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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagggcagcctagaatttcatcatgcttgcattgataacaataaaccttgaatttccatgttttgctacatcttcaaatttttttccatgacttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTTGATACATTTGTATTCTTAGACAAGAACAAGGATGGATATGTCAGCAAAA

Basic information

species Glycine max
transcript GLYMA08G33830.2
intron # 3
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G33830.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g40720.1 (Oryza sativa), 3'ss of exon 3
--cagggcagcctagaatttcatcatgcttgcattgataacaataaaccttgaatttccatgttttgctac-atcttcaaatttttttccatgacttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTTGATACATTTGTATTCTTAGACAAGAACAAGGATGGATATGTCAGCAAAA
   |||  | | ||| |  |     | | || ||     |   || | ||    |  |    || ||| |  | ||||    |||  |  |     | |  ||||       || ||  |   ||| || ||||  || |||||||| ||||||||| ||||||| || || || |||||||| |||||||||||||| ||  
gataggata-cttagtaactttctgtacctgtatc--ctattttagatctgtcttaactcatttctgccaggagcttctctgtttccttgacataatgcacagAAGATTAAGATGGGATTAGGAAATCTTGAGGCAACTTTTGAGACCTTGGTTGATGCATTTGTTTTTTTGGATAAGAACAAAGATGGATATGTCAGTAAGG

upper sequence: GLYMA08G33830.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g10470.1 (Oryza sativa), 3'ss of exon 3
cagggcagcctagaatttcatcatgct-tgcattgataacaataaaccttgaatttccatgttttgctacatcttcaa---atttttttccatgac----ttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTTGATACATTTGTATTCTTAGACAAGAACAAGGATGGATATGTCAGCAAAA
      |    | | | ||   ||  | ||||| ||    | |   | |   |||||   ||| || |   |  |  |   |||| |  || ||||    | |  |||| |  | |||| ||  |    |  || ||    || || ||||| ||||||||| |||| || ||||| ||||| ||||| ||||| ||||||||||| |
------aatggatattctctatataatctgcatcgaatttattc--cttatcatttctccgttgtgtttatttctggatacatttatacccttgacactatgctttagAGAAAAAGAATGGGACTAGGTAGTCTTGAACCAACTTTCGAGACATTGGTTGATTCATTCGTCTTCTTGGACAAAAACAAAGATGGGTATGTCAGCAAGA

upper sequence: GLYMA08G33830.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G142693_T02 (Zea mays), 3'ss of exon 3
---cagggcagcctagaatttcatcatgcttgcattgataacaataaaccttgaatttccatgttttgctacatcttcaaatttttttccatgacttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTTGATACATTTGTATTCTTAGACAAGAACAAGGATGGATATGTCAGCAAAA
    || | |   ||||  | | ||| | |    |        |  |    |    ||| ||   ||   | ||           ||  ||| | | || |||| |  | |||| ||| |    || || ||    |||||||| || ||||||||  ||||||| ||||| ||||||||||| |||||||||||||| || |
tgttagagta--ttagacatgcctcaagttgatttcctattttacgagttcttttattctatcactttggatattgcttgtgcccttgacatta-taccttagAGAAAAAGAATGGGGTTAGGGAACCTTGAACCAACATTTGAAACATTGGTTGAGTCATTTGTCTTCTTGGACAAGAACAAAGATGGATATGTCAGTAAGA

upper sequence: GLYMA08G33830.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G142693_T01 (Zea mays), 3'ss of exon 1
cagggcagcctagaatttcatcatgcttgcattgataacaataaaccttgaatttccatgttttgctacatc-ttcaaatttttttccatgacttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACT-TTGGTTGATACATTTGTATTCTTAGACAAGAACAAGGATGGATATGTCAGCAAAA
                                                    |||  |   || | |   || ||    || ||   || ||        | |      | |  |  ||   | | |  |||  | |  ||||||  ||||  || |     |   ||||      | | | | |||   |  |  |     
----------------------------------------------------tttgaaacattggttgagtcatttgtcttcttggacaagaacaaagatggatatgtcagtaagagtga-gatgatacaggcaataaatgagaccattggagGAGA-----GCGCTCTTCAGGGCGCATAGGCATGAGAAGATTTG-----

upper sequence: GLYMA08G33830.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G155822_T01 (Zea mays), 3'ss of exon 3
cagggcagcctagaat-ttcatcatgcttgcattgataacaataaaccttgaatttccatgttttgctacatcttcaaatttttttccatgac----ttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTTGATACATTTGTATTCTTAGACAAGAACAAGGATGGATATGTCAGCAAAA
      |   |||| | ||   ||||| |  | |    |   ||     ||  |||   |   || ||    ||    || | | ||| ||||    |    |||| |  | |||| ||| |    |  || ||    |||||||| || ||||| ||  | ||||| ||||| ||||||||||| ||||||||||||||||| |
----ataagttagagtatttggcatgcctcgagttgagatcctattttatgtgttttttttaatt-ctgtccctctggatgtatgtccttgacatgatattttagAGAAAAAGAATGGGGTTAGGTAGCCTTGAACCAACATTTGAAACATTGGTCGAGTCTTTTGTCTTCTTGGACAAGAACAAAGATGGATATGTCAGCAAGA

upper sequence: GLYMA08G33830.2 (Glycine max), 3'ss of exon 3
lower sequence: AT4G26470.1 (Arabidopsis thaliana), 3'ss of exon 3
-------cagggcagcct-agaatttcatcatgcttgcattgataacaataaaccttgaatttccat--gttttgctacatcttcaaatttttttccatgacttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTTGATACATTTGTATTCTTAGACAAGAACAAGGATGGATATGTCAGCAAAA
       ||    |   | |    |     ||||| |  ||||||    |     ||  ||||  ||  ||| | | |    || |||  | |||   ||   |   |||||||    ||| || ||||||||||||||    ||||| |||||  | ||||| |||||||| ||| ||||| |||||||||| |||||||| |||    
gtacccgcaaaatacttttatcgatctcctatgctcggtttgata---tttcgttttagattttgattggttattcaatggttttaaagctatttttgtgtgatgaatagAAATGGACAATGGGAATGCCAAAGCTGGAACCAACATTCGAGACGCTTGTTGACACATTTGTGTTCCTAGACGAGAACAAGGACGGATATGTTAGCCGCG

upper sequence: GLYMA08G33830.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0015g01200.t01 (Vitis vinifera), 3'ss of exon 3
cagggcagcctagaatttcatcatgcttgcattgataacaataaaccttgaatttccatgttttgctacatcttcaaattttttt-----ccatgacttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTTGATACATTTGTATTCTTAGACAAGAACAAGGATGGATATGTCAGCAAAA
   | |||  |  | |||| || | || |||     | | | | |   ||   ||   |  ||   |    | | | ||||||||     |||||||    |||||||||||| || ||||||||||| |||||||  || ||||| ||  |||||||| ||||||| ||| | |||||||| |||||||| ||||| ||||| |
---gccagttttcattttcctc-tcctggcacccccaccca-acattatgtgcttatgtagttctttcttcccttacatttttttgtattccatgacactgctagAAATCACGGATGGGGATGCCAAATCTGGAGGCAACCTTTGAAACACTGGTTGATGCATTTGTGTTCCTGGACAAGAATAAGGATGGTTATGTGAGCAAGA

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|151409948|gb|EV279756.1|EV279756
EST:     TCTTTTGTGTTGTCTACCTTCTCAAGAATGACCCTGCAGCTCTTCATGCT                         AAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTT
genomic: TCTTT-GTGTTGTCTACCTTCTCAAGAATGACCCTGCAGCTCTTCATGCTgtatcctagc ... acttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTT
EST: gi|254316174|gb|GR827711.1|GR827711
EST:     TTCTTTGTGTTGTCTACCTTCTCAAGAATGACCCTGCAGCTCTTCATGCT                         AAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTT
genomic: TTCTTTGTGTTGTCTACCTTCTCAAGAATGACCCTGCAGCTCTTCATGCTgtatcctagc ... acttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTT
EST: gi|193478531|gb|FK447558.1|FK447558
EST:     TTCTTTGTGTTGTCTACCTTCTCAAGAATGACCCTGCAGCTCTTCATGCT                         AAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTT
genomic: TTCTTTGTGTTGTCTACCTTCTCAAGAATGACCCTGCAGCTCTTCATGCTgtatcctagc ... acttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTT
EST: gi|298170086|gb|HO018710.1|HO018710
EST:     TTCTTTGTGTTGTCTACCTTCTCAAGAATGACCCTGCAGCTCTTCATGCT                         AAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTT
genomic: TTCTTTGTGTTGTCTACCTTCTCAAGAATGACCCTGCAGCTCTTCATGCTgtatcctagc ... acttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTT
EST: gi|298194650|gb|HO043122.1|HO043122
EST:     TTCTTTGTGTTGTCTACCTTCTCAAGAATGACCCTGCAGCTCTTCATGCT                         AAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTT
genomic: TTCTTTGTGTTGTCTACCTTCTCAAGAATGACCCTGCAGCTCTTCATGCTgtatcctagc ... acttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTT
EST: gi|192305727|gb|FG995697.1|FG995697
EST:     TTCTTTGTGTTGTCTACCTTCTCAAGAATGACCCTGCAGCTCTTCATGCT                         AAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTT
genomic: TTCTTTGTGTTGTCTACCTTCTCAAGAATGACCCTGCAGCTCTTCATGCTgtatcctagc ... acttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTT
EST: gi|13481965|gb|BG511308.1|BG511308
EST:     TTCTTTGTGTTGTCTACCTTCTCAAGAATGACCCTGCAGCTCTTCATGCT                         AAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTT
genomic: TTCTTTGTGTTGTCTACCTTCTCAAGAATGACCCTGCAGCTCTTCATGCTgtatcctagc ... acttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTT
EST: gi|22523171|gb|BU081982.1|BU081982
EST:     TTCTTTGTGTTGTCTACCTTCTCAAGAATGACCCTGCAGCTCTTCATGCT                         AGATCACGAATTGTGATGCCA
genomic: TTCTTTGTGTTGTCTACCTTCTCAAGAATGACCCTGCAGCTCTTCATGCTgtatcctagc ... acttccctagAAATCACGAATTGGGATGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgaatttccatgttttgctacatcttcaaatttttttccatgacttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTTGATACATTTGTATTCTTAGACAAGAACAAGGATGGATATGTCAGCAAAA
                                      ttccatgac  putative branch site 
                                              cttccct  CT-rich tract
                        atcttcaaattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagggcagcctagaatttcatcatgcttgcattgataacaataaaccttgaatttccatgttttgctacatcttcaaatttttttccatgacttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTTGATACATTTGTATTCTTAGACAAGAACAAGGATGGATATGTCAGCAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - tcatgct
- - - - - - - - - - - - - -tgcattg
- - - - - - - - - - - - - - - - - - - - - - -ccttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctaca