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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttccttcgctaaccacttacatgctgtcttccttctgtcctaaatttcccatctcacttattaccctggtttgttgatctgttttgcttccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAATATCATGGAGTTCCTTATTCTGGCTGGAGATCATCTGTACCGTATGGATT

Basic information

species Zea mays
transcript GRMZM2G106213_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106213_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 2
--------tttccttcgctaaccacttacatgctgtcttccttctgtcctaaatttcccatctcacttattaccctggtttgttgatctgttttgcttccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAATATCATGGAGTTCCTTATTCTGGCTGGAGATCATCTGTACCGTATGGATT
          || |  | || | |||| |||| | | |   ||||||   | | | ||        | |  || |||  |  || || |  |||  |||  | ||||||||||||||||||| ||||| |||||  | |||||||||||||| || ||| | |||||||| || ||| ||||||||||||| |||||||||||||| |
atagatgagctcttaggttaccaactttcatgttatatggtttctgtatgacaatacct-------taaggacgctgcctaatttattttgtttctttctgt-ctcagGGTACTGCAGATGCTGTGCGACAATACTTATGGCTATTTGAGGAACACAATGTTATGGAGTTTCTCATTTTGGCTGGAGATCACCTGTACCGTATGGACT
















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|148987334|gb|EE031175.2|EE031175
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|60355358|gb|DN222331.1|DN222331
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCACAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|67027741|gb|CO456490.1|CO456490
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATGTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|71303914|gb|DR788076.1|DR788076
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|148966536|gb|EE017559.2|EE017559
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCCACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|148950461|gb|EC896031.2|EC896031
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|31354893|gb|CD439250.1|CD439250
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|154130546|gb|EC872338.2|EC872338
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|31356252|gb|CD440609.1|CD440609
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|211191066|gb|FL114963.1|FL114963
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCG
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCG
EST: gi|148967973|gb|EE019294.2|EE019294
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|6564057|gb|AW231679.1|AW231679
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcccatctcacttattaccctggtttgttgatctgttttgcttccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAATATCATGGAGTTCCTTATTCTGGCTGGAGATCATCTGTACCGTATGGATT
                                     ttttgcttccattctc  CT-rich tract
           acttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttccttcgctaaccacttacatgctgtcttccttctgtcctaaatttcccatctcacttattaccctggtttgttgatctgttttgcttccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAATATCATGGAGTTCCTTATTCTGGCTGGAGATCATCTGTACCGTATGGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA