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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaaacatatttaagtcactcccctaattattattactattattgtgtctcatcagatttcactggttcttctaagttgcaacttatgattgagttgcagGTTGATATTGCTATTCCCGAAGTTTTCGTTGGTGGGCTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTGCTGCTGTTGGCAGAACTG

Basic information

species Glycine max
transcript GLYMA07G00350.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 11
ctaaacatatttaagtcactcccctaattattattactattattgtgtctcatcagattt-cactggttcttctaagttgcaacttatgattgagttgcagGTTGATATTGCTATTCCCGAAGTTTTCGTTGGTGGGCTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTGCTGCTGTTGGCAGAACTG
       ||||| | | |||     |   |  ||   || | |     || || | || |  | ||||  |       || ||        ||  ||||||||||| || || || || || ||||| ||||||||  | || ||||| |||||||||||  | |||||||| ||||| ||| ||||||||||||||||||
------gtatttta-ttacttagacacgcaaaatacttactttctgtgcttataacatatataatggtcttg------tgtaa--------tggattgcagGTTGACATAGCAATCCCAGAGGTTTTTGTTGGTGGTTTACTTGGTTCAATGCTTATATTCCTGTTTAGTGCATGGGCTTGTTCTGCTGTTGGCAGAACTG

upper sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 11
ctaaacatatttaagtcactcccctaattattattac-tattattg-tgtctcatcagatttcactggttcttctaagttgcaacttatgattgagttgcagGTTGATATTGCTATTCCCGAAGTTTTCGTTGGTGGGCTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTGCTGCTGTTGGCAGAACTG
                        ||  | |  |||   ||  ||| ||| |  || ||| |        ||||| |    || | |  |||  | |  ||||||||||||||||| || ||||| |||||||||||  |  | ||| |||||||||| ||  | |||||||||||||| || || || |||||  ||||||
-----------------------gtagatttcgttatgcatcgttgctgtattctc-gatgttgagacaacttctcatactcatcctcggataaaat--cagGTTGATATTGCTATCCCAGAAGTGTTCGTTGGTGGATTATTGGGTGCCATGCTTATTTTCCTCTTTAGTGCTTGGGCATGCGCGGCAGTTGGTCGAACTG

upper sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 12
ctaaacatatttaagtcactcccctaattattattactattattgtgtctcatcagatttcactggttcttctaagttgcaacttatgattgagttgcagGTTGATATTGCTATTCCCGAAGTTTTCGTTGGTGGGCTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTGCTGCTGTTGGCAGAACTG
    |||| ||| | ||  |    || || |  || || |||||   |  ||   |  | |     |  | || | |     | |   ||  |    |||||||||||||| || || ||||| ||| |||| ||| |  ||||| |||||||||||||  | ||||| |||||||| ||||| || |||||  ||||||
--gtacattttttactctttggtgta-ttctgtttcctcttattccattccactcgcatac-----tcatcctgattcttgtcctcacatctaa--acagGTTGATATTGCGATCCCAGAAGTCTTCATTGGAGGGTTATTAGGTGCCATGCTTATATTCCTGTTTAGCGCTTGGGCTTGTGCAGCAGTTGGTCGAACTG

upper sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 11
ctaaacatatttaagtcactcccctaattattattactattattgtgtctcatcagatttcactggttcttctaagttgcaacttatgattgagttgcagGTTGATATTGCTATTCCCGAAGTTTTCGTTGGTGGGCTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTGCTGCTGTTGGCAGAACTG
       ||  |    |||| |  | ||  |  | |   |  ||   |    |   |  |||||| || || || |||          ||    || |||||||||||||| ||||| |||||||| ||||||||| || | || || |||||||| ||  | |||||||| ||||| ||| |||| |||||| | ||||
------gtaagtgga-cactactttgatc-tcttcatcgtgtttacattctct---aactcactgcttttt-tatgtt---------aatcaccttacagGTTGATATTGCCATTCCAGAAGTTTTTGTTGGTGGGTTGTTGGGCTCTATGCTTATTTTCCTATTTAGTGCATGGGCATGTTCTGCAGTTGGCCGGACTG

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|15286246|gb|BI470137.1|BI470137
EST:     GTGCTTATATGGACGAGGTTTCTGCATTTGCTCATGAACCTTTTAAACAG                         GTTGATATTGCTATTCCCGAAGTTTTCGTTGGTGGGCTGCTAGGTTCCATG
genomic: GTGCTTATATGGACGAGGTTTCTGCATTTGCTCATGAACCTTTTAAACAGgtgcgcagaa ... tgagttgcagGTTGATATTGCTATTCCCGAAGTTTTCGTTGGTGGGCTGCTAGGTTCCATG
EST: gi|58016814|gb|CX703556.1|CX703556
EST:     GTGCTTATATGGACGAGGTTTCTGCATTTGCTCATGAACCTTTTAAACAG                         GTTGATATTGCTATTCCCGAAGTTTTCGTTGGTGGGCTGCTAGGTTCCATG
genomic: GTGCTTATATGGACGAGGTTTCTGCATTTGCTCATGAACCTTTTAAACAGgtgcgcagaa ... tgagttgcagGTTGATATTGCTATTCCCGAAGTTTTCGTTGGTGGGCTGCTAGGTTCCATG
EST: gi|192305808|gb|FG995736.1|FG995736
EST:     GTGCTTATATGGACGAGGTTTCTGCATTTGCTCATGAACCTTTTAAACAG                         GTTGATATTGCTATTCCCGAAGTTTTCGTTGGTGGGCTGCTAGGTTCCATG
genomic: GTGCTTATATGGACGAGGTTTCTGCATTTGCTCATGAACCTTTTAAACAGgtgcgcagaa ... tgagttgcagGTTGATATTGCTATTCCCGAAGTTTTCGTTGGTGGGCTGCTAGGTTCCATG
EST: gi|58015021|gb|CX701763.1|CX701763
EST:     GTGCTTATATGGACGAGGTTTCTGCATTTGCTCATGAACCTTTTAAACAG                         GTTGATATTGCTATTCCCGAAGTTTTCGTTGGTGGGCTGCTAGGTTCCATG
genomic: GTGCTTATATGGACGAGGTTTCTGCATTTGCTCATGAACCTTTTAAACAGgtgcgcagaa ... tgagttgcagGTTGATATTGCTATTCCCGAAGTTTTCGTTGGTGGGCTGCTAGGTTCCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctcatcagatttcactggttcttctaagttgcaacttatgattgagttgcagGTTGATATTGCTATTCCCGAAGTTTTCGTTGGTGGGCTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTGCTGCTGTTGGCAGAACTG
                                      ttatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaaacatatttaagtcactcccctaattattattactattattgtgtctcatcagatttcactggttcttctaagttgcaacttatgattgagttgcagGTTGATATTGCTATTCCCGAAGTTTTCGTTGGTGGGCTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTGCTGCTGTTGGCAGAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
ctaaaca
- - - - - - - - - ctcccct
- - - - - - - - - - - - - - - - - - - - - - gtgtctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaact