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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttctttaaatatccacataacgctcaattggagtaatactgttagtaaatggtcgaagatattaatttcttgtgtaccgatcatgtcttaactgggcccatattgtagatattgaaatgtagacgctaccttttcagGTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGATAATGATACTGTTGCTGCAGTTATACTGGGTACTGGCACTAATGCAGCGTACATAG

Basic information

species Zea mays
transcript GRMZM2G171373_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171373_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g52450.2 (Oryza sativa), 3'ss of exon 4
gttagtttctttaaatatccacataacgctcaattggagtaatactgttagtaaatggtcgaagatattaatttcttgtgtaccgatcatgtcttaactgggcccatattgtagatattgaaatgtaga-cgctaccttttcagGTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGATAATGATACTGTTGCTGCAGTTATACTGGGTACTGGCACTAATGCAGCGTACATAG
||||| ||||||  |||||||  | | ||||||| |||| || |||| ||| | ||             ||| |  ||  ||  | |||||| |||     || |      || | |||||| |||| | | ||||| |||||||| |||||||||||||||||||| |||||||||||||||||| || |||||||| ||||||| ||||||||||| || || | |||||||||||||||||
gttagcttcttttgatatccatcttatgctcaataggagaaacactgctagaagat-------------aatgttgtggctattg-tcatgttttatt---gcactggccatacaaattgaagtgtaaaacactaccctttcagGTTAATGATACAGTAGGGACATTAGCTGCTGGGAGATATGTGAATCATGATACTATTGCTGCTGTTATACTGGGAACAGGTAGTAATGCAGCGTACATAG
















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|78087466|gb|DV515859.1|DV515859
EST:     TAAACAAGGCTATCAAACGCCAAGGAGTTGATATGGAAGTCACAGTACTG                         GTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGATAATGAT
genomic: TAAACAAGGCTATCAAACGCCAAGGAGTTGATATGGAAGTCACAGTACTGgttagtttct ... accttttcagGTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGATAATGAT
EST: gi|71757201|gb|DR955138.1|DR955138
EST:     TAAACAAGGCTATCAAACGCCAAGGAGTTGATATGGAAGTCACAGTACTG                         GTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGATAATGAT
genomic: TAAACAAGGCTATCAAACGCCAAGGAGTTGATATGGAAGTCACAGTACTGgttagtttct ... accttttcagGTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGATAATGAT
EST: gi|78106048|gb|DV524466.1|DV524466
EST:     TAAACAAGGCTATCAAACGCCAAGGAGTTGATATGGGAGTCACAGTACTG                         GTCAATGATACAGTANGGACATTGGCTGCTGGGAGATATGTGGATAATGAT
genomic: TAAACAAGGCTATCAAACGCCAAGGAGTTGATATGGAAGTCACAGTACTGgttagtttct ... accttttcagGTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGATAATGAT
EST: gi|71448675|gb|DR829725.1|DR829725
EST:     TAAACAAGGCTATCAAACGCCAAGGAGTTGATATGGAAGTCACAGTACTG                         GTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGGATA-TGA
genomic: TAAACAAGGCTATCAAACGCCAAGGAGTTGATATGGAAGTCACAGTACTGgttagtttct ... accttttcagGTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGG-ATAATGA
EST: gi|78089619|gb|DV517993.1|DV517993
EST:     TAAACAAGGCTATCAAACGCCAAGGAGTTGATATGGAAGTCACAGTACTG                         GTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGATAATGAT
genomic: TAAACAAGGCTATCAAACGCCAAGGAGTTGATATGGAAGTCACAGTACTGgttagtttct ... accttttcagGTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGATAATGAT
EST: gi|78080649|gb|DV509061.1|DV509061
EST:     TAAACAAGGCTATCAAACGCCAAGGAGTTGATATGGAAGTCACAGTACTG                         GTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGATAATGAT
genomic: TAAACAAGGCTATCAAACGCCAAGGAGTTGATATGGAAGTCACAGTACTGgttagtttct ... accttttcagGTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGATAATGAT
EST: gi|94477216|gb|EB706174.1|EB706174
EST:     TAAACAAGGCTATCAAACGCCAAGGAGTTGATATGGAAGTCACAGTACTG                         GTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGATAATGAT
genomic: TAAACAAGGCTATCAAACGCCAAGGAGTTGATATGGAAGTCACAGTACTGgttagtttct ... accttttcagGTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGATAATGAT
EST: gi|149112472|gb|EE295341.2|EE295341
EST:     TAAACAAGGCTATCAAACGCCAAGGAGTTGATATGGAAGTCACAGTACTG                         GTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGATAATGAT
genomic: TAAACAAGGCTATCAAACGCCAAGGAGTTGATATGGAAGTCACAGTACTGgttagtttct ... accttttcagGTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGATAATGAT
EST: gi|149047925|gb|EE048253.2|EE048253
EST:     TAAACAAGGCTATCAAACGCCAAGGAGTTGATATGGAAGTCACAGTACTG                         GTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGATAATGAT
genomic: TAAACAAGGCTATCAAACGCCAAGGAGTTGATATGGAAGTCACAGTACTGgttagtttct ... accttttcagGTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGATAATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtcttaactgggcccatattgtagatattgaaatgtagacgctaccttttcagGTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGATAATGATACTGTTGCTGCAGTTATACTGGGTACTGGCACTAATGCAGCGTACATAG
   tcttaac  putative branch site (score: 2)
                                           ctaccttttc  putative PPT
                 atattgtagatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttctttaaatatccacataacgctcaattggagtaatactgttagtaaatggtcgaagatattaatttcttgtgtaccgatcatgtcttaactgggcccatattgtagatattgaaatgtagacgctaccttttcagGTCAATGATACAGTAGGGACATTGGCTGCTGGGAGATATGTGGATAATGATACTGTTGCTGCAGTTATACTGGGTACTGGCACTAATGCAGCGTACATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG