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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGATGTCCCAATCAAATACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactacagatttgtgttgtatatacataatttatcattgtgaaaacacttaagttgtgcttacatttgcaaacacaaacaccag

Basic information

species Zea mays
transcript GRMZM2G002687_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002687_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os12g35570.3 (Oryza sativa), 5'ss of exon 9
-------------------GTGGATGTCCCAATCAAATACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattacta-------cagatttgt-gttgtatatacataatttatcattgtgaaaacacttaagttgt--gcttacatttgcaaacacaaacaccag-------------
                   |||||||| |||||||| ||||||||||||||||||||||||||  | ||||| | ||||||||| |||||| ||| |        | || ||| |  |  || |  ||||||  | |  ||       ||||  |||   |||  | |      | | ||||                 
TTGTGATTGTGATGTTCAGGTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAGCTCGAGCACATAAAGAAGgtaatacaaattatgctatatatgtagaggcgtagagctaatttgcc-tgatgtgtttctttaacatgttttcttcaactgatttccgctaacatttctgaaactcatcag

upper sequence: GRMZM2G002687_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os12g35570.2 (Oryza sativa), 5'ss of exon 8
GTGGATGTCCCAATCAAATACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattacta-------cagatttgt-gttgtatatacataatttatcattgtgaaaacacttaagttgt--gcttacatttgcaaacacaaacaccag-------------
|||||||| |||||||| ||||||||||||||||||||||||||  | ||||| | ||||||||| |||||| ||| |        | || ||| |  |  || |  ||||||  | |  ||       ||||  |||   |||  | |      | | ||||                 
GTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAGCTCGAGCACATAAAGAAGgtaatacaaattatgctatatatgtagaggcgtagagctaatttgcc-tgatgtgtttctttaacatgttttcttcaactgatttccgctaacatttctgaaactcatcag

upper sequence: GRMZM2G002687_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os07g17770.1 (Oryza sativa), 5'ss of exon 7
GTGGATGTCCCAATCAAATACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactacagatttgtgttgtatatacataatttatcattgtg---aaaacacttaagttgtgcttacatttgcaaacacaaacaccag
||||||||| ||||||| ||||| |||||||||||  |||| ||||| ||||||| ||||||||| |||||   | | |  ||| |||    |   |  |    || |||| |     |||| | | |    |  | | ||||       | || |||||
GTGGATGTCTCAATCAAGTACCTAAACTTCTTCCTACAAGACGATGATGAGCTTGAGCACATAAAGAAGgtgc-atttcttatt-gtggaaaactaagttgcactaccattatatatgaaactcattatccattataaaatttatt--tcccaataccag

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|37395551|gb|CF635056.1|CF635056
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|6020814|gb|AW065742.1|AW065742
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGAGGGA
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGA
EST: gi|91876014|gb|EB405971.1|EB405971
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|211179082|gb|FL345825.1|FL345825
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|71765216|gb|DR963153.1|DR963153
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|148935573|gb|EC879616.2|EC879616
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTGGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|9953034|gb|BE639617.1|BE639617
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|149010068|gb|EE041875.2|EE041875
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|149108285|gb|EE292625.2|EE292625
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|111192905|gb|EE291041.1|EE291041
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|110520053|gb|EE024360.1|EE024360
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|67030403|gb|CO459152.1|CO459152
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|211149406|gb|FL319865.1|FL319865
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|37373821|gb|CF623233.1|CF623233
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|149073833|gb|EE162155.2|EE162155
EST:     ACCTGAACTTTTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|60354415|gb|DN221388.1|DN221388
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|113701058|gb|EE678562.1|EE678562
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGTGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|5871148|gb|AW017589.1|AW017589
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|7844633|gb|AW787855.1|AW787855
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|211181701|gb|FL465356.1|FL465356
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGA-STTGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|71305907|gb|DR789080.1|DR789080
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
EST: gi|211274585|gb|FL461449.1|FL461449
EST:     ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG                         GAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT
genomic: ACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATT

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), 47 (downstream exon)
Score: 292

GTGGATGTCCCAATCAAATACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATTGCAGTTCTATCTGAGATTGTTGCTAGACACCAGAGAGCTAGAGCTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 323

GTGGATGTCCCAATCAAATACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATTGCAGTTCTATCTGAGATTGTTGCTAGACACCAGAGAGCTAGAGCTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 349

GTGGATGTCCCAATCAAATACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATTGCAGTTCTATCTGAGATTGTTGCTAGACACCAGAGAGCTAGAGCTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 253

GTGGATGTCCCAATCAAATACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactac ... caaacaccagGAGTACAAGGAGGGAAGGATGTTGACTGGTGAAGTGAAGCAACGGCTTATTGCAGTTCTATCTGAGATTGTTGCTAGACACCAGAGAGCTAGAGCTCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGATGTCCCAATCAAATACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAGgtattactacagatttgtgttgtatatacataatttatcattgtgaaaacacttaagttgtgcttacatttgcaaacacaaacaccag

- - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - GAGCTT