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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATTACAGCGGTCTGTTCAGACGACCCCGTGGGATGTATTTCAGTGCAAAGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctgaaagtgctgtctaaatgcacgttttcaagtaatgcctctagtgtagcgattaagattgagattatttgagtgtgggttcaactaatgagat...

Basic information

species Zea mays
transcript GRMZM2G085747_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085747_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os10g35960.2 (Oryza sativa), 5'ss of exon 4
AAATTACAGCGGTCTGTTCAGACGACCCCGTGGGATGTATTTCAGTGCAAAGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctgaa------agtgctgtctaaatgcacgttttcaag----taatgcctctagtgtagcgattaagattgagattatttgagtgtgggttcaactaatgagat
 |||||||| ||  ||||||| || |||||||||||||||||||| || ||||||||||||||||||||||| |||||||||||||||||||| ||||||||| | ||||       | || | |  ||   ||  || |   |      |||    || |         ||||  ||||||  |  ||   |   |  |          
GAATTACAGTGGCTTGTTCAGGCGCCCCCGTGGGATGTATTTCAGCGCCAAGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAGgtacacctgagtacttgactgttatagaataacaatttatttggacaccgatgttcttactagtatatcaaagaaagagattggtcaagatcgaaattca----------

upper sequence: GRMZM2G085747_T04 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA07G08110.1 (Glycine max), 5'ss of exon 4
AAATTACAGCGGTCTGTTCAGACGACCCCGTGGGATGTATTTCAGTGCAAAGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctgaaagtgctgtctaaatgcacgttttcaagtaatgcctctagtgtagcgattaagattgagattatttgagtgtgggttcaactaatgagat----
||||||    ||  | || || || || ||||| |||||||| ||||| || ||||| || ||||||||||||||||| || |||||||||||  |  |||||| ||   |   | | |  |||| ||   |         |   |  | | | |  |||   | |     | ||| | | |    ||  ||  | |       
AAATTATTCAGGGTTATTTAGGCGTCCACGTGGAATGTATTTTAGTGCCAAAGATAAAGGAGAGATGATGTCAATGATCTATAACTGGCCAGCTCACGAGgtattgc---attagttttggaaattcagtctcattttctttctgttcattattgaaattggaaatattcatttttca-tatattctccccttctaattcttac

upper sequence: GRMZM2G085747_T04 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA03G01680.1 (Glycine max), 5'ss of exon 5
AAATTACAGCGGTCTGTTCAGACGACCCCGTGGGATGTATTTCAGTGCAAAGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctgaaagtgctgtctaaatgcacgttttcaagtaatgcctctagtgtagcgattaagattgagattatttgagtgtgggttcaactaatgagat---
||||||   |||  | || || || || ||||| |||||||| ||||| || ||||| || ||||||||||||||||| || |||||||||||  |  |||||| ||   |   | | |  |||| ||   |         |   |  | | | |  |||   | |     | |||   | |    |   ||  | |      
AAATTATTCCGGGTTATTTAGGCGTCCACGTGGAATGTATTTTAGTGCCAAAGATAAAGGAGAGATGATGTCAATGATCTATAACTGGCCAGCTCATGAGgtattgc---attagttttagaaattcagtatcatcttctttttgttcattattgaaattggaaatagtcattttttcatatattcttcccttctaattctta

upper sequence: GRMZM2G085747_T04 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA09G39870.1 (Glycine max), 5'ss of exon 4
AAATTACAGCGGTCTGTTCAGACGACCCCGTGGGATGTATTTCAGTGCAAAGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctgaaagtgctgtctaaatgc-acgttttcaagtaatgcctctagtgtagcgattaagattgagattatttgagtgtgggttcaactaatgagat--
||||||    ||  | || ||||| || ||||| |||||||| ||||| || ||||| || ||||||||||||||||| || ||||||||| | ||  |||||| |    || |  ||   || |||  | ||         | | |  |   |||  | |  ||  |  | | |||   | |   ||   ||  | | ||  
AAATTATTCAGGGTTATTTAGACGCCCACGTGGAATGTATTTTAGTGCCAAAGATAAAGGAGAGATGATGTCAATGATCTATAACTGGCCATCTGATCAGgtattgaactaa-tcttggtaaagtgctgcattccttttcttttcattcatgatagtaaatggga--gcaactttttctatttatttttcccttttaatatca

upper sequence: GRMZM2G085747_T04 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA18G46340.1 (Glycine max), 5'ss of exon 4
-AAATTACAGCGGTCTGTTCAGACGACCCCGTGGGATGTATTTCAGTGCAAAGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctgaaagtgctgtctaaatgc-acgttttcaagtaatgcctctagtgtagcgattaagattgagattatttgagtgtgggttcaactaatgagat
 ||||||   |||  | || ||||| || ||||| |||||||| ||||| || ||||| || ||||||||||||||||| || ||||||||| | ||  |||||| |     | |  ||   ||||||  | ||         | | |  |   |||  | |  ||||||  || ||  |       |   |  | || || 
AAAATTATTCCGGGTTATTTAGACGCCCGCGTGGAATGTATTTTAGTGCGAAAGATAAAGGAGAGATGATGTCAATGATCTATAACTGGCCATCTGATCAggtattgaactca-tcttggtaaaatgctgcattccttttcttttcattcatgatagaaaatg-gattgacttttttctatatccattcttaagattgtgac

upper sequence: GRMZM2G085747_T04 (Zea mays), 5'ss of exon 4
lower sequence: Vv15s0046g03670.t01 (Vitis vinifera), 5'ss of exon 4
AAATTACAGCGGTCTGTTCAGACGACCCCGTGGGATGTATTTCAGTGCAAAGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctgaaagtgctgtctaaatgcacgttttcaagtaatgcctctagtgtagcgattaagattgagattatttgagtgtgggttcaactaatgagat-
||| |||   ||  |||| ||||| || ||||| |||||||||||||  |||||||| || ||||||||||| ||||| ||||||||||||||  |  |||||  | ||  | |  ||    |  |    ||   |  |  |   ||   | || | ||    |||       | | | |     ||| | |  | | || 
AAACTACTCGGGGTTGTTTAGACGTCCACGTGGAATGTATTTCAGTGGCAAGGATAAAGGAGAGATGATGTCCATGATCTACAACTGGCCAGCTCACCAGgtactg-tgtgaatcttggaagagagttaattaaaacatggtatttcccctttatctatccctattccatagttattatttaacattccatttgttatatc

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|211274711|gb|FL015918.1|FL015918
EST:     GGATAAGGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCT
genomic: GGATAAGGGGG-AGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCT
EST: gi|74238358|gb|DT646272.1|DT646272
EST:     AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
genomic: AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
EST: gi|149102281|gb|EE287658.2|EE287658
EST:     AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
genomic: AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
EST: gi|211384290|gb|FL369291.1|FL369291
EST:     GATAAGGGGGGAGATGATGTCAATGATTTTACA-CTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGGCTTAGGTGA
genomic: GATAAGGGGG-AGATGATGTCAATGATTT-ACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGG-CTTAGGTGA
EST: gi|33094812|gb|CF054806.1|CF054806
EST:     AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
genomic: AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
EST: gi|32838032|gb|CD977710.1|CD977710
EST:     AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
genomic: AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
EST: gi|32836374|gb|CD976052.1|CD976052
EST:     AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
genomic: AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
EST: gi|211016654|gb|FL375789.1|FL375789
EST:     GATAAGGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAAGA-G                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTGAG-CTTAGGTG
genomic: GATAAGGGGG-AGATGATGTCAATGATTTACAACTGGCCAGCAGA-GAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCT-AGGCTTAGGTG
EST: gi|32801635|gb|CD953871.1|CD953871
EST:     AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
genomic: AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
EST: gi|71437509|gb|DR818559.1|DR818559
EST:     AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
genomic: AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATTACAGCGGTCTGTTCAGACGACCCCGTGGGATGTATTTCAGTGCAAAGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctgaaagtgctgtctaaatgcacgttttcaagtaatgcctctagtgtagcgattaagattgagattatttgagtgtgggttcaactaatgagat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG