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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagattccttcttgctgttccaaaattctaaacagttggggaagtttttttttaacttctaatgtgcgtttctgttagTGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTGCCATCCAAGAGCTTCATGCAACTGTTCAAGTTCTACCACCACAAGAGA

Basic information

species Zea mays
transcript GRMZM2G464000_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G464000_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 5
gtagattccttcttgctgttccaaaattctaaacagttggggaagtttttttttaacttctaatgtgcgtttctgttagTGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTGCCATCCAAGAGCTTCATGCAACTGTTCAAGTTCTACCACCACAAGAGA
|||  ||| |  ||  | | | |   |   |   |  |  | ||| |        | ||||||   |  ||||| |||||||| ||||||||||| || ||||| ||||| || || ||||| |||||||| ||||||||||| |  |||||||||| ||||||||| |||||||| |
gtaagttcttgattattttccaagcgtgaaacgaacctctgaaagct-------gatttctaaacggtctttcttttagTGCTTATGCATACTGGTTACTGCTCCCCTACATCATCACCTCCACCATCTGCAATCCAAGAGCTACGAGCAACTGTTCGAGTTCTACCGCCACAAGACA
















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|211146179|gb|FK958443.1|FK958443
EST:     TCAACTTTGGGGAACAGATATATATACAAATGATTCAGATCTTGTGGCTG                         TGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTG
genomic: TCAACTTTGGGGAACAGATATATATACAAATGATTCAGATCTTGTGGCTGgtagattcct ... tttctgttagTGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTG
EST: gi|32823438|gb|CD963160.1|CD963160
EST:     GATCTTGTGGCTG                         TGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTG
genomic: GATCTTGTGGCTGgtagattcct ... tttctgttagTGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTG
EST: gi|26558158|gb|CA830393.1|CA830393
EST:     TCAACTTTGGGGAACAGATATATATACAAATGATTCAGATCTTGTGGCTG                         TGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTG
genomic: TCAACTTTGGGGAACAGATATATATACAAATGATTCAGATCTTGTGGCTGgtagattcct ... tttctgttagTGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTG
EST: gi|67024103|gb|CO452852.1|CO452852
EST:     TCAACTTTGGGGAACAGATATATATACAAATGATTCAGATCTTGTGGCTG                         TGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCNCATCTG
genomic: TCAACTTTGGGGAACAGATATATATACAAATGATTCAGATCTTGTGGCTGgtagattcct ... tttctgttagTGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTG
EST: gi|58029867|gb|CX725294.1|CX725294
EST:     GGGGAACAGATATATATACAAATGATTCAGATCTTGTGGCTG                         TGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTG
genomic: GGGGAACAGATATATATACAAATGATTCAGATCTTGTGGCTGgtagattcct ... tttctgttagTGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTG
EST: gi|21987866|gb|BQ779394.1|BQ779394
EST:     TCAACTTTGGGGAACAGATATATATACAAATGATTCAGATCTTGTGGCTG                         TGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTG
genomic: TCAACTTTGGGGAACAGATATATATACAAATGATTCAGATCTTGTGGCTGgtagattcct ... tttctgttagTGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTG
EST: gi|32931653|gb|CF036465.1|CF036465
EST:     TCAACTTTGGGGAACAGATATATATACAAATGATTCAGATCTTGTGGCTG                         TGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTG
genomic: TCAACTTTGGGGAACAGATATATATACAAATGATTCAGATCTTGTGGCTGgtagattcct ... tttctgttagTGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTG
EST: gi|32822990|gb|CD962699.1|CD962699
EST:     GATCTCGTGGCTG                         TGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTG
genomic: GATCTTGTGGCTGgtagattcct ... tttctgttagTGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTG
EST: gi|32934961|gb|CF039773.1|CF039773
EST:     TCAACTTTGGGGAACAGATATATATACAAATGATTCAGATCTTGTGGCTG                         TGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTG
genomic: TCAACTTTGGGGAACAGATATATATACAAATGATTCAGATCTTGTGGCTGgtagattcct ... tttctgttagTGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattctaaacagttggggaagtttttttttaacttctaatgtgcgtttctgttagTGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTGCCATCCAAGAGCTTCATGCAACTGTTCAAGTTCTACCACCACAAGAGA
                                 ttctaat  putative branch site (score: 2)
                                             tttctgtt  putative PPT
                  aagtttttttttaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagattccttcttgctgttccaaaattctaaacagttggggaagtttttttttaacttctaatgtgcgtttctgttagTGCTAATGCATACTGGCTATTGCTCGCCTACGTCCTCCCCTCCCCCATCTGCCATCCAAGAGCTTCATGCAACTGTTCAAGTTCTACCACCACAAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA