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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccctagttatttcaacacatttatatgacacccgaatttaaggacaaatccgaatgcatcttacatgcgtgacaggatcaagtatcacacata...

Basic information

species Zea mays
transcript GRMZM2G128877_T03
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128877_T03 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 16
CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccctagttatttcaacacatttatatgacacccgaatttaaggacaaatccgaatgcatcttacatgcgtgacaggatcaagtatcacacata
|||||||||||||| || |||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||||||||| |||||||||||     |   |||| |    | || ||  | ||| |  |   |   || ||           | |  |  ||  || ||   ||           
CTTGTTGGTAAAGACGCACTGGCAGAATCTGACAAGATTACACTGGAGACAGCAAAACTTCTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCCgtgagtgttaaacccatttga---tagttctacta-acctgtgtcataatccatattaactaattgatcaattctgttgcatgaaacag-----------

upper sequence: GRMZM2G128877_T03 (Zea mays), 5'ss of exon 13
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 17
CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtccc----ctagttatttcaacacatttatatgacacccga-----atttaaggacaaat-ccgaatgcatc---ttacatgcgtgac-aggatcaagtatcacacata----------------------------
||||| || ||||||||  | || ||| | || || ||||| || ||||| ||||||||  |||| ||||| ||| | |||||||||||||||||||||| ||||||      |||| ||    || ||||   |        |      ||||   || | | ||  |||   |   ||  ||||  | | || |     | |  ||| ||                            
CTTGTCGGAAAAGATGCTTTAGCTGAAACAGATAAAATTACTCTAGAGACTGCAAAGCTTTTGAGGGAAGACTATCTTGCACAAAATGCATTTACCCCgtaagtcccagattaagtttttgattcaaattttcgtcctttttaatttttgtttacttactatttccttatgttcccctttttatgctggtctagaaattctttttccacttaatatatgtatctcatgtggctgtgacag
















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|32929207|gb|CF034019.1|CF034019
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|60338201|gb|DN205174.1|DN205174
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|5770168|gb|AI973342.1|AI973342
EST:     CACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: CACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|13149764|gb|BG320086.1|BG320086
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|32831320|gb|CD970998.1|CD970998
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|4646572|gb|AI491316.2|AI491316
EST:     AAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: AAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|32928400|gb|CF033212.1|CF033212
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|32837774|gb|CD977452.1|CD977452
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|5296280|gb|AI783050.1|AI783050
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|5846764|gb|AI999847.1|AI999847
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|32939925|gb|CF044744.1|CF044744
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGC-CAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|211532168|gb|FL123442.1|FL123442
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTT
EST: gi|211152801|gb|FL123511.1|FL123511
EST:     ACAGCRAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGAWAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|5847131|gb|AW000210.1|AW000210
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|5804554|gb|AI979524.1|AI979524
EST:     AAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: AAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|33092495|gb|CF052489.1|CF052489
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAAATCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|5846817|gb|AI999900.1|AI999900
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|5846863|gb|AI999946.1|AI999946
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|67040096|gb|CO466351.1|CO466351
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|149076737|gb|EE165383.2|EE165383
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|32836684|gb|CD976362.1|CD976362
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|83278503|gb|DV942511.1|DV942511
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|5343199|gb|AI795384.1|AI795384
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|5296225|gb|AI782905.1|AI782905
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|5325051|gb|AI783242.1|AI783242
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|211156008|gb|FL123543.1|FL123543
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|32910829|gb|CF015641.1|CF015641
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
EST: gi|67025855|gb|CO454604.1|CO454604
EST:     ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC                         ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT
genomic: ACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccc ... ttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCCgtgagtcccctagttatttcaacacatttatatgacacccgaatttaaggacaaatccgaatgcatcttacatgcgtgacaggatcaagtatcacacata

- - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaggacaa