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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttgcattggttgaatgttacaagttggatcggtagcacccttttgaattataattatgcaaattgtcctaacatgttgagtgatttggtatcatgcagAATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACTTGTTTCTGTTCTTTGGCTAGACGATCAATTGGAGTCGTCAATTGTGCTG

Basic information

species Zea mays
transcript GRMZM5G862931_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G862931_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g40790.1 (Oryza sativa), 3'ss of exon 2
tcttgcattggt--tgaatgttacaagttggatcggtagcacccttttgaattataattatgcaaattgtcctaacatg--ttgagtgatttggtatcatgcagAATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACTTGTTTCTGTTCTTTGGCTAGACGATCAATTGGAGTCGTCAATTGTGCTG
      ||||||  |   | || |   |   ||  ||||   | || |     |      || |||||        |||  ||||  |||    | |  |||||||||||||| |||||||| ||||||||||| ||||| |||||||| || ||||| ||| |||||||||||||||| || |||||||| ||||||   || 
---aagattggtgttttttttttctgataacattagtagtttcattatactacagtgccttgtaaattacgacggtatgaattgaa-gatactatgtgctgcagAATGGATCACATATTACTAGAGACAACAGGATTGGCTGATCCTGCACCTCTTGTCTCTATTCTTTGGCTAGACGACCAGTTGGAGTCATCAATTAAACTA
















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|40336013|gb|CK370083.1|CK370083
EST:     AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAG                         AATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
genomic: AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAGgtaaaataca ... tatcatgcagAATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
EST: gi|78112342|gb|DV530736.1|DV530736
EST:     AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAG                         AATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
genomic: AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAGgtaaaataca ... tatcatgcagAATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
EST: gi|211125209|gb|FL458514.1|FL458514
EST:     AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAG                         AATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
genomic: AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAGgtaaaataca ... tatcatgcagAATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
EST: gi|76926513|gb|DV170904.1|DV170904
EST:     AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAG                         AATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
genomic: AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAGgtaaaataca ... tatcatgcagAATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
EST: gi|211017329|gb|FL293924.1|FL293924
EST:     AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAG                         AATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
genomic: AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAGgtaaaataca ... tatcatgcagAATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
EST: gi|71435591|gb|DR816641.1|DR816641
EST:     AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAG                         AATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
genomic: AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAGgtaaaataca ... tatcatgcagAATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
EST: gi|89760831|gb|DY689083.1|DY689083
EST:     AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAG                         AATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
genomic: AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAGgtaaaataca ... tatcatgcagAATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
EST: gi|33467642|gb|CF244691.1|CF244691
EST:     AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAG                         AATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
genomic: AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAGgtaaaataca ... tatcatgcagAATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
EST: gi|50335360|gb|CO530486.1|CO530486
EST:     AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAG                         AATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
genomic: AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAGgtaaaataca ... tatcatgcagAATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
EST: gi|71434868|gb|DR815918.1|DR815918
EST:     AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAG                         AATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
genomic: AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAGgtaaaataca ... tatcatgcagAATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
EST: gi|78108723|gb|DV527141.1|DV527141
EST:     AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAG                         AATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
genomic: AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAGgtaaaataca ... tatcatgcagAATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
EST: gi|211020108|gb|FL293928.1|FL293928
EST:     AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAG                         AATGGATCATATATTACTTGAG
genomic: AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAGgtaaaataca ... tatcatgcagAATGGATCATATATTACTTGAG
EST: gi|71446369|gb|DR827419.1|DR827419
EST:     AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAG                         AATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT
genomic: AAACACAGTCTGGTTCAAGCACTTGAGCAGCTTGTGCAGAGAAAGGATAGgtaaaataca ... tatcatgcagAATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaattataattatgcaaattgtcctaacatgttgagtgatttggtatcatgcagAATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACTTGTTTCTGTTCTTTGGCTAGACGATCAATTGGAGTCGTCAATTGTGCTG
                      tcctaac  putative branch site (score: 1)
     tataattatgcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttgcattggttgaatgttacaagttggatcggtagcacccttttgaattataattatgcaaattgtcctaacatgttgagtgatttggtatcatgcagAATGGATCATATATTACTTGAGACAACAGGGTTGGCCGATCCTGCTCCACTTGTTTCTGTTCTTTGGCTAGACGATCAATTGGAGTCGTCAATTGTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG