Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtcctttccctcattgaagtatgtagctatgctatttttaatcgtatgctactatgttaaatactagtcaatttcactatagGAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTACAGGACCTGAGCAGTGCCCCCCTGAGGGGAAACTTCCTG

Basic information

species Zea mays
transcript GRMZM2G120517_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120517_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g35520.2 (Oryza sativa), 3'ss of exon 4
-----gtctgtcctttccctcat--------------tgaagtatgtagctatgctatttttaat---cgtatgcta----ctatgttaa------atactagtcaatttcactatagGAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTACAGGACCTGAGCAGTGCCCCCCTGAGGGGAAACTTCCTG
      ||    |   ||| ||               |||||||  || |||  ||  |||||||   || |  |||    |||  ||||      ||  | |||||  |     |||||||||||||| |||||||||||||||| ||| |||||  ||||||| ||||| ||||||||||| || ||||||||||| ||||| |
gtctgatcccctcacgcccccaaaaaataatgaaaaatgaagtacctaactagtctggttttaatgtacgaacactatattctaccttaatgatccatttttgtcaaacttgtactagGAAGCTGGTGGTCCAAAGATTCCAATGACATATGGACGGATTGATGTCACAGGTCCTGAGCAGTGTCCACCTGAGGGGAAGCTTCCCG
















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|22489220|gb|BU049143.1|BU049143
EST:     GTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGAG                         GAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTA
genomic: GTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGAGgtctgtcctt ... ttcactatagGAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTA
EST: gi|24934386|gb|CA452604.1|CA452604
EST:     GTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGAG                         GAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTACA
genomic: GTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGAGgtctgtcctt ... ttcactatagGAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTACA
EST: gi|101393103|gb|EB818482.1|EB818482
EST:     TGGCAAGTGCTACAGCAATTGAG                         GAAGCTGGGGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTACA
genomic: TGGCAAGTGCTACAGCAATTGAGgtctgtcctt ... ttcactatagGAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTACA
EST: gi|18181579|gb|BM382789.1|BM382789
EST:     GTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGAG                         GAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTACA
genomic: GTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGAGgtctgtcctt ... ttcactatagGAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTACA
EST: gi|89106264|gb|DY576481.1|DY576481
EST:     GTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGAG                         GAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTA
genomic: GTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGAGgtctgtcctt ... ttcactatagGAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTA
EST: gi|7238058|gb|AW573325.1|AW573325
EST:     GTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGAG                         GAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTACA
genomic: GTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGAGgtctgtcctt ... ttcactatagGAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTACA
EST: gi|74246091|gb|DT654005.1|DT654005
EST:     GTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGAG                         GAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTACA
genomic: GTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGAGgtctgtcctt ... ttcactatagGAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTACA
EST: gi|18383811|gb|BM417011.1|BM417011
EST:     GTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGAG                         GAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGA
genomic: GTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGAGgtctgtcctt ... ttcactatagGAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGA
EST: gi|18383818|gb|BM417018.1|BM417018
EST:     GTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGAG                         GAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTAC
genomic: GTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGAGgtctgtcctt ... ttcactatagGAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTAC
EST: gi|22489146|gb|BU049069.1|BU049069
EST:     GTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGAG                         GAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTAC
genomic: GTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGAGgtctgtcctt ... ttcactatagGAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgctatttttaatcgtatgctactatgttaaatactagtcaatttcactatagGAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTACAGGACCTGAGCAGTGCCCCCCTGAGGGGAAACTTCCTG
        ttttaat  putative branch site (score: 3)
                                            tttcact  putative PPT
     tatttttaatcgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtcctttccctcattgaagtatgtagctatgctatttttaatcgtatgctactatgttaaatactagtcaatttcactatagGAAGCTGGTGGCCCAAAGATTCCAATGAAATACGGACGAGTTGATGTTACAGGACCTGAGCAGTGCCCCCCTGAGGGGAAACTTCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG