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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGGTATATCTAGggctgtgaatccgtaaaaggttcatccagtttttttcctgcacacatgttaatatttctgaaacaaaatattctattgtag

Basic information

species Zea mays
transcript GRMZM2G110185_T03
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110185_T03 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA19G45140.1 (Glycine max), 5'ss of exon 7
----------ACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGGT----ATATCTAGg--gctgtgaatccgtaaaaggttcatccagtttttttcctgcacacatgttaatatttctgaaacaaaatattctattgtag
          |||||||||||||| ||  | || ||||||||||||||||||||||| |||||||| || |||||||| |||||  | ||||| || |||||    ||  ||| |  ||  |   |   ||||   ||  ||| ||| ||| | || |||    || ||    || |||    || | || | |   
GGCTAATAGGACTGATGCTTGTTTTATAAGAGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgagaatggctaagatgcactttttttttaaattttttttcccgttatttccatg-acatgatttcatcgaactaaaattttatgtcctctag---

upper sequence: GRMZM2G110185_T03 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA03G42370.2 (Glycine max), 5'ss of exon 7
----------ACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGGTATAT--CTAGggctgtgaatccgtaaaaggttcatccagtttttttcctgc-acacatgttaatatttctgaaacaaaatattctattgtag
          |||||||||||||| ||  | || ||||||||||||||||||||||| |||||||| || |||||||| |||||  | ||||| || |||||  ||  ||| |        ||  |  |   |  ||      || || |    |||    || || |  || |||    || | || | |   
GGCTAATAGGACTGATGCTTGTTTTATAAGAGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggctaagatgcaccttctatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctag---

upper sequence: GRMZM2G110185_T03 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA16G01810.1 (Glycine max), 5'ss of exon 7
----------ACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGGTATATCTAGggctgtgaatccgtaaaaggttcatccagtttttttcctgcacacatgttaatatttctgaaacaaaatattctattgtag
          |||||||||||||| ||  | || ||||||||||||||||||||||| ||||| || || || ||| |||||||  | ||||| || |||||| ||  |       |   |    |    || |||  ||| ||| | || | |     | || |  || |||    || |  | | |   
GGCTAATAGGACTGATGCTTGTTTTATAAGGGTTATTGGAAGTGAGCTAGTTCAGAAATATGTCGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaatacataag-acgtgccttctagcttttgatc--gttgtttccatg-aaattcaatcatttgactaaaattttatctcttgtag---

upper sequence: GRMZM2G110185_T03 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA07G05220.1 (Glycine max), 5'ss of exon 7
----------ACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGGTATA-TCTAGggctgtgaatccgtaaaaggttcatccagtttttttcctgcacacatgttaatatttctgaaacaaaatattctattgtag-
          |||||||||||||| ||  | || ||||||||||||||||||||||| |||||||| || || ||| |||||||  | ||||| || |||||| | |  |      |    |  ||     ||  |    || ||| | || | | |  | |     | |||   ||| | |   ||| |   
GGCTAATAGGACTGATGCTTGTTTTATAAGGGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaaatgcacaagactcgtcctctagcttttttttatcattgtttccatgaaaataaatca-----tttgactaaaattttctcatttttag

upper sequence: GRMZM2G110185_T03 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA03G42370.4 (Glycine max), 5'ss of exon 7
----------ACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGGTATAT--CTAGggctgtgaatccgtaaaaggttcatccagtttttttcctgc-acacatgttaatatttctgaaacaaaatattctattgtag---------------
          |||||||||||||| ||  | || ||||||||||||||||||||||| |||||||| || |||||||| |||||  | ||||| || |||||  ||  ||| |        ||  |  |   |  ||      || || |    |||    || || |  || |||    || | || | |  |               
GGCTAATAGGACTGATGCTTGTTTTATAAGAGTTATTGGAAGTGAGCTAGTTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggctaagatgcaccttctatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctagatggcccgctctaagaag

upper sequence: GRMZM2G110185_T03 (Zea mays), 5'ss of exon 7
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 5'ss of exon 7
----------ACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGGTATATCTAGggctgtgaatccgtaaaaggt--tcatccagtttttttcctgcacacatgttaatatttctgaaacaaaatattctattgtag---
          |||||||| ||||| || ||||| ||||||||||| || |||||||| || ||||| || || ||| |||||||  | ||||| || |||||  |      ||      |    |    ||  ||||  | ||| ||         |||    |||||     |     |  || | |||  |   
GGCTAACAGAACTGATGCATGTTTTATTCGTGTTATTGGAAGTGAACTTGTTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgt-cacaagctgccacatgtttacagtttgtcttcatttattttattgttcttgatcattgctatattgtccgactgctacctttttttgctgcag

upper sequence: GRMZM2G110185_T03 (Zea mays), 5'ss of exon 7
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 5'ss of exon 7
----------ACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGGTATATCTAGggctg-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|60342770|gb|DN209743.1|DN209743
EST:     TGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTT-C--------C-AG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
genomic: TGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGGTATATCTAGggctgtgaat ... tctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
EST: gi|78085798|gb|DV514191.1|DV514191
EST:     TGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTT-C--------C-AG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
genomic: TGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGGTATATCTAGggctgtgaat ... tctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
EST: gi|60350973|gb|DN217946.1|DN217946
EST:     TGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGGTATATCTAG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
genomic: TGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGGTATATCTAGggctgtgaat ... tctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
EST: gi|29129891|gb|CB380595.1|CB380595
EST:     TGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTT-C--------C-AG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
genomic: TGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGGTATATCTAGggctgtgaat ... tctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
EST: gi|60344174|gb|DN211147.1|DN211147
EST:     TGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTT-C--------C-AG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
genomic: TGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGGTATATCTAGggctgtgaat ... tctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
EST: gi|33104358|gb|CF064318.1|CF064318
EST:     TGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTT-C--------C-AG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
genomic: TGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGGTATATCTAGggctgtgaat ... tctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
EST: gi|60398345|gb|DN231161.1|DN231161
EST:     TGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTT-C--------C-AG                         ATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCA
genomic: TGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGGTATATCTAGggctgtgaat ... 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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGCTAGTTCAGAAGTATGTTGGAGAAGGTGCTCGGATGGTCAGGGAACTGTTCCAGGTATATCTAGggctgtgaatccgtaaaaggttcatccagtttttttcctgcacacatgttaatatttctgaaacaaaatattctattgtag

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