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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGATGTTTTTGGAAATTTATCTGCATTCAGTCACATTGTATTATTCGAGTCAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacatcattgtgccttagatataacttgttttcttttaatttttttcacttaagagttcaatagacacacattagctaccgctttctagcattctt...

Basic information

species Zea mays
transcript GRMZM2G000937_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000937_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g02110.1 (Oryza sativa), 5'ss of exon 7
---CGATGTTTTTGGAAATTTATCTGCATTCAGTCACATTGTATTATTCGAGTCAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacatcattgtgccttagatataacttgttttcttttaatttttttcacttaagagttcaatagacacacattagctaccgctttctagcattctt---
   | | |||||||||||||||||| | |||||||||||||||||||| ||||| |||||||| |||   ||| ||||||||||||||||||| |||   ||||||| ||    |||   |||| |   | ||  | |||  | | |||  |   | || |  |  |           || | ||        |  | || |    
GGGCAAGGTTTTTGGAAATTTATCTTCTTTCAGTCACATTGTATTATTTGAGTCTGAAGAAAGGCAT---CTCAAGTTGCTTCTGCACAATTCTTTTAGAGAGgtaaaaccatgttgaatcttaaa---atctcttcttccctcagtttaataggcatatgcatataccttttttctgtttggtagtttagatttcccttttgtaa

upper sequence: GRMZM2G000937_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g39810.4 (Oryza sativa), 5'ss of exon 6
---CGATGTTTTTGGAAATTTATCTGCATTCAGTCACATTGTATTATTCGAGTCAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacatcattgtgccttagatataacttgttttcttttaatttttttcacttaagagttcaatagacacacattagctaccgctttctagcattctt----
   ||| |||||||||||||||||| | |||||||| ||||||||||| || || |||||||| |||||   | |||||||||||| |||||| ||||  ||||||| |||   |||   |||| | ||  ||  | |||  | | ||   |     || |  || | |    |  |  |   ||    | | |    || |     
GGGCGAGGTTTTTGGAAATTTATCTTCGTTCAGTCATATTGTATTATTTGAATCTGAAGAAAGGCATGT---CAAGTTGCTTCTGCGCAATTCATTTCAAGAGgtaaaacactgttgaatcttaaaaat--ctcttcttccctcagttcaataggtatacgcatttatttagtagcc--tgtttataaatatatgatgttttagtaa
















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|110506408|gb|EE017968.1|EE017968
EST:     CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAG                         ATGAGGAGGTTTTTCCACTCACATTTCAAGATTGACAGAGACCTTCAGTCG
genomic: CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacatc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGATTGACAGAGACCTTCAGTCG
EST: gi|148929350|gb|EC875261.2|EC875261
EST:     CAGAAGAAAGACATGTTCTCCAGTTGCTTTTGCACAATTCCTTTCTTGAG                         ATGAGGAGGTTTTTCCACTCCCATTTCAAGATTGACAGAGACCTTCAGTCG
genomic: CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacatc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGATTGACAGAGACCTTCAGTCG
EST: gi|6653847|gb|AW267252.1|AW267252
EST:     CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCCCAATTCCTTTCTTGAG                         ATGGGGAGGTTTTTCCCCTCACATTTCAAGATTGACAGAGACCTTCAGTCG
genomic: CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacatc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGATTGACAGAGACCTTCAGTCG
EST: gi|211018072|gb|FL437095.1|FL437095
EST:     CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAG                         ATGGGGAGGTTTTTCCACTCACATTTCAAGATTGACAGAGACCTTCAGTCG
genomic: CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacatc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGATTGACAGAGACCTTCAGTCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGATGTTTTTGGAAATTTATCTGCATTCAGTCACATTGTATTATTCGAGTCAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacatcattgtgccttagatataacttgttttcttttaatttttttcacttaagagttcaatagacacacattagctaccgctttctagcattctt

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA