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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTCAGAGTCGGAGATTAAGCAGCTCTGCGCTGCCGCCAAGGAGATCTTCCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccccctttcccgtggctcctgagcaatttcttcatgtctaggatccaagatgacatcttggggactgctttggttggtcaacggggtatggcg...

Basic information

species Zea mays
transcript GRMZM2G112240_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112240_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g57450.2 (Oryza sativa), 5'ss of exon 1
CTGTCAGAGTCGGAGATTAAGCAGCTCTGCGCTGCCGCCAAGGAGATCTTCCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccccctttcccgtggctcctgagcaatttcttca----tgtctaggatccaagatgacatcttggggactgctttggttggtcaacggggtatggcg
|| || ||||||||||||||||||||||||||  || ||||||||||||||||| | |||||||||||||| ||||||||||||||||||||||||||||||| |  |||  ||||  ||  | | |||||||| ||||      || ||    || || ||| ||||||||||| |   ||||||||||||||||        
CTTTCGGAGTCGGAGATTAAGCAGCTCTGCGCAACCTCCAAGGAGATCTTCCTGAATCAGCCCAACCTGCTCGAGCTCGAGGCCCCCATCAAAATCTGCGgtaatttccctgtttcttgtcacgcgtgagcaatatctttgatgttggctgccctcgaaaatgtcatcttggggatttgcttggttggtcaacgggtagc----

upper sequence: GRMZM2G112240_T01 (Zea mays), 5'ss of exon 1
lower sequence: EDO97337 (Chlamydomonas reinhardtii), 5'ss of exon 1
CTGTCAGAGTCGGAGATTAAGCAGCTCTGCGCTGCCGCCAAGGAGATCTTCCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccccctttcccgtg---gctcctgagcaatttcttcatgt--ctaggatccaagatgacatcttggggactgctttggttggtcaacggggtatggcg---------------
||| | |||   ||||||   | |||||||    | ||||||||||||||  ||   |||||||||||||||||||| ||||| |||||||| || ||||||       |       ||      |    | ||  |  |  |  |   |  ||  ||  |  |   | ||  ||    |  |       |      ||| | ||               
CTGGCGGAGAATGAGATTCGTCTGCTCTGCTTGACGGCCAAGGAGATCTTTATGAGCCAGCCCAACCTGCTGGAGCTGGAGGCGCCCATCAAGATTTGCGgtgcgtaggcatggcagcgaacgaacgtgcgggcggtaacgacccgctacggggcccctgggcgttgtttttcggcgctccatcaccaacctgacttgtacg-cgcttccggggctgcag

upper sequence: GRMZM2G112240_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ20637 (Selaginella moellendorffii), 5'ss of exon 1
CTGTCAGAGTCGGAGATTAAGCAGCTCTGCGCTGCCGCCAAGGAGATCTTCCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccccctttcccgtggctcctgagcaatttcttcatgtctaggatccaagatgacatcttggggactgctttggttggtcaacggggtatggcg-------------
|| |  || |||||| |   |||||| || |  | | ||||||| |||||| ||  ||||||||| || |||||||||||||| |||||||||||||| ||||  | ||            ||   |||||| |    ||| |||||| |   |||  ||| | |  ||   || |||  || | |       | |                 
CTCTTGGAATCGGAGGTGCGGCAGCTTTGTGTGGTCTCCAAGGACATCTTCATGTCGCAGCCCAATCTTCTGGAGCTCGAGGCGCCCATCAAAATCTGTGgtaagctcc------------gcgaatgagcattgcgctcaagtctagcagagaagtggac-tttgaggttttgttttcttttgcctgtttattgtctttgttccacttctct

upper sequence: GRMZM2G112240_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ32796 (Selaginella moellendorffii), 5'ss of exon 1
CTGTCAGAGTCGGAGATTAAGCAGCTCTGCGCTGCCGCCAAGGAGATCTTCCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccccctttcc-cgtggctcctgagcaatttcttcatgtctaggatccaagatgacatcttggggactgctttggttggtcaacggggtatggcg-
|| |  || |||||| |   |||||| || |  | | ||||||| |||||| ||  ||||||||| || |||||||||||||| |||||||||||||| ||||  | || |   |   | | || |   ||    |     |    | |  |   || |    | ||       |  ||  |||         || ||    
CTCTTGGAATCGGAGGTGCGGCAGCTTTGTGTAGTCTCCAAGGACATCTTCATGTCGCAGCCCAATCTTCTGGAGCTCGAGGCGCCCATCAAAATCTGTGgtaagctccgcgaatgagcattgcgctcaagt--ctagcagagaagtggactttgaggttttgttttcttttgcgtgtttattgtctttgtttgtttgatct

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|31360679|gb|CD445036.1|CD445036
EST:     CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCG                         GTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
genomic: CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccc ... ttctgatcagGTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
EST: gi|31358693|gb|CD443050.1|CD443050
EST:     CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCG                         GTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
genomic: CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccc ... ttctgatcagGTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
EST: gi|60354715|gb|DN221688.1|DN221688
EST:     CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCG                         GTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
genomic: CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccc ... ttctgatcagGTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
EST: gi|47961397|gb|CN844106.1|CN844106
EST:     CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCG                         GTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
genomic: CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccc ... ttctgatcagGTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
EST: gi|32867250|gb|CF006932.1|CF006932
EST:     CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCG                         GTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
genomic: CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccc ... ttctgatcagGTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
EST: gi|78081005|gb|DV509417.1|DV509417
EST:     CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCG                         GTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
genomic: CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccc ... ttctgatcagGTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
EST: gi|60398519|gb|DN231335.1|DN231335
EST:     CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCG                         GTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
genomic: CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccc ... ttctgatcagGTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
EST: gi|32862758|gb|CF002440.1|CF002440
EST:     CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCG                         GTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
genomic: CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccc ... ttctgatcagGTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
EST: gi|71326725|gb|DR800025.1|DR800025
EST:     CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCG                         GTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
genomic: CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccc ... ttctgatcagGTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
EST: gi|78109282|gb|DV527698.1|DV527698
EST:     CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCG                         GTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
genomic: CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccc ... ttctgatcagGTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
EST: gi|44682198|gb|CK787246.1|CK787246
EST:     CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCG                         GTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
genomic: CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccc ... ttctgatcagGTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
EST: gi|13516130|gb|BG518406.1|BG518406
EST:     CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCG                         GTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
genomic: CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccc ... ttctgatcagGTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
EST: gi|78085668|gb|DV514061.1|DV514061
EST:     CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCG                         GTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
genomic: CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccc ... ttctgatcagGTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
EST: gi|67039396|gb|CO465651.1|CO465651
EST:     CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCG                         GTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG
genomic: CCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccc ... ttctgatcagGTGATGTCCATGGCCAGTACTCTGATCTCCTGAGGCTATTTGATTATGGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTCAGAGTCGGAGATTAAGCAGCTCTGCGCTGCCGCCAAGGAGATCTTCCTGCAGCAGCCCAACCTGCTGGAGCTCGAGGCCCCCATCAAAATCTGCGgtattccccccctttcccgtggctcctgagcaatttcttcatgtctaggatccaagatgacatcttggggactgctttggttggtcaacggggtatggcg

- - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT