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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTTTGAAGACTgtatccttccaaaaatgcaaattctaatgtttggttttcaaattttctatttgttaacgtctatgtacatgattaaatcatgaaatgcgttggtccttttcagtgcagcatgtgaaatgaatgttattgttgttttccttcataaaggatttag

Basic information

species Glycine max
transcript GLYMA03G33000.4
intron # 9
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33000.6 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os05g02310.1 (Oryza sativa), 5'ss of exon 7
ATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTTTGAAGACTgtatccttccaaaaatgcaaattctaatgtttggttttcaaatt---ttctatttgttaacgtctatgtacatgattaaatcatgaaatgcgttggtccttttcagtgcagcatgtgaaatgaatgttattgttgttttccttcataaaggatttag
||||| || |||||||||||||| |||||    ||||||||||||||||||||||| || || || || || ||||||||  | || |||||||| ||||||||||||    |    |  | | | | |||  |  ||| || |   |||||     ||||   | |    |   | || ||    |||  |||| |||                                                          
ATTGCCGTTTGTGCTGATGATCCTGAGTACAAGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatccttttttatcaacttaatatcaagttctgcattctaaatgaattctaggcaataactcatgtcctaaccttgaactccaccaatatgttgttccc---------------------------------------------------------

upper sequence: GLYMA03G33000.6 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os01g74350.1 (Oryza sativa), 5'ss of exon 8
ATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTTTGAAGACTgtatccttccaaaaatgcaaattctaatgtttggttttcaaattttctatttgttaacgtctatgtacatgattaaatcatgaaatgcgt-tggtccttttcagtgcagcatgtgaaatgaatgttattgttgttttccttcataaaggatttag
||||| ||||||||||||||||| |||||    |||||||| ||||||||||| || || || || || |||||||||||  | ||||| || || ||||||||||||                |||| | | | | | ||    | || |||||     |||| | |||   || | ||| ||||     |||  || | |  || | || |   |   |   |                              
ATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACTgtatccttt---------------taatttattgctcttaa----tgtacttgtt-----ctatttgcattcatagagcataaaatattcatggaactctac--tgaaacaagctcagctagcttc-----------------------------

upper sequence: GLYMA03G33000.6 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G137930_T02 (Zea mays), 5'ss of exon 7
ATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTTTGAAGACTgtatccttccaaaaatgcaaattctaatgtttggttttcaaattttctatttgttaacgtctatgtacatgattaaatcatgaaatgcgttggtccttttcagtgcagcatgtgaaatgaatgttattgttgttttccttcataaaggatttag
||||| || || |||||||||||||||||  | ||||||||||||||||||||||| || || || || || ||||||||  | || || || || ||||||||||||   |  || ||      | | ||| ||  |     |  | |      |  ||||| ||||   || || | ||    ||  ||| || |  | | |      | | |                                       
ATTGCAGTGTGCGCTGATGATCCCGAGTACAGGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTCTTCGAGGACTgtatcctttttatgattca----tcagtatttcgtcct---gctaacca------agagtcta-gtactacataaagtgattgc-tgttttgatcatgcttaataagttctttta---------------------------------------

upper sequence: GLYMA03G33000.6 (Glycine max), 5'ss of exon 9
lower sequence: AT3G53620.1 (Arabidopsis thaliana), 5'ss of exon 7
ATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTTTGAAGACTgt-atccttccaaaaatgcaaattctaatgtttggttttcaaattttctatttgttaacgtctatgtacatgattaaatcatgaaatgcgttggtccttttcagtgcagcatgtgaaatgaatgttattgttgttttccttcataaaggatttag
||||||||||| ||||| ||||| |||||||| |||||||| || ||||  |||||||| || |||||| | ||||| || || ||||| |||||||||||| |   |||      | |||| | |  || ||||||    |   |   |       ||   | |   | || |  |                                                                              
ATTGCTGTCTGCGCTGACGATCCAGAGTATCGCCATTACAACGACATCAGTGAGCTTCCGCCTCATCGTATGGCTGAGATCCGCCGTTTCTTTGAAGACTgtgagtgttcttttcttacaaacttt--tggttggttaaggatgatatgaggctcatactcttgtaatcttgttgcag-----------------------------------------------------------------------------

upper sequence: GLYMA03G33000.6 (Glycine max), 5'ss of exon 9
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 5'ss of exon 7
ATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTTTGAAGACTgtatccttccaaaaatgc--aaattctaatgtttggttttcaaattttctatttgttaacgtctatgtacatgattaaatcatgaaatgcgttggtccttttcagtgcagcatgtgaaatgaatgttattgttgttttccttcataaaggatttag
||||| || |||||||||||||| ||||| ||||| |||| ||||||||| ||||| ||||| || ||||| ||||| || || ||||| |||||||| |||||||||| |||||| |  ||    ||        |  |  ||    | |||  | ||      ||| | | |   | |  |  | |   ||  |  | |  | |  || |  |   ||  |  | ||  || |||||||| |||||  | | ||
ATTGCAGTTTGTGCTGATGATCCTGAGTACCGACACTACACTGATATCAATGAGCTCCCTCCGCACCGTTTGGCTGAGATCCGCCGTTTCTTTGAAGATTgtatccttctaaaaattcttaatccttagcaaacactagtttaaaa--cgattcttcaagcatactgtccttaaaatacttgtttatttt-tttataatctcaaatctagaaaattggatctaaatcatcctttttttccttaataaaccaatcag

upper sequence: GLYMA03G33000.6 (Glycine max), 5'ss of exon 9
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 5'ss of exon 8
ATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTTTGAAGACTgtatccttccaaaaatgcaaattctaatgtttggttttcaaattttctatttgttaacgtctatgtacatgattaaatcatgaaatgcgttggtccttttcagtgcagcatgtgaaatgaatgttattgttgttttccttcataaaggatttag
|| |||||||||||||| ||||| |||||| |||| | ||| || ||||| ||| |||||||||||||  | || ||||||||||| ||||| ||||| ||||       || ||    | ||| |||  || ||    ||  ||  |   |  ||  |  ||  |  |   ||  ||       ||| || ||  |||  | ||    |  |  ||| | |  | |||     |||                 
ATCGCTGTCTGTGCTGACGATCCGGAGTATAGACACTTCAAAGACATCAATGAGTTTCCTCCACATCGACTTGCCGAAATTCGTCGGTTTTTCGAAGATTgtaagtcctgaataa----atttcaaatacttcgt----aagcttcattgataatagaggttacatgaaatcttgtatttct---tgcatttgtggtttcaaatg----acttacaatcattact-ttgagccgttcag---------------

upper sequence: GLYMA03G33000.6 (Glycine max), 5'ss of exon 9
lower sequence: PP1S142_132V6.1 (Physcomitrella patens), 5'ss of exon 4
ATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTTTGAAGACTgta---tccttccaaaaatgcaaat-tctaatgtttggttttcaaattttctatttgttaacgtctatgtacatgattaaatcatgaaatgcgttggtccttttcagtgcagcatgtgaaatgaatgttattgttgtt--ttccttcataaagg-atttag-------------------------------
|| |||||||||||||| |||||||||||  | || | ||| || |||||||| || ||||| || ||||| ||||| || ||||| |||||||| |||||||      || ||    | || |  |||   |      |||    ||||    | |||    |   | |   || ||   |       || ||  |    | ||| | || |||| ||  | ||||   ||||| |   |   || |||  |  ||| |                                
ATCGCTGTCTGTGCTGACGATCCCGAGTACAGGCACTTCAAGGACATCAAGGAACTCCCTCCCCACCGTTTGGCTGAGATCCGTCGGTTTTTTGAGGACTgtaagtcattttcatgcgttcatacctctggcgcactaatttattttttttcggtagttttttttgttttttttgttttttttcctccctgtgtatgctgctgtca-tacatcatg-gattttaatgggtttgttttaggtctattaatatggacattcacttcactgactagcacgcaaccattgttacag

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|192298048|gb|FG991328.1|FG991328
EST:     GGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGNNNNNNNGAAGACT                         ACAAGAAGAATGAAAACAAGGAAGTCGCAGTAAACGACTTTTTGCCTGCCT
genomic: GGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTTTGAAGACTgtatccttcc ... aaggatttagACAAGAAGAATGAAAACAAGGAAGTCGCAGTAAACGACTTTTTGCCTGCCT
EST: gi|10236851|gb|BE805739.1|BE805739
EST:     GGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTGTTTTGAAGACT                         ACAAGAAGAATGAAAACAAGGAAGTCGCAGTAAACGACTTGTTGCCTGCCT
genomic: GGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTTTGAAGACTgtatccttcc ... aaggatttagACAAGAAGAATGAAAACAAGGAAGTCGCAGTAAACGACTTTTTGCCTGCCT
EST: gi|192296495|gb|FG989111.1|FG989111
EST:     GGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTCTTGAAGACT                         ACAAGAAGAATGAAAACAAGGAAGTCGCAGTAAACGACTTTTTGCCTGCCT
genomic: GGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTTTGAAGACTgtatccttcc ... aaggatttagACAAGAAGAATGAAAACAAGGAAGTCGCAGTAAACGACTTTTTGCCTGCCT
EST: gi|16105384|gb|BI893124.1|BI893124
EST:     GGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGNNNNNNNGAAGACT                         ACNAGAAGAATGAAAACAAGGAAGTCGCAGTAAACGACTTTTTGCCTGCC
genomic: GGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTTTGAAGACTgtatccttcc ... aaggatttagACAAGAAGAATGAAAACAAGGAAGTCGCAGTAAACGACTTTTTGCCTGCC
EST: gi|8827754|gb|BE211484.1|BE211484
EST:     GGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGGTTTTTTGAAGACT                         ACAAGAAGAATGAAAACCAGGAAAGTCG-AGTAAACGACTTTATGCCTGCC
genomic: GGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTTTGAAGACTgtatccttcc ... aaggatttagACAAGAAGAATGAAAACAAGGAA-GTCGCAGTAAACGACTTTTTGCCTGCC
EST: gi|192324459|gb|FK015810.1|FK015810
EST:     GGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTT-GAAGACT                         ACAAGAAGAATGAAAACAAAGAAGTCGCAGTAAACGACTTTTTGCCTGCCT
genomic: GGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTTTGAAGACTgtatccttcc ... aaggatttagACAAGAAGAATGAAAACAAGGAAGTCGCAGTAAACGACTTTTTGCCTGCCT
EST: gi|151404690|gb|EV274504.1|EV274504
EST:     GGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGNNNNNNNGAAGACT                         ACAAGAAGAATGAAAACAAAGAAGTCGCAGTAAACGACTTTTTGCCTGCCT
genomic: GGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTTTGAAGACTgtatccttcc ... aaggatttagACAAGAAGAATGAAAACAAGGAAGTCGCAGTAAACGACTTTTTGCCTGCCT
EST: gi|17022987|gb|BM094021.1|BM094021
EST:     GGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGNNNNNNNGAAGACT                         ACAAGAAGAATGAAAACAAGGAAGTCGCAGTAAACGACTTTTTGCCTGCCT
genomic: GGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTTTGAAGACTgtatccttcc ... aaggatttagACAAGAAGAATGAAAACAAGGAAGTCGCAGTAAACGACTTTTTGCCTGCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTTTGAAGACTgtatccttccaaaaatgcaaattctaatgtttggttttcaaattttctatttgttaacgtctatgtacatgattaaatcatgaaatgcgttggtccttttcagtgcagcatgtgaaatgaatgttattgttgttttccttcataaaggatttag

- - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA