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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATAGACCCATTGAGAGCAATGGCTATGGGTGGACCCCTGGAAGATGCTCGTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTCgtatgtactagtggcttaatcctttgctgcaagtgagcaaattcctattactgctacttccatttaccctgacccttcttgtttgttcaatag

Basic information

species Zea mays
transcript GRMZM2G179459_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179459_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g32460.1 (Oryza sativa), 5'ss of exon 5
TATAGACCCATTGAGAGCAATGGCTATGGGTGGACCCCTGGAAGATGCTCGTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTCgtatgtactagtggcttaatcctttgctgcaagtgagcaaattcctattactgctacttccat-ttaccctgacccttcttgtttgttcaatag-------------------------
|||||| |||||||| || ||||||   || |  ||||||||||||||||||||||||||||| || |||||| ||||||||||||||||||||||||| ||||||| |||   |||  ||| |   ||||||  |||||  || || || ||||||||| ||  | |   ||    | ||     ||   ||                          
TATAGATCCATTGAGGGCTATGGCTGCAGGCGCTCCCCTGGAAGATGCTCGTGGTCTTGCACAACGTTATAGCCGGATGAGACATGAAGCTGAGATCCTTgtatgtattagcaacttgttccat-attgcaagcaagcaa--tcttactattgctacttctatgcttcatagaatacttttccccattatgtatcttaaccctcttgtttgtcatacag
















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|149001142|gb|EE038404.2|EE038404
EST:     GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTC                         TCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
genomic: GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTCgtatgtacta ... tgttcaatagTCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
EST: gi|149088736|gb|EE177860.2|EE177860
EST:     GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTC                         TCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
genomic: GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTCgtatgtacta ... tgttcaatagTCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
EST: gi|149032717|gb|EE154943.2|EE154943
EST:     GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTC                         TCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
genomic: GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTCgtatgtacta ... tgttcaatagTCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
EST: gi|148996112|gb|EE035378.2|EE035378
EST:     GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTC                         TCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
genomic: GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTCgtatgtacta ... tgttcaatagTCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
EST: gi|88757167|gb|DY541308.1|DY541308
EST:     GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTC                         TCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
genomic: GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTCgtatgtacta ... tgttcaatagTCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
EST: gi|149013869|gb|EE043354.2|EE043354
EST:     GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTC                         TCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
genomic: GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTCgtatgtacta ... tgttcaatagTCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
EST: gi|93014497|gb|EB640017.1|EB640017
EST:     GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTC                         TCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
genomic: GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTCgtatgtacta ... tgttcaatagTCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
EST: gi|149085767|gb|EE175287.2|EE175287
EST:     GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTC                         TCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
genomic: GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTCgtatgtacta ... tgttcaatagTCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
EST: gi|101389748|gb|EB816808.1|EB816808
EST:     GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTC                         TCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCCATTGCT
genomic: GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTCgtatgtacta ... tgttcaatagTCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
EST: gi|149086994|gb|EE176539.2|EE176539
EST:     GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTC                         TCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
genomic: GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTCgtatgtacta ... tgttcaatagTCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
EST: gi|6564150|gb|AW231772.1|AW231772
EST:     GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTC                         TCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
genomic: GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTCgtatgtacta ... tgttcaatagTCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
EST: gi|148983017|gb|EE028919.2|EE028919
EST:     GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTC                         TCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
genomic: GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTCgtatgtacta ... tgttcaatagTCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
EST: gi|148951274|gb|EC896976.2|EC896976
EST:     GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTC                         TCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT
genomic: GTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTCgtatgtacta ... tgttcaatagTCTACTGAAATTGCTAGAAGAAAGGCACGGGTAAGAGAAGCTCCAATTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATAGACCCATTGAGAGCAATGGCTATGGGTGGACCCCTGGAAGATGCTCGTGGTCTTGCACAGCGCTATAGCAGGATGAGACATGAAGCTGAGATCCTCgtatgtactagtggcttaatcctttgctgcaagtgagcaaattcctattactgctacttccatttaccctgacccttcttgtttgttcaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC