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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttttctctctctctcgtataccggtgttttccatcgaccagggggcttgtggtgggcgggcaggatttgggctccaggaggggggtaattgttaactgcgtttcctttgccgtgcttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG

Basic information

species Zea mays
transcript GRMZM2G112865_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112865_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g62210.1 (Oryza sativa), 3'ss of exon 2
gtattttttctctctctctcgtataccggtgttttccatcgaccagggggcttgtggtgggcgggcaggatttgggctccaggaggggggtaattgttaactgcgtttcctttgccgtgcttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
                    |||      | | | |  ||  ||  ||  || ||      ||  ||    |||      ||   |||||    |   |  |  ||       | |||| ||  || |||||||||||||| ||||| ||||||||||||||||||||||| ||||| |||
--------------------gtacgt-actctctcctttccgcctaggatctggt------cgaacac--cttg-----tagagtgggggcgcctcggatttatgtgctgggagtcgtggttgattccagGCGAAGGAGGTGCGGCGCAAGGCGGATCAGATGGTGCAGCTCGGGAAAGAG

upper sequence: GRMZM2G112865_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g38580.1 (Oryza sativa), 3'ss of exon 2
---gtattttttctctctctctcgtataccggtgttttccatcgaccagggggcttgtggtgggcgggcaggatttgggctccaggaggggggtaattgttaactgcgtttcctttgccgtgcttc-----gtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
   |      | || ||||||     | ||||  |||  | |||| ||     || | ||||||   ||||| |||  || ||||||      | ||| ||   |   ||| || ||   ||||||     |||||||||||||||||| |||  ||| |||||||||||||||||||| || || |||
gtagcccgcgtcctgtctctccgtggttccggcattt--cgtcgaacac----ctagcggtgggaatgcaggttttctgcgccaggaaatt--tgatttttttttttcttttctgtgtgttgcttcttgacgtttcagGCGAAGGAGGTGCGGACGAAAGCGGATCAGATGGTGCAGCTCGGCAAAGAG
















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|37393499|gb|CF634015.1|CF634015
EST:     TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG                         GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
genomic: TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
EST: gi|110963515|gb|EE183415.1|EE183415
EST:     TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG                         GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
genomic: TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
EST: gi|60356193|gb|DN223166.1|DN223166
EST:     TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG                         GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
genomic: TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
EST: gi|21987566|gb|BQ779094.1|BQ779094
EST:     TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTCGCCAAG                         GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
genomic: TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
EST: gi|32909297|gb|CF014109.1|CF014109
EST:     TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTCGCCAAG                         GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
genomic: TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
EST: gi|50337603|gb|CO532729.1|CO532729
EST:     TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG                         GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
genomic: TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
EST: gi|22545985|gb|BU098344.1|BU098344
EST:     TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTCGCCAAG                         GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
genomic: TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
EST: gi|148963908|gb|EE015020.2|EE015020
EST:     TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG                         GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
genomic: TGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtattttttc ... ttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctccaggaggggggtaattgttaactgcgtttcctttgccgtgcttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG
                   tgttaac  putative branch site (score: 2)
                                            cttcgtttc  putative PPT
               taattgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttttctctctctctcgtataccggtgttttccatcgaccagggggcttgtggtgggcgggcaggatttgggctccaggaggggggtaattgttaactgcgtttcctttgccgtgcttcgtttcagGCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG