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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttggaaataagattttacattacttgcatcttgacaactgctttctttagaatattgcattttgtgttcctatacaaccatcttgctgcatcttg...

Basic information

species Zea mays
transcript GRMZM2G147145_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147145_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os06g49810.1 (Oryza sativa), 5'ss of exon 8
TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttggaaataagattttac-attacttgcatcttgaca-actgctttctttagaatattgcattttgtgttcctatacaaccatcttgctgcatcttg
||||||||| ||||| ||||| ||||||||||| ||||||||| ||||||||||||||||||| ||||||||||| ||||| |||||||||||||||||||| ||||| ||  | | || ||  | |  || ||| ||     |    ||||  | | | ||| | ||| |   |   || |||   |   | | |  |   
TCCTAATGCTTGTGGCTGGGCGTATGGAATGAATATGTTTGATTTGGAAGAATGGAAGAAGAAGGACATTACTGGCATTTATCACAAATGGCAGAACATGgtaagttgaaataaggtttatattactgtttccatttttctgtagaaatttcaatggcaaatttc-tttcgctataacatgcaatatttcagtttctgcaa-

upper sequence: GRMZM2G147145_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA18G45750.1 (Glycine max), 5'ss of exon 8
TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgag---ttggaaataagatt---ttacattacttgcatcttgacaactgctttctttagaatattgcattttgtgttcctatacaaccatcttgctgcatcttg
 || ||||| ||||||||||| || || ||||||||||||||| || | |  ||||| ||||| ||||| ||||| || || ||||| ||||||||  |||||||   ||| | || | |||   |||||| |  ||  | ||   |  |  |    | |  | |   ||  ||    | || || |   ||   | | |   |  
-CCAAATGCTTGTGGTTGGGCATACGGGATGAACATGTTTGATTTGAAGGTGTGGAAAAAGAAGGACATCACTGGCATATATCACAAGTGGCAGAATTTGGtgagaagttgaacattacattggtttacatcaaatgtctattcttacataataagatgactacag-acagatttaactgctctaaagggata--gttaccctt--

upper sequence: GRMZM2G147145_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA07G08910.1 (Glycine max), 5'ss of exon 6
TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttgg-aaataagattttacattacttgcatcttgacaactgctttctttagaatattgcattttgtgttcctatacaaccatcttgctgcatcttg-
|||  |||| ||||||||||| || || |||||||||||||||||| | |  ||||| ||||| || || || || || || ||||| |||||||| ||||| ||  |   || ||    ||   |||| |  ||  |     ||  | ||      |||    |  || |   |  |        |  || |  ||  |  
TCCACATGCTTGTGGTTGGGCATACGGGATGAACATGTTTGATCTGAAGGTGTGGAAAAAGAAGGATATCACCGGCATATATCACAAGTGGCAGAATATGgtaagcagatgaacaaagcattggtttacataaattgt-----ctattctcgcacagatagaagagatt-ttcactgacttgttttttctgtttgattctag

upper sequence: GRMZM2G147145_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA03G02250.1 (Glycine max), 5'ss of exon 14
TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttg-gaaataagattttacattacttgcatcttgacaactgctttctttagaatattgcattttgtgttcctatacaaccatcttgctgcatcttg------
||| ||||| ||||||||||| || || |||||||||||||||||| | |  ||||| ||||| || || || || || || ||||| |||||||| ||||| ||    | ||  |    ||   |||| |  ||  |     ||        ||||||   |   |     ||  |     ||    ||| |   | |        
TCCAAATGCTTGTGGTTGGGCATACGGGATGAACATGTTTGATCTGAAGGTGTGGAAAAAGAAGGATATCACCGGCATATATCACAAGTGGCAGAATATGgtaagcaaaggaacgaagcattggtttacatcaattgtctattctcacacaaatagaatgcaggtatggagatttttcactgacttgtttgttatgtttgattctag

upper sequence: GRMZM2G147145_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA09G40260.1 (Glycine max), 5'ss of exon 9
TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgag---ttggaaataagatt---ttacattacttgcatcttgacaactgctttctttagaatattgcattttgtgttcctatacaaccatcttgctgcatcttg
||| ||||| ||||||||||| || || ||||||||||||||| || | |  ||||| ||||| ||||| ||||| || || ||||| ||||||||  |||||||   ||| | |||| |||   |||||| || ||  | ||   |  |  |    | |  | |   ||  ||    |||| || |   |    | | |      
TCCAAATGCTTGTGGTTGGGCATACGGGATGAACATGTTTGATTTGAAGGTGTGGAAAAAGAAGGACATCACTGGCATATATCACAAGTGGCAGAATTTGgtgagcagttgaacataacattggtttacatcacatgtctgttcttacataataagatgactacag-acagatttaactcctctaaagggaga--gttaccct---

upper sequence: GRMZM2G147145_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT2G46480.1 (Arabidopsis thaliana), 5'ss of exon 5
TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttggaaataagattttacattacttgcatcttgacaactgctttct-ttagaatattgcattttgtgttcctatacaaccatcttgctgcatcttg
||| ||    || || ||||||||||| |||||||| || || ||| ||||||||||||||||  ||||||| | || ||| |||   ||||| ||| |||| || |          | ||   |||  |  |   | | ||||| | |   ||  | |   |  |  | ||||  |   |     | |||| |       
TCCCAAGTTCTGCGGATGGGCTTATGGGATGAACATCTTCGACCTGAAAGAATGGAAGAAGAACAACATTACAGAAACTTATCACTTTTGGCAAAACCTGgtcagct-----cttcttcttggcttatctttaatctaa-aactgttgtagatttaagttgagagtgatatgttattcccctgt--ttttgcag-------

upper sequence: GRMZM2G147145_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv15s0048g01300.t01 (Vitis vinifera), 5'ss of exon 9
TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttggaaataagattttacattacttgcat-cttgacaactgctttctttagaat--attgcattttgtgttcctatacaaccatcttgctgcatcttg
||| ||||| ||||| ||||| |||||||||||||| ||||||||  | || ||||  |  |  || |||||||| || || || || ||||||||||||||||||     |  | || |    ||| |||||| |||      |  ||  |||| ||   |||   |||  ||    |  |     || ||  |  | |   
TCCAAATGCTTGTGGGTGGGCATATGGAATGAACATTTTTGATCTCAAGGAGTGGACAAGAAGGGATATTACTGGCATATATCATAAGTGGCAGAACATGgtgagtctttgaataaatctcgttttatttgcatgctttgtgtttttttcttttacaaacaattttttttcatgcatgtgaatgtttatgttatttgacc---

upper sequence: GRMZM2G147145_T02 (Zea mays), 5'ss of exon 5
lower sequence: PP1S251_8V6.1 (Physcomitrella patens), 5'ss of exon 9
TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttggaaataagattttacattacttgcatcttgacaactgctttctttagaatattgc--attttgtgttcctatacaaccatcttgctgcatcttg
  |  |||| ||||||||||| |||||||||||||| |||||| || |  ||||||| |   ||||||| || || |||||||| |||||||| | ||||||  || | |  |  |||||     ||           ||| |   |||   | ||  ||  |  | ||  ||| | ||| ||    |  | |   ||  | 
ATCAGATGCTTGTGGTTGGGCCTATGGAATGAACATTTTTGATTTGAAGCAATGGAAAATCCAAGACATCACGGGTATTTACCATAAATGGCAAAGCATGgtatgt-gaacctctgatttccatatatccttgagcaaacaccatttttaactggatcatctctaagttattgtgcatat-cagttgtgcttcaatatactt

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|211270161|gb|FL453294.1|FL453294
EST:     AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATG                         AACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
genomic: AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttgga ... ctttgtacagAACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
EST: gi|148962191|gb|EE013006.2|EE013006
EST:     AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATG                         AACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
genomic: AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttgga ... ctttgtacagAACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
EST: gi|60396687|gb|DN229554.1|DN229554
EST:     AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATG                         AACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
genomic: AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttgga ... ctttgtacagAACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
EST: gi|67019228|gb|CO447977.1|CO447977
EST:     AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATG                         AACGAGAATAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
genomic: AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttgga ... ctttgtacagAACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
EST: gi|60347201|gb|DN214174.1|DN214174
EST:     AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATG                         AACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
genomic: AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttgga ... ctttgtacagAACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
EST: gi|32849365|gb|CD989046.1|CD989046
EST:     AATGGAAGAAGAAAGACATTACTGGAATTTCCCACAAATGGCAGAACATG                         AACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
genomic: AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttgga ... ctttgtacagAACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
EST: gi|76018864|gb|DT946034.1|DT946034
EST:     AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATG                         AACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
genomic: AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttgga ... ctttgtacagAACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
EST: gi|51592296|gb|CV071442.1|CV071442
EST:     AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATG                         AACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
genomic: AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttgga ... ctttgtacagAACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
EST: gi|60345745|gb|DN212718.1|DN212718
EST:     AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATG                         AACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
genomic: AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttgga ... ctttgtacagAACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
EST: gi|211198454|gb|FL128767.1|FL128767
EST:     AATGGAAGAAGAAAGACATTACTGTAATTTACCACAAATGGCAGAACATG                         AACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
genomic: AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttgga ... ctttgtacagAACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
EST: gi|149081488|gb|EE170623.2|EE170623
EST:     AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATG                         AACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
genomic: AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttgga ... ctttgtacagAACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
EST: gi|71312998|gb|DR793023.1|DR793023
EST:     AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATG                         AACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA
genomic: AATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttgga ... ctttgtacagAACGAGAACAGGCTGCTCTGGAAACTGGGGACATTGCCACCAGGGCTTCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATTTACCACAAATGGCAGAACATGgtgagttggaaataagattttacattacttgcatcttgacaactgctttctttagaatattgcattttgtgttcctatacaaccatcttgctgcatcttg

- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA