Skip to another splice site:
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 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaacagcataagcatttcgctgcctgggcacctgtggcaagtgcattgtgtatcctcatccatagcttacaatttgtgtttgtcatatgtatcccatgccttcactccag

Basic information

species Zea mays
transcript GRMZM2G143213_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143213_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g02680.1 (Oryza sativa), 5'ss of exon 5
GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagaca--acagcataagcatttcgctgcctgggcacctgtggcaagtgcattgtgtatcctcatccatagcttacaatttgtgtttgtcatatgtatcccatgccttcactccag
||| ||||| || || ||||||||| ||||||| ||||| || |  || ||||||| |||| |||||||||||| ||||||||| |||||| ||||  |||||||||  ||||   |    |||          || |||||    ||| ||   |||   || | | |   ||  ||  || |  ||||||              
GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAAGCACAGgtatgacaaaacagcataaagattttattaggcgggtg--------aactgcatc-catatactgtgcca---ctaatattccttgactgaaatcttcatcccag-------------

upper sequence: GRMZM2G143213_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g01850.2 (Oryza sativa), 5'ss of exon 6
GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagaca--acagcataagcatttcgctgcctgggcacctgtggcaagtgcattgtgtatcctcatccatagcttacaatttgtgtttgtcatatgtatcccatgccttcactccag
||| ||||| || || ||||||||| ||||||| ||||| || |  || ||||||| |||| |||||||||||| |||||| || |||||| ||||  |||||||||  ||||   |    |||          || |||||    ||| ||   |||   || | | |   ||  ||  || |  ||||||              
GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaaacagcataaagattttattaggcgggtg--------aactgcatc-catatactgtgcca---ctgatattccttgactgaaatcttcatcccag-------------
















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|18166338|gb|BM336177.1|BM336177
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|78093070|gb|DV521444.1|DV521444
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|60397283|gb|DN230099.1|DN230099
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|27575994|gb|CA998688.1|CA998688
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|5847313|gb|AW000392.1|AW000392
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|91051178|gb|EB161596.1|EB161596
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|32916297|gb|CF021109.1|CF021109
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|31910663|gb|CD651537.1|CD651537
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|60394332|gb|DN227202.1|DN227202
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|110194217|gb|EC876115.1|EC876115
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|60344999|gb|DN211972.1|DN211972
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|60394730|gb|DN227600.1|DN227600
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|78074515|gb|DV502949.1|DV502949
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|60398759|gb|DN231575.1|DN231575
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|67024512|gb|CO453261.1|CO453261
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|31909621|gb|CD651010.1|CD651010
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|18166704|gb|BM336543.1|BM336543
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|18650116|gb|BM498935.1|BM498935
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAATCTCAG                         GACCTGGCAACAATAGTCCCAAATCTTGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|4967063|gb|AI692029.1|AI692029
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTGAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|37384260|gb|CF629190.1|CF629190
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAATCTCAG                         GACCTGGCAATAATAGTCCCAAATCTTGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|17929629|gb|BM266589.1|BM266589
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|18162372|gb|BM332211.1|BM332211
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|18167215|gb|BM337054.1|BM337054
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|60398446|gb|DN231262.1|DN231262
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAATCTCAG                         GACCTGGCAATAATAGTCCCAAATCTTGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|12968998|gb|BG265943.1|BG265943
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTGAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|78025082|gb|DV493469.1|DV493469
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTGAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|18163570|gb|BM333409.1|BM333409
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|5525594|gb|AI861487.1|AI861487
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|5819371|gb|AI987577.1|AI987577
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
EST: gi|211268426|gb|FL478582.1|FL478582
EST:     TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG                         GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC
genomic: TCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 113

GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 67

GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 44

GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 59

GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaac ... ttcactccagGACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagacaacagcataagcatttcgctgcctgggcacctgtggcaagtgcattgtgtatcctcatccatagcttacaatttgtgtttgtcatatgtatcccatgccttcactccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA