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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaatcttctaatgctgttgaaagttgctagatagacagtttagtggaaaaattatgggtgagagtagttgaaggatgacaactcatattcttttgtagGTGGAGGGTATGTTATATCACCAGTGAACAAAGGAAAGCAATCAGTTGTAAAGCATATGCTTGCTATTGATTGGAAATGCTGGAGATTATATCTTAAATC

Basic information

species Glycine max
transcript GLYMA13G40010.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G40010.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G069976_T01 (Zea mays), 3'ss of exon 12
---attaatcttctaatgctgttgaaagttgctagatagacagtttagtggaaaaattatgggtgagagtagttgaaggatgacaactcatattcttttgtagGTGGAGGGTATGTTATATCACCAGTGAACAAAGGAAAGCAATCAGTTGTAAAGCATATGCTTGCTATTGATTGGAAATGCTGGAGATTATATCTTAAATC
   ||  ||  | || |     | |||  | ||      ||   |||     |  ||| ||  |     |   |||    || |   |   ||  ||    ||||||||| ||||| ||||||||||| ||  ||||||  ||||||||||||||||| |||||||| || |||||||||| |||||  |  |||||     |
gtaatgtatgctttactttcagtcaaatct-ctgtgggaac---ttaactatagtatt-tgcttacacttcactgatatgtgcctttttgaatattt----agGTGGAGGTTATGTAATATCACCAGTCAATCAAGGAAGACAATCAGTTGTAAAGCACATGCTTGCCATAGATTGGAAATTCTGGAAGTCTTATCTGTTTAC

upper sequence: GLYMA13G40010.1 (Glycine max), 3'ss of exon 11
lower sequence: AT2G28320.1 (Arabidopsis thaliana), 3'ss of exon 11
attaatcttctaatgctgttgaaagttgctag-atagacagtttagtggaaaaattatgggtgagagtagt-tgaaggatgacaactcatattcttttgtagGTGGAGGGTATGTTATATCACCAGTGAACAAAGGAAAGCAATCAGTTGTAAAGCATATGCTTGCTATTGATTGGAAATGCTGGAGATTATATCTTAAATC
|  ||| |    || |||| ||     || |  | | |  | | | |     || ||| | |       || | |   |||    ||| |||  | |   |||||| || ||||| || || ||  |  |||| ||||| ||||||||||| ||||| ||||||||| |||||||||| | ||||||||  ||| | ||  |
aagaatatatatat-ctgtggatgtaggccaatacatattgatcactaatgcaactattgatctcttctgtgtaactaatgttttctcctatg-tatcacagGTGGCGGTTATGTGATTTCTCCCATAGACAACGGAAAACAATCAGTTGTGAAGCACATGCTTGCTGTTGATTGGAAGTCCTGGAGATCTTATGTGAAGCC

upper sequence: GLYMA13G40010.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv06s0004g02720.t01 (Vitis vinifera), 3'ss of exon 11
attaatcttctaatgctgttgaaagttgctagatagacagt--ttagtggaaaaatt--atgggt--gagagtagt---tgaaggatgacaactcatattcttttgtagGTGGAGGGTATGTTATATCACCAGTGAACAAAGGAAAGCAATCAGTTGTAAAGCATATGCTTGCTATTGATTGGAAATGCTGGAGATTATATCTTAAATC
        | |    | |   |    || |  |||  || |  ||| ||||  ||||  |||| |  || |||| |   |  || ||||||  |   | ||||||| ||||||||| |||||  |||| || || ||| | || || |||||||||||||| || |||||||||||||| ||||||| ||||||||  |||||  || |
--------tttttctcagcaaaggactg-tgaatacccaatatttactggaggaatttcatggtttagaaagtaatgcattgagtatgacattttgcactcttttgcagGTGGAGGATATGTGGTATCTCCTGTAAACCAGGGGAAACAATCAGTTGTAAAACACATGCTTGCTATTGACTGGAAATTCTGGAGATCTTATCTACAAAC

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|208271826|gb|GE068706.1|GE068706
EST:     TCACAAGAAGTGCCCTCCCCAGAAAGGCTATGTGCGTGCTTGTCTTAAAA                         GTGGAGGGTATGTTATATCACCAGTGAACAAAGGAAAGCAATCAGTTGTAA
genomic: TCACAAGAAGTGCCCTCCCCAGAAAGGCTATGTGCGTGCTTGCCTTAAAAgtaatgtatg ... tcttttgtagGTGGAGGGTATGTTATATCACCAGTGAACAAAGGAAAGCAATCAGTTGTAA
EST: gi|19452839|gb|BM954249.1|BM954249
EST:     CGTGCTTGCCTTAAAA                         GTGGAGGGTATGTTATATCACCAGTGAACAAAGGAAAGCAATCAGTTGTAA
genomic: CGTGCTTGCCTTAAAAgtaatgtatg ... tcttttgtagGTGGAGGGTATGTTATATCACCAGTGAACAAAGGAAAGCAATCAGTTGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaaaaattatgggtgagagtagttgaaggatgacaactcatattcttttgtagGTGGAGGGTATGTTATATCACCAGTGAACAAAGGAAAGCAATCAGTTGTAAAGCATATGCTTGCTATTGATTGGAAATGCTGGAGATTATATCTTAAATC
                                          tattctttt  CT-rich tract
                                         atattctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaatcttctaatgctgttgaaagttgctagatagacagtttagtggaaaaattatgggtgagagtagttgaaggatgacaactcatattcttttgtagGTGGAGGGTATGTTATATCACCAGTGAACAAAGGAAAGCAATCAGTTGTAAAGCATATGCTTGCTATTGATTGGAAATGCTGGAGATTATATCTTAAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - -tgctgtt
- - - - - - - - - - - - gttgcta
- - - - - - - - - - - - - - - - - - - - - - - -gaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caactca