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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttttaactgatagattatatagtggtatagataaaggtgatatataatatactcgtaactgatttgctgctcgcttatatttttgttgtctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACGTGCTGGTCCATCAGTTGGTATCGTCGTTTCCTTCTACGAGGTTGTCAAG

Basic information

species Zea mays
transcript GRMZM2G106703_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106703_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os08g29720.1 (Oryza sativa), 3'ss of exon 9
-agttttaactgatag-attatatagtggtatagataaaggtgatatataatatactcgtaactgatttgctgctcgcttatatttttgttgtctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACGTGCTGGTCCATCAGTTGGTATCGTCGTTTCCTTCTACGAGGTTGTCAAG
 || | ||| |  | | |||| ||  |  | ||  ||    ||| |  |  |    | |  | |   || | | | |  |   ||  | ||  |  |||||| ||||||||  |||||||  |||||||||| || || |||||||| ||||| ||||| ||||||||||| |||||| |||| |||||||||||||| |||
taggtgtaatttcttgtattacattttcat-tatttacccctgagaggtcttggcttggggagtcgatttcagttggactgatttaattttaacc-tggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACGAGCTGGCCCATCAGTTGGAATCGTCATTTCTTTCTACGAGGTTGTGAAG
















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|71330462|gb|DR801990.1|DR801990
EST:     GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
genomic: GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
EST: gi|78080372|gb|DV508784.1|DV508784
EST:     GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
genomic: GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
EST: gi|37391227|gb|CF632855.1|CF632855
EST:     GAGAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCATGAAAGGGCTGTTCACTGGCGTCGGCCCACGTGTTGCACG
genomic: GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
EST: gi|50331807|gb|CO526933.1|CO526933
EST:     GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
genomic: GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
EST: gi|40303051|gb|CK347438.1|CK347438
EST:     GAGAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCATGAAAGGGCTGTTCACTGGCGTCGGCCCACGTGTTGCACG
genomic: GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
EST: gi|71766047|gb|DR963984.1|DR963984
EST:     GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
genomic: GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
EST: gi|89247187|gb|DY618973.1|DY618973
EST:     GAAAAGGCAATGAGGATGACTCCAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
genomic: GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
EST: gi|108953060|gb|EC364565.1|EC364565
EST:     GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
genomic: GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
EST: gi|71425694|gb|DR806840.1|DR806840
EST:     GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
genomic: GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
EST: gi|148996296|gb|EE035578.2|EE035578
EST:     GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
genomic: GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
EST: gi|78125235|gb|DV543619.1|DV543619
EST:     GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
genomic: GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
EST: gi|78122434|gb|DV540818.1|DV540818
EST:     GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
genomic: GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
EST: gi|67023452|gb|CO452201.1|CO452201
EST:     GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
genomic: GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
EST: gi|91057184|gb|EB167602.1|EB167602
EST:     GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
genomic: GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
EST: gi|149000842|gb|EE038070.2|EE038070
EST:     GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
genomic: GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
EST: gi|60343202|gb|DN210175.1|DN210175
EST:     GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
genomic: GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
EST: gi|37389305|gb|CF631871.1|CF631871
EST:     TGACTACAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCATGAAAGGGCTGTTCACTGGCGTCGGCCCACGTGTTGCACG
genomic: TGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
EST: gi|88746967|gb|DY531108.1|DY531108
EST:     GAAAAGGCAATGAGGATGACTCCAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
genomic: GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
EST: gi|71443271|gb|DR824321.1|DR824321
EST:     GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
genomic: GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
EST: gi|71441616|gb|DR822666.1|DR822666
EST:     GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAG                         GTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG
genomic: GAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaat ... tctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatatactcgtaactgatttgctgctcgcttatatttttgttgtctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACGTGCTGGTCCATCAGTTGGTATCGTCGTTTCCTTCTACGAGGTTGTCAAG
                               ttatatttttgttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttttaactgatagattatatagtggtatagataaaggtgatatataatatactcgtaactgatttgctgctcgcttatatttttgttgtctgtggcagGTCTGGAGGCTTGAAAGGGCTGTTCACCGGCGTCGGCCCACGTGTTGCACGTGCTGGTCCATCAGTTGGTATCGTCGTTTCCTTCTACGAGGTTGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgctc