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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAAACCGGACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtatatctagggctgtgaatccgtaaaaggttcatccagtttttttcctgcacacatgttaatatttctgaaacaaaatattctattgtag

Basic information

species Zea mays
transcript GRMZM2G110185_T04
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110185_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA19G45140.1 (Glycine max), 5'ss of exon 7
AGCAAACCGGACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgt----atatctagg--gctgtgaatccgtaaaaggttcatccagtttttttcctgcacacatgttaatatttctgaaacaaaatattctattgtag
 || ||  |||||||||||||||| ||  | || ||||||||||||||||||||||| |||||||| || |||||||| |||||  | ||||| || |||||    ||  ||| |  ||  |   |   ||||   ||  ||| ||| ||| | || |||    || ||    || |||    || | || | |   
GGCTAATAGGACTGATGCTTGTTTTATAAGAGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgagaatggctaagatgcactttttttttaaattttttttcccgttatttccatg-acatgatttcatcgaactaaaattttatgtcctctag---

upper sequence: GRMZM2G110185_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA03G42370.2 (Glycine max), 5'ss of exon 7
AGCAAACCGGACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtatat--ctagggctgtgaatccgtaaaaggttcatccagtttttttcctgc-acacatgttaatatttctgaaacaaaatattctattgtag
 || ||  |||||||||||||||| ||  | || ||||||||||||||||||||||| |||||||| || |||||||| |||||  | ||||| || |||||  ||  ||| |        ||  |  |   |  ||      || || |    |||    || || |  || |||    || | || | |   
GGCTAATAGGACTGATGCTTGTTTTATAAGAGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggctaagatgcaccttctatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctag---

upper sequence: GRMZM2G110185_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA16G01810.1 (Glycine max), 5'ss of exon 7
AGCAAACCGGACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtatatctagggctgtgaatccgtaaaaggttcatccagtttttttcctgcacacatgttaatatttctgaaacaaaatattctattgtag
 || ||  |||||||||||||||| ||  | || ||||||||||||||||||||||| ||||| || || || ||| |||||||  | ||||| || |||||| ||  |       |   |    |    || |||  ||| ||| | || | |     | || |  || |||    || |  | | |   
GGCTAATAGGACTGATGCTTGTTTTATAAGGGTTATTGGAAGTGAGCTAGTTCAGAAATATGTCGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaatacataag-acgtgccttctagcttttgatc--gttgtttccatgaa-attcaatcatttgactaaaattttatctcttgtag---

upper sequence: GRMZM2G110185_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA07G05220.1 (Glycine max), 5'ss of exon 7
AGCAAACCGGACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtata-tctagggctgtgaatccgtaaaaggttcatccagtttttttcctgcacacatgttaatatttctgaaacaaaatattctattgtag-
 || ||  |||||||||||||||| ||  | || ||||||||||||||||||||||| |||||||| || || ||| |||||||  | ||||| || |||||| | |  |      |    |  ||     ||  |    || ||| | || | | |  | |     | |||   ||| | |   ||| |   
GGCTAATAGGACTGATGCTTGTTTTATAAGGGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaaatgcacaagactcgtcctctagcttttttttatcattgtttccatgaaaataaatca-----tttgactaaaattttctcatttttag

upper sequence: GRMZM2G110185_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA03G42370.4 (Glycine max), 5'ss of exon 7
AGCAAACCGGACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtatat--ctagggctgtgaatccgtaaaaggttcatccagtttttttcctgc-acacatgttaatatttctgaaacaaaatattctattgtag---------------
 || ||  |||||||||||||||| ||  | || ||||||||||||||||||||||| |||||||| || |||||||| |||||  | ||||| || |||||  ||  ||| |        ||  |  |   |  ||      || || |    |||    || || |  || |||    || | || | |  |               
GGCTAATAGGACTGATGCTTGTTTTATAAGAGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggctaagatgcaccttctatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctagatggcccgctctaagaag

upper sequence: GRMZM2G110185_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 5'ss of exon 7
AGCAAACCGGACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtatatctagggctgtgaatccgtaaaaggt--tcatccagtttttttcctgcacacatgttaatatttctgaaacaaaatattctattgtag---
 || ||| | |||||||| ||||| || ||||| ||||||||||| || |||||||| || ||||| || || ||| |||||||  | ||||| || |||||  |      ||      |    |    ||  ||||  | ||| ||         |||    |||||     |     |  || | |||  |   
GGCTAACAGAACTGATGCATGTTTTATTCGTGTTATTGGAAGTGAACTTGTTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgt-cacaagctgccacatgtttacagtttgtcttcatttattttattgttcttgatcattgctatattgtccgactgctacctttttttgctgcag

upper sequence: GRMZM2G110185_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 5'ss of exon 7
AGCAAACCGGACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtatatctagggctg-tgaatccgta-----aaaggttcatccagtttt--tttcctgcacacatgttaatatttctgaaacaaaatattctattgtag-
 || ||  |||| |||||||| ||||| ||||| ||||| |||||||| |||||||| ||||| ||||| ||||||||||||||| | || || ||||||| |  || |  | |  | | | |  |      | | || ||   ||||   |||   |   |    ||| |  |||      ||  | |    |   |  
TGCCAATAGGACAGATGCTTGCTTCATTCGTGTTATTGGCAGTGAGCTTGTTCAGAAATATGTAGGAGAGGGTGCTCGGATGGTCCGTGAGCTTTTCCAGgcaagtcaatcgttaatcacttcacatccctgaggtttgatatggtttggatttagagactatcctttagtcattcgcctggaacctgtatactcacatc

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|166501194|gb|EG039388.1|EG039388
EST:     GCTCGGATGGTCAGGGAACTGTTCCAG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
genomic: GCTCGGATGGTCAGGGAACTGTTCCAGgtatatctag ... tctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
EST: gi|78085798|gb|DV514191.1|DV514191
EST:     TTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
genomic: TTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtatatctag ... tctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
EST: gi|60350973|gb|DN217946.1|DN217946
EST:     TTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGGTATATCTAG                
genomic: TTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTT-C--------C-AGgtatatctag ... t
EST: gi|29129891|gb|CB380595.1|CB380595
EST:     CAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
genomic: CAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtatatctag ... tctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
EST: gi|60344174|gb|DN211147.1|DN211147
EST:     TCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
genomic: TCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtatatctag ... tctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
EST: gi|5846988|gb|AW000067.1|AW000067
EST:     TTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAA
genomic: TTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtatatctag ... tctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAA
EST: gi|211328324|gb|FL186215.1|FL186215
EST:     TTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
genomic: TTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtatatctag ... tctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
EST: gi|60395089|gb|DN227958.1|DN227958
EST:     GAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
genomic: GAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtatatctag ... tctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
EST: gi|33104358|gb|CF064318.1|CF064318
EST:     TTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
genomic: TTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtatatctag ... tctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
EST: gi|5296364|gb|AI783134.1|AI783134
EST:     TTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATG
genomic: TTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtatatctag ... tctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATG
EST: gi|60398345|gb|DN231161.1|DN231161
EST:     TTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
genomic: TTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtatatctag ... tctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
EST: gi|60342770|gb|DN209743.1|DN209743
EST:     TTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
genomic: TTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtatatctag ... tctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
EST: gi|60397964|gb|DN230780.1|DN230780
EST:     AAGGTGCTCGGATGGTCAGGGAACTGTTCCAG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
genomic: AAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtatatctag ... tctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
EST: gi|60351568|gb|DN218541.1|DN218541
EST:     TTCAGAAGTATTTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
genomic: TTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtatatctag ... tctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAAACCGGACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGgtatatctagggctgtgaatccgtaaaaggttcatccagtttttttcctgcacacatgttaatatttctgaaacaaaatattctattgtag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA