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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGGCAGCGGTGGCTCAGCCGGCGAGCCCGACCTCGCCGCACGTCGCGCACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAGgtaaaagcctccatcaattaggatctagattaccaatcattagctgttagctcagcatgctcataactgtttttttatttttttatttttttgctgtcga...

Basic information

species Zea mays
transcript GRMZM2G123986_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123986_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g06970.1 (Oryza sativa), 5'ss of exon 1
CATGGCAGCGGTGGCTCAGCCGGCGAGCCC---GACCTCGCCGCACGTCGCGCACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAGgta---aaagcctccatcaattaggatctagattaccaatcatta--gctgttagctcagcatgctcataactgtttttttatttttttatttttttgctgtcga
   | | ||| |||| | |||| |||||||   | |  || ||||||||||| ||||||||||| ||||||||||||| |||||  |||||||||||| |||||||   | |  |||  |    |     |    ||             || |    |   |     | ||| || | | | ||| |   | | ||| |        
--CGTCGGCG-TGGCGCGGCCGTCGAGCCCCTCGGCGGCGGCGCACGTCGCGTACAAGATCCCGGCCGGCGACGGGCCGTACGCTCGGGCCAAGCACTACCAGgtatatataagctctgttttctctcgccggcgttcatggctggcgccgccgcgtccatggggaaattatagctctctctatatatgcatttatttatata-----
















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|211206187|gb|FL360004.1|FL360004
EST:     ACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAG                         CTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC
genomic: ACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAGgtaaaagcct ... aataattaagCTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC
EST: gi|78085599|gb|DV513992.1|DV513992
EST:     ACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAG                         CTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC
genomic: ACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAGgtaaaagcct ... aataattaagCTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC
EST: gi|211494830|gb|FL326696.1|FL326696
EST:     ACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAG                         CTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC
genomic: ACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAGgtaaaagcct ... aataattaagCTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC
EST: gi|211412707|gb|FL360157.1|FL360157
EST:     ACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAG                         CTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC
genomic: ACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAGgtaaaagcct ... aataattaagCTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC
EST: gi|211012372|gb|FL318437.1|FL318437
EST:     ACAAGATCCCGCCCGGCGAC-GGSCTTACGCGAGGGCCAAGCACTTCCAG                         CTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC
genomic: ACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAGgtaaaagcct ... aataattaagCTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC
EST: gi|211134099|gb|FL315804.1|FL315804
EST:     ACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAG                         CTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC
genomic: ACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAGgtaaaagcct ... aataattaagCTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC
EST: gi|154130487|gb|EC872220.2|EC872220
EST:     ACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAG                         CTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC
genomic: ACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAGgtaaaagcct ... aataattaagCTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC
EST: gi|211143627|gb|FL314870.1|FL314870
EST:     ACAAGATCCCGCCCGGCGACGGSCTTTACGCGAGGGCCAAGCACTTCCAG                         CTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC
genomic: ACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAGgtaaaagcct ... aataattaagCTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC
EST: gi|211396429|gb|FL326121.1|FL326121
EST:     ACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAG                         CTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC
genomic: ACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAGgtaaaagcct ... aataattaagCTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC
EST: gi|211185361|gb|FL306752.1|FL306752
EST:     ACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAG                         CTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC
genomic: ACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAGgtaaaagcct ... aataattaagCTGGTGGAGAAGGACCTGGACGCGTCGATCGCGTGGTTCTGGAAGGCGATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGGCAGCGGTGGCTCAGCCGGCGAGCCCGACCTCGCCGCACGTCGCGCACAAGATCCCGCCCGGCGACGGGCCTTACGCGAGGGCCAAGCACTTCCAGgtaaaagcctccatcaattaggatctagattaccaatcattagctgttagctcagcatgctcataactgtttttttatttttttatttttttgctgtcga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctccatc