Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatctcgtcgttcacaaccatacatttctgatcatctatccgatcgaggcgtacgtgtgcccatgcatgcatggtgtgtttatgtcatggtgtcgtcatggcatgcagCCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGTGAAGAAAGAGCACGCCTCCGTGCCCTTCGATGACCAGTGCTCCATCCTG

Basic information

species Zea mays
transcript GRMZM2G094165_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094165_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g45274.2 (Oryza sativa), 3'ss of exon 7
-----------------------------gtaagtatctcgtcgttcacaac-----catacatttctg---atcatctatccgatcgaggcgtacgtgtgcccatgcatg-----catggtgtgtttatgtcatgg--tgtcgtcatggc--atgcagCCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGTGAAGAAAGAGCACGCCTCCGTGCCCTTCGATGACCAGTGCTCCATCCTG
                             |  ||||        ||  ||||     ||||  | | ||   |  | | |   | |  ||   ||    ||     |  |      ||| || ||||| || |  ||  |  |    ||     | |||||||||||||||| ||||||||| || ||| ||||| ||||||   |||||  |||  |||||||||||  |||| ||||||||||| ||| ||||| ||
gtaagttgctgaacaaaagaaaacttagtgatagtactatagtattggcaacttgggcataactgtatgcagacaaacaaagggttgaagaaataaaaatgttagcgtgtcttgatcatcgtttgtttctgactcgggtttgcactttgattggttcagCCACTTCGTCGAGGACTGGGTCAGGACCGGTTTCCCCGCCAAGAAGAAGGTTCAGACCGAGCACGCCTCGCTGCCTTTCGATGACCAATGCGCCATCTTG
















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|18174547|gb|BM349935.1|BM349935
EST:     GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTT                         CCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
genomic: GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTTgtaagtatct ... tggcatgcagCCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
EST: gi|18164148|gb|BM333987.1|BM333987
EST:     GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTT                         CCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
genomic: GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTTgtaagtatct ... tggcatgcagCCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
EST: gi|18171549|gb|BM341383.1|BM341383
EST:     GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTT                         CCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
genomic: GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTTgtaagtatct ... tggcatgcagCCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
EST: gi|28986076|gb|CB350958.1|CB350958
EST:     GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTT                         CCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
genomic: GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTTgtaagtatct ... tggcatgcagCCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
EST: gi|18166370|gb|BM336209.1|BM336209
EST:     GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTT                         CCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
genomic: GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTTgtaagtatct ... tggcatgcagCCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
EST: gi|13125899|gb|BG316574.1|BG316574
EST:     GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTT                         CCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
genomic: GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTTgtaagtatct ... tggcatgcagCCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
EST: gi|40334515|gb|CK368585.1|CK368585
EST:     GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTT                         CCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
genomic: GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTTgtaagtatct ... tggcatgcagCCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
EST: gi|14529433|gb|BI096566.1|BI096566
EST:     GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTT                         CCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGNCAAGGT
genomic: GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTTgtaagtatct ... tggcatgcagCCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
EST: gi|16920707|gb|BM074789.1|BM074789
EST:     GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTT                         CCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
genomic: GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTTgtaagtatct ... tggcatgcagCCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
EST: gi|211367575|gb|FL222562.1|FL222562
EST:     GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTT                         CCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAA
genomic: GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTTgtaagtatct ... tggcatgcagCCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAA
EST: gi|18176297|gb|BM351302.1|BM351302
EST:     GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTT                         CCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
genomic: GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTTgtaagtatct ... tggcatgcagCCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
EST: gi|18165287|gb|BM335126.1|BM335126
EST:     GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTT                         CCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT
genomic: GGTGGCATCCGGGCGCTGCTCTCCCTCCAGGACGGTGCACCCGACAACTTgtaagtatct ... tggcatgcagCCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtgtgcccatgcatgcatggtgtgtttatgtcatggtgtcgtcatggcatgcagCCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGTGAAGAAAGAGCACGCCTCCGTGCCCTTCGATGACCAGTGCTCCATCCTG
                       tgtttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatctcgtcgttcacaaccatacatttctgatcatctatccgatcgaggcgtacgtgtgcccatgcatgcatggtgtgtttatgtcatggtgtcgtcatggcatgcagCCACTTCGTCGAGAACTGGGTCAAGATCGGCTTCCCTGCCAAGGTCAAGGTGAAGAAAGAGCACGCCTCCGTGCCCTTCGATGACCAGTGCTCCATCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA