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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatatgttagtctagtggattgcccagttacctggtttgctatgtttggttgtccgttgtatagtggtagattctgattccatattttgttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGATATCAAGCAGTAGATTTTACATCTAGTTTACCAAGAATTGGACACTGCCT

Basic information

species Zea mays
transcript GRMZM2G125300_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G125300_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT5G27700.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------ttatatgttagtctagtggattgcccagttacctggtttgcta--tgtttggttgtccgttgtatagtggtagatt--ctgattccatattttgttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGATATCAAGCAG---TAGATTTTACATCTAGTTTACCAAGAATTGGACACTGCCT
                                                  | || ||||  |   ||| ||         |  ||     | |    ||||  | ||   | |||  |  ||| ||   | | |    || |    |    ||||| ||||| |||||     | |||||||||||||||||||||||||||||   ||| ||    ||     |  ||||   ||        | | |   ||   
gtttgtaacaatttctcaatgctttgtccataattgagtcagaagagagttgatttgtt--ttgtgtgtatcataagaagagttgaacaaccaaccctttgaatttctact-tatcttcataggttaattaactattgatgtacacgattgcagGGAGACGCTGACAGTGGTGTCGACAGGTTGTGGCAGAAGAAGAAGGTTGAAGCCAAACAAAACTAAGAGCTTAATCTGTCTTGTTTTTTGTCGAATCTTG---
















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|32836843|gb|CD976521.1|CD976521
EST:     ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGCGACGCAGACAGCTCCTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAT
genomic: ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgacagttc ... ttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
EST: gi|9730947|gb|BE509699.1|BE509699
EST:     ATGATGGTCACTTCACAACATTTGCTCTTTCTGGGTTTGTCCGTGCTCAG                         GGCGATGCAGACAGCTCCTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAT
genomic: ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgacagttc ... ttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
EST: gi|15426862|gb|BI542684.1|BI542684
EST:     ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTTCGTGCTCAG                         GGCGACGCAGACAGCCCCTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAT
genomic: ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgacagttc ... ttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
EST: gi|32836427|gb|CD976105.1|CD976105
EST:     ACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGCGACGCAGACAGCTCCTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAT
genomic: ACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgacagttc ... ttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
EST: gi|32932877|gb|CF037689.1|CF037689
EST:     ATGATGGTCACTTCACAACATTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGCGATGCAGACAGCTCCTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAT
genomic: ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgacagttc ... ttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
EST: gi|91869600|gb|EB400457.1|EB400457
EST:     ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
genomic: ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgacagttc ... ttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
EST: gi|60346165|gb|DN213138.1|DN213138
EST:     ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTTCGTGCTCAG                         GGCGACGCAGACAGCTCCTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAT
genomic: ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgacagttc ... ttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
EST: gi|32793079|gb|CD945315.1|CD945315
EST:     ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGCGACGCAGACAGCTCCTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAT
genomic: ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgacagttc ... ttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
EST: gi|71431500|gb|DR812550.1|DR812550
EST:     ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
genomic: ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgacagttc ... ttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
EST: gi|113590052|gb|DW756033.1|DW756033
EST:     TTTGTCCGTGCTCAG                         GGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
genomic: TTTGTCCGTGCTCAGgtgacagttc ... ttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
EST: gi|33094595|gb|CF054589.1|CF054589
EST:     ATGATGGTCACTTCACAACATTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGCGATGCAGACAGCTCCTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAT
genomic: ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgacagttc ... ttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
EST: gi|32843230|gb|CD982911.1|CD982911
EST:     ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGCGACGCAGACAGCTCCTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAT
genomic: ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgacagttc ... ttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
EST: gi|9824794|gb|BE575101.1|BE575101
EST:     ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGCGACGCAGACAGCTCCTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAT
genomic: ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgacagttc ... ttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
EST: gi|33091065|gb|CF051059.1|CF051059
EST:     ATGATGGTCACTTCACAACATTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGCGATGCAGACAGCTCCTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAT
genomic: ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgacagttc ... ttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
EST: gi|211133498|gb|FL122205.1|FL122205
EST:     ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGACGCAGACAGCTCCTTGGACAGGCTGTGGCAAAAGAAGAAGGCTGAT
genomic: ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgacagttc ... ttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
EST: gi|6695761|gb|AW288839.1|AW288839
EST:     ATGATGGTCACTTCACAACATTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGCGACGCAGACAGCTCCTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAT
genomic: ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgacagttc ... ttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
EST: gi|9952632|gb|BE639320.1|BE639320
EST:     ATGATGGTCACTTCACAACATTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGCGATGCAGAC
genomic: ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgacagttc ... ttgtgcacagGGCGACGCAGAC
EST: gi|32843719|gb|CD983400.1|CD983400
EST:     ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGCGACGCAGACAGCTCCTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAT
genomic: ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgacagttc ... ttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
EST: gi|211181607|gb|FL122698.1|FL122698
EST:     ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT
genomic: ATGATGGTCACTTCACAACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgacagttc ... ttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggttgtccgttgtatagtggtagattctgattccatattttgttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGATATCAAGCAGTAGATTTTACATCTAGTTTACCAAGAATTGGACACTGCCT
                           ttctgat  putative branch site (score: 3)
                                        ttttgtt  putative PPT
                                     atattttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatatgttagtctagtggattgcccagttacctggtttgctatgtttggttgtccgttgtatagtggtagattctgattccatattttgttgtgcacagGGCGACGCAGACAGCTCCTTGGACAGGTTGTGGCAGAAGAAGAAGGTTGATATCAAGCAGTAGATTTTACATCTAGTTTACCAAGAATTGGACACTGCCT

- - - - - - - - - - -tgcccag
- - - - - - - - - - - - - - -tacctgg
- - - - - - - - - - - - - - - - - - - tgctatg
- - - - - - - - - - - - - - - - - - - - - - - ttggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gattctg