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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGAAGCCGCCGCCGTACAAGGACCCTGACAATGGGAGTCAGCGATTCCTACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtactgtcctccattctcttgtttcatctcaccttgttgggattagctaatctgatgttgcacgcatctatagaacgttttcctgtaccggtttg...

Basic information

species Zea mays
transcript GRMZM2G139683_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139683_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g41450.1 (Oryza sativa), 5'ss of exon 2
GGGAAGCCGCCGCCGTACAAGGACCCTGACAATGGGAGTCAGCGATTCCTACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtactgtcctccattctcttgtttcatctcaccttgttgggattagctaatctgatgttgcacgcatctatagaacgttttcctgtaccggtttg----
  | || |   ||||      |||||  || | | ||| ||||| ||| |  | ||| | |||||| | ||||||||||| |||||||||||||||||||||||||||||||  |||    ||| |||||| ||   ||||  ||| ||  |        | ||       | ||| ||||   ||  |||      ||     
CCGGAGGCAATGCCGGCGCCTGACCCCAACGACGCGAGGCAGCGGTTCTTGTTGGAGCTCGAGTTCATCCAGTGCCTCGCAAACCCTACCTACATCCACTgtactgtactgta-tcctcgttctcgtttca-cttggcttg--gggttttaccgcggatcttttcattaggtttattgaacaaattagtgtttaatctttgact

upper sequence: GRMZM2G139683_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g07020.2 (Oryza sativa), 5'ss of exon 1
---GGGAAGCCGCCGCCGTACAAGGACCCTGACAATGGGAGTCAGCGATTCCTACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtactgtcctccattctcttgtttcatctc-----accttgttgggatt----agctaatctgatgttgcacgcatctatagaacgttttcctgtaccggtttg
   |  | |||  |||||      |||||  || | | ||| ||||| ||| |  | ||| | |||||| | |||||||||||||||||||||||||||||||||| |   |  | | |     |    ||||| |||     |  || || || ||    | | ||| |   ||   | |||  ||   ||| |  |    |         
GAGGCAAGGCCCGCGCCGCCT---GACCCCAACGACGCGAGGCAGCGGTTCTTGTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACTgtaattctcgtttcacttggtttggatttcacctcgggtcattttattaggtttctgaaacaaattttgggtgata-gcacatagctaacttcgtttcttc--------

upper sequence: GRMZM2G139683_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA10G38750.2 (Glycine max), 5'ss of exon 3
GGGAAGCCGCCGCCGTACAAGGACCCTGACAATGGGAGTCAGCGATTCCTACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtactgtcc--tccattctcttgtttcatctcaccttgttgggattagcta-atctgatgttgcacgcatctatagaacgttttcctgtaccggtttg
|  ||    |     ||||| || || ||  |||||   ||||| ||  | || || |||||||| || |||||||| ||||| ||||||||||||||||||||  |  |  |   |  |||   | |||||| ||  | |||     | || ||  ||||| || |    |||  ||   |  ||| |     ||       
GCCAAAGAAC--ATATACAAAGATCCAGATGATGGGCAGCAGCGCTTTTTGCTTGAATTGGAGTTTGTTCAGTGCCTTGCCAATCCTACCTACATCCACTgtacgattttaactatttgatttgatggtttcagctt-cattgaacaaaatatctgcatctgttgattgttgcaagtaattagtgttctttgacacaacag--

upper sequence: GRMZM2G139683_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA20G28990.1 (Glycine max), 5'ss of exon 2
GGGAAGCCGCCGCCGTACAAGGACCCTGACAATGGGAGTCAGCGATTCCTACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtactgtcctccattctcttgtttcatctcaccttgttgggattagcta-atctgatgttgcacgcatctatagaacgttttcctgtac--cggtttg
|  ||    |     ||||| || || ||  |||||   ||||| ||  | || || |||||||| || |||||||| ||||| |||||||||||||||||||   |  |  | |  |||   | |||||| ||  | |||     | || ||  ||||| || |    |||  ||   |   || |     ||  | | |  
GCCAAAGAAC--ATATACAAAGATCCAGATGATGGGCAGCAGCGGTTTTTGCTTGAATTGGAGTTTGTTCAGTGCCTTGCCAATCCTACCTACATCCACTgtatgattttcactttgatttgatagtttcagctt-cattgaacaaaatacctgcatctgttgattgttgcaagtaattagttttctttgacacaacagct--

upper sequence: GRMZM2G139683_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ18119 (Selaginella moellendorffii), 5'ss of exon 1
--GGGAAGCCGCCGCCGTACAAGGACCCTGACAATGGGAGTCAGCGATTCCTACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtactgtcctccattctcttgtttcatctcaccttgttgggattagctaatctgatgttgcacgcatctatagaacgttttcctgtaccggtttg
   | ||      |  ||  |  |  |  ||    ||| | ||| ||||  |  | ||| |||||||||| ||||||||||| ||||| |||||||| |||||||| ||| |||  ||| | || | | ||  |     ||  | ||   | | |   ||  ||  |                                   
TTAGCAATGGAGAGTGGTGAAGAGGTC--GATGGAGGGCGGCAGAGATTTTTGTTGGAGCTGGAGTTCGTCCAGTGCCTCGCAAACCCGACCTACATTCACTgtac-gtattgtt-tccctgctttggctttgtgatcgctgatgggtgattgttg-ccttttgcag-----------------------------------

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|211343281|gb|FL146112.1|FL146112
EST:     ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATT-ATCGGGTACCTCA
genomic: ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtact ... tcccaaatagATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
EST: gi|211340893|gb|FL146102.1|FL146102
EST:     ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
genomic: ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtact ... tcccaaatagATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
EST: gi|211343280|gb|FL146111.1|FL146111
EST:     ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
genomic: ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtact ... tcccaaatagATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
EST: gi|71765862|gb|DR963799.1|DR963799
EST:     ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
genomic: ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtact ... tcccaaatagATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
EST: gi|211343276|gb|FL146107.1|FL146107
EST:     ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATT-ATCGGGTACCTCA
genomic: ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtact ... tcccaaatagATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
EST: gi|28910217|gb|CB331329.1|CB331329
EST:     ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
genomic: ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtact ... tcccaaatagATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
EST: gi|26559121|gb|CA831356.1|CA831356
EST:     ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
genomic: ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtact ... tcccaaatagATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
EST: gi|211343275|gb|FL146106.1|FL146106
EST:     ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
genomic: ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtact ... tcccaaatagATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
EST: gi|94479606|gb|EB708564.1|EB708564
EST:     ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
genomic: ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtact ... tcccaaatagATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
EST: gi|87157028|gb|DY401817.1|DY401817
EST:     ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
genomic: ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtact ... tcccaaatagATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
EST: gi|22521504|gb|BU080315.1|BU080315
EST:     ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
genomic: ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtact ... tcccaaatagATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
EST: gi|211340894|gb|FL146103.1|FL146103
EST:     ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
genomic: ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtact ... tcccaaatagATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
EST: gi|60352751|gb|DN219724.1|DN219724
EST:     ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
genomic: ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtact ... tcccaaatagATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
EST: gi|211343278|gb|FL146109.1|FL146109
EST:     ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
genomic: ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtact ... tcccaaatagATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
EST: gi|211340891|gb|FL146100.1|FL146100
EST:     ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACKCTACCTACATCCACT                         ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTA
genomic: ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtact ... tcccaaatagATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTA
EST: gi|211340890|gb|FL146099.1|FL146099
EST:     ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATT-ATCGGGTACCTCA
genomic: ACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtact ... tcccaaatagATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
EST: gi|5901084|gb|AW042184.1|AW042184
EST:     CCAACCCTACCTACATCCACT                         ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA
genomic: CCAACCCTACCTACATCCACTgtactgtact ... tcccaaatagATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGAAGCCGCCGCCGTACAAGGACCCTGACAATGGGAGTCAGCGATTCCTACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtactgtcctccattctcttgtttcatctcaccttgttgggattagctaatctgatgttgcacgcatctatagaacgttttcctgtaccggtttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG