTGATCCATTTAATGAACACAATGATGCTGACCTATGGCAAGCTTTAGAAAGGGCGCATTTGAAGGATGTAATAAGAAGAAA
                           | |||||  ||      |   || |   | ||||  | | ||   |||| | ||  |    ||||  | ||||| || ||  | |||||| | |||||||||| ||||||||||||||||||||| ||| | ||| |||||||||||||| | || ||||| ||    || ||
---------------------------gtttgtgtgtagtttaagacgat-attgtaagtatga-tcctgaattctgagaaaca--gttcttcttgttagGGACGGTGAGATTCAATATCGATCCATTTAGTGAACACAATGATGCTGACCTCTGGGAGGCTCTAGAAAGGGCGCATATAAAAGATGTCATCGATAGGAA

upper sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 25
lower sequence: Vv10s0003g04470.t01 (Vitis vinifera), 3'ss of exon 24
acattgtattatcttaaatt--ttcccttggttgtgaataaa-cattgtttattagcttcagtaaaacttctcccttctaaaaattatcactctttctct-tagGAACTGTTCGTTTCAATCTTGATCCATTTAATGAACACAATGATGCTGACCTATGGCAAGCTTTAGAAAGGGCGCATTTGAAGGATGTAATAAGAAGAAA
    | |    |  || |||  |  ||  ||||     ||   ||| ||  | | |  |  |   |  |      | ||||      |   |   | | |  |||||||||  | || ||||||||||| || |||||||||||||| |||||||| ||| | |||||||| ||||| ||| | |||||||| || || |||||
----ttttcccttatacattggtgtccagggttacagctatgtcatagtacacttggatatggtgagttgtgttatactaatggcagttttttactttgtgcagGAACTGTAAGATTTAATCTTGATCCTTTCAATGAACACAATGACGCTGACCTTTGGGAGGCTTTAGAGAGGGCACATCTCAAGGATGTCATCAGGAGAAA

upper sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 25
lower sequence: Vv10s0003g04460.t01 (Vitis vinifera), 3'ss of exon 5
acattgtattatcttaaattttcccttggttgtgaataaacattgtttattagcttcagtaaaacttctcccttctaaaaattatcactctttctct-tagGAACTGTTCGTTTCAATCTTGATCCATTTAATGAACACAATGATGCTGACCTATGGCAAGCTTTAGAAAGGGCGCATTTGAAGGATGTAATAAGAAGAAA
   |     |     |||   |        |     |   ||   | | ||   ||| |  ||  | ||   |  |   |||| ||| | ||    | |||| |||||  | || ||||||||||| || ||||| ||||||||||||||||| ||| | ||| || | || || ||| | |||||  | || || |  ||
-tttcacggtgaaacaaaacatgataaaaatcattttcctcaacatatttttctttccgagaatatactgtataattctaattgtcatttttataatgtagGTACTGTGAGATTTAATCTTGATCCTTTCAATGAGCACAATGATGCTGACCTTTGGAAGGCTCTAAAGAGAGCACATCTCAAGGACTTCATTAGGATGAA

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|22524594|gb|BU083405.1|BU083405
EST:     TGTTCGAAAAGTTCTTACTATCATACCACAATCTCCAGTTCTTTTCTCTG                         GAACTGTTCGTTTCAATCTTGATCCATTTAATGAACACAATGATGCTGACC
genomic: TGTTCGAAAAGTTCTTACTATCATACCACAATCTCCAGTTCTTTTCTCTGgtattttcca ... tttctcttagGAACTGTTCGTTTCAATCTTGATCCATTTAATGAACACAATGATGCTGACC
EST: gi|22522303|gb|BU081114.1|BU081114
EST:     TGTTCGAAAAGTTCTTACTATCATACCACAATCTCCAGTTCTTTTCTCTG                         GAACTGTTCGTTTCAATCTTGATCCATTTAATGAACACAATGATGCTGACC
genomic: TGTTCGAAAAGTTCTTACTATCATACCACAATCTCCAGTTCTTTTCTCTGgtattttcca ... tttctcttagGAACTGTTCGTTTCAATCTTGATCCATTTAATGAACACAATGATGCTGACC
EST: gi|9902417|gb|BE611385.1|BE611385
EST:     GTTCGAAAAGTTCTTACTATTATACTCACAATCTCCAGTTCTTTTCTCTG                         GAACTGTTCGTTTCAATCTTGATCCATTTAATGAACACAATGATTCTGACC
genomic: GTTCGAAAAGTTCTTACTATCATAC-CACAATCTCCAGTTCTTTTCTCTGgtattttcca ... tttctcttagGAACTGTTCGTTTCAATCTTGATCCATTTAATGAACACAATGATGCTGACC
EST: gi|22524556|gb|BU083367.1|BU083367
EST:     TGTTCGAAAAGTTCTTACTATCATACCACAATCTCCAGTTCTTTTCTCTG                         GAACTGTTCGTTTCAATCTTGATCCATTTAATGAACACAATGATGCTGACC
genomic: TGTTCGAAAAGTTCTTACTATCATACCACAATCTCCAGTTCTTTTCTCTGgtattttcca ... tttctcttagGAACTGTTCGTTTCAATCTTGATCCATTTAATGAACACAATGATGCTGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattagcttcagtaaaacttctcccttctaaaaattatcactctttctcttagGAACTGTTCGTTTCAATCTTGATCCATTTAATGAACACAATGATGCTGACCTATGGCAAGCTTTAGAAAGGGCGCATTTGAAGGATGTAATAAGAAGAAA
                           ttctaaa  putative branch site (score: 2)
                                    ttatcactctttctct  putative PPT
                           ttctaaaaattatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acattgtattatcttaaattttcccttggttgtgaataaacattgtttattagcttcagtaaaacttctcccttctaaaaattatcactctttctcttagGAACTGTTCGTTTCAATCTTGATCCATTTAATGAACACAATGATGCTGACCTATGGCAAGCTTTAGAAAGGGCGCATTTGAAGGATGTAATAAGAAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - ttccctt
- - - - - - - - - - - - - -ggttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - gcttcag