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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATAAGCACTGTCGCGGACAAGGGTTTAAAAAAGCCACTCTACACATCTGCTCGTTTGAAGAAGGGAGAAGTTTTGTATTTGGAGACACATTTGTCCAGgtattttttatatgaaagttcttgttctaaatcagtgtctgtatttcaactgtcactccattaattgttaaatgtcacatgcaagtgcaacaggaatgtg...

Basic information

species Glycine max
transcript GLYMA10G31960.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G31960.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G464000_T02 (Zea mays), 5'ss of exon 9
GTATAAGCACTGTCGCGGACAAGGGTTTAAAAAAGCCACTCTACACATCTGCTCGTTTGAAGAAGGGAGAAGTTTTGTATTTGGAGACACATTTGTCCAGgtatt----ttttatatgaaagttcttgttctaaatcagtgtctgtatttcaa--ctgtcactccat-----taattgttaaatgtcacatgcaagtgcaacaggaatgtg-----
||||||||| ||| || |||||||| || |||||| |||| || || |||||| |  ||||||| ||||||||  | |||||||||||||||||    ||||||     |||  ||  |    | | ||||| |     |||   |  ||| |   |||   | |||     | | || | | |||  | | ||| |     |  | | |      
GTATAAGCATTGTGGCAGACAAGGGATTGAAAAAGTCACTTTATACTTCTGCTAGACTGAAGAAAGGAGAAGTAATATATTTGGAGACACATTTTAATAGgtatggacgtttgctactacttctttagttctgatgatatgttcttgcttccagtttgtgcttgcatggaactcactgctcactgtt-ctttcaattttgttacaagtctccacag

upper sequence: GLYMA10G31960.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G464000_T04 (Zea mays), 5'ss of exon 9
GTATAAGCACTGTCGCGGACAAGGGTTTAAAAAAGCCACTCTACACATCTGCTCGTTTGAAGAAGGGAGAAGTTTTGTATTTGGAGACACATTTGTCCAGgtatt----ttttatatgaaagttcttgttctaaatcagtgtctgtatttcaa--ctgtcactccat-----taattgttaaatgtcacatgcaagtgcaacaggaatgtg
||||||||| ||| || |||||||| || |||||| |||| || || |||||| |  ||||||| ||||||||  | |||||||||||||||||    ||||||     |||  ||  |    | | ||||| |     |||   |  ||| |   |||   | |||     | | || | | |||  | | ||| |     |  |     
GTATAAGCATTGTGGCAGACAAGGGATTGAAAAAGTCACTTTATACTTCTGCTAGACTGAAGAAAGGAGAAGTAATATATTTGGAGACACATTTTAATAGgtatggacgtttgctactacttctttagttctgatgatatgttcttgcttccagtttgtgcttgcatggaactcactgctcactgtt-ctttcaattttgttacaag----

upper sequence: GLYMA10G31960.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv07s0130g00270.t01 (Vitis vinifera), 5'ss of exon 9
GTATAAGCACTGTCGCGGACAAGGGTTTAAAAAAGCCACTCTACACATCTGCTCGTTTGAAGAAGGGAGAAGTTTTGTATTTGGAGACACATTTGTCCAGgtattttttatatgaaagttcttgttctaaatcagtgtctgtatttcaactgtcactccattaattgttaaatgtcacatgcaagtgcaacaggaatgtg--
| ||||||| ||| || ||||| ||  |||| ||||| || || |||||||| || |||||||||||||||||||||||||| || |||||||    ||||||||   | |||  |  ||   ||   |     ||| || |  ||    |  |       ||| |    | | |  |||| ||    | ||    | |   
GCATAAGCATTGTTGCTGACAAAGGCCTAAAGAAGCCCCTTTATACATCTGCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAGgtattcactttattgacattga-gtgagattctggtggctcttcttttg-taccttagatctaagttcccatttttccatggaatgagatcatatttctttt

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|51343542|gb|CO984275.1|CO984275
EST:     GCTCGTTTGAAGAAGGGAGAAGTTTTGTATTTGGAGACACATTTGTCCAG                         ATATGAACTTTGTTTTACTGGAGAGAAGATGGTCAAGGTTACACCAGCAAC
genomic: GCTCGTTTGAAGAAGGGAGAAGTTTTGTATTTGGAGACACATTTGTCCAGgtatttttta ... ttctgtgtagATATGAACTTTGTTTTACTGGAGAGAAGATGGTCAAGGTTACACCAGCAAC
EST: gi|254344049|gb|GR850959.1|GR850959
EST:     GCTCGTTTGAAGAAGGGAGAAGTTTTGTATTTGGAGACACATTTGTCCAG                         ATATGAACTTTGTTTTACTGGAGAGAAGATGGTCAAGGTTACACCAGCAAC
genomic: GCTCGTTTGAAGAAGGGAGAAGTTTTGTATTTGGAGACACATTTGTCCAGgtatttttta ... ttctgtgtagATATGAACTTTGTTTTACTGGAGAGAAGATGGTCAAGGTTACACCAGCAAC
EST: gi|17963267|gb|BM270018.1|BM270018
EST:     GCTCGTTTGAAGAAGGGAGAAGTTTTGTATTTGGAGACACATTTGTCCAG                         ATATGAACTTTGTTTTACTGGAGAGAAGATGGTCAAGGTTACACCAGCAAC
genomic: GCTCGTTTGAAGAAGGGAGAAGTTTTGTATTTGGAGACACATTTGTCCAGgtatttttta ... ttctgtgtagATATGAACTTTGTTTTACTGGAGAGAAGATGGTCAAGGTTACACCAGCAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATAAGCACTGTCGCGGACAAGGGTTTAAAAAAGCCACTCTACACATCTGCTCGTTTGAAGAAGGGAGAAGTTTTGTATTTGGAGACACATTTGTCCAGgtattttttatatgaaagttcttgttctaaatcagtgtctgtatttcaactgtcactccattaattgttaaatgtcacatgcaagtgcaacaggaatgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA