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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttctctttttgttgcaaattttccgtttggtttattctctttcataatagcttacattttctctgctaacttgggttctcaccag

Basic information

species Zea mays
transcript GRMZM2G113592_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113592_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os10g02630.1 (Oryza sativa), 5'ss of exon 7
GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttctctttttgttgcaaattttccgtttggtttattct--------ctttcataa-----tagcttacattttctctgctaacttgggttctcaccag
|| || ||||| || || || || |||| |||||||||||||||||||||||| |||||| ||||||| || ||||||||||||||   |     |||     |  |  ||  |   ||  | | |        |  | || |     |  |||||||||||||||||||  || |||||| |   
GTACGGCTTGTGACCGACAAGGAAACAAATAAACCTAGAGGATATGCATTCATCGAGTATATGCACACCCGGGACATGAAAAgtaaagcttctggtttagcatatctcctctatacagtccaatttggcgtcatcactgatgaagtgctgtcttacattttctctgctaatatgtgttctcgcag-

upper sequence: GRMZM2G113592_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA01G38120.1 (Glycine max), 5'ss of exon 7
GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttctctttttgttgcaaattttccgtttggtttattctctttcataatagcttacattttctctgctaacttgggttctcaccag
|||||  | ||  |||| |||||||||| ||| || || || ||||| |||||||||||| |||| ||| ||||||||||| ||             ||   |  |||      ||  ||| ||   | |||  || ||||  | ||    |  |   || | ||  ||    
GTTCGATTAGTTGCTGACAAAGATACAAATAAGCCCAGGGGTTATGCTTTCATTGAGTATCTGCATACAAGAGACATGAAAGgt-------------tgacactgatt----acttaatttgtttattatcactatggcttttaattcacatctttggtttgttttgcag---

upper sequence: GRMZM2G113592_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv04s0023g01580.t01 (Vitis vinifera), 5'ss of exon 7
GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttctctttttgttgcaaattttccgtttggtttattctctttcataatagcttacattttctctgctaacttgggttctcaccag
|| || ||  | || || ||||| || |||||||||||||| ||||| |||||||| ||| |||| ||||| || |||||| ||  | |       |||  |||  | ||   |||  | |  | |  || ||| |   || | |   | |  ||   ||| ||      |||
GTCCGACTCATTACCGACAAAGAGACTAGTAAACCTAGAGGTTATGCTTTCATTGAATATATGCATACACGGGATATGAAAGgtttgctatatagcttga-gcatttattggttttcatctgatgtgctttatattttgtttc-tgaacaccacttgtttgtgtcaaattcag

upper sequence: GRMZM2G113592_T02 (Zea mays), 5'ss of exon 7
lower sequence: PP1S42_265V6.1 (Physcomitrella patens), 5'ss of exon 7
GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagt----ttctctttttgttgcaaattt-tccgtttggtttattctctttcataatagcttacattttctctgctaacttg---ggttctcaccag-------------------------------------
|| || ||||||  ||| |||  | |||     ||  ||||||||||||| |||||||||  |||||| || ||||||||||||| ||    ||||    ||||       || ||| | |  |  ||| |   | |    |   | ||     |   | ||||||   | || |  |                                        
GTCCGACTTGTACATGATAAAACTTCAAAGGCTCCCCGAGGATATGCATTTATTGAGTATCAGCACACTCGGGACATGAAAAgtatgtgaagttcttcgcttgtcttgtccttatccatatcatacatttttggtga-ggcatgctgcagcgcttgcacaaacttgatagattgttgcttttggtagctttttgaagctatcatctgtgtgtgtgcag

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|148969418|gb|EE020215.2|EE020215
EST:     ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA                         ATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
genomic: ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
EST: gi|30087143|gb|CB885351.1|CB885351
EST:     ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA                         ATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
genomic: ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
EST: gi|15323613|gb|BI478906.1|BI478906
EST:     ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA                         ATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
genomic: ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
EST: gi|16137393|gb|BI894258.1|BI894258
EST:     TATGTGCACACACGAGACATGAAAA                         A-GCCTAC-AGCAAGCAGATGGGAGAAATGTGGACAACAGGGGGGTATTAG
genomic: TATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
EST: gi|16137326|gb|BI894191.1|BI894191
EST:     ACCTAGAGGA-ATGCA-TCATTGAGTATG-GCACACACGAGACATGAAAA                         ATGCCTACAAGCAAGCAGATGGGAGAAAAG-GGACAACAGGAGGGTATTAG
genomic: ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
EST: gi|149078708|gb|EE167506.2|EE167506
EST:     ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA                         AATGCCTACAAGCAAGCAGATGGG-GAAAA
genomic: ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagA-TGCCTACAAGCAAGCAGATGGGAGAAAA
EST: gi|71312602|gb|DR792823.1|DR792823
EST:     ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA                         ATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
genomic: ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
EST: gi|91873232|gb|EB403189.1|EB403189
EST:     ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA                         ATGCCTACCAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
genomic: ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
EST: gi|31358158|gb|CD442515.1|CD442515
EST:     ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA                         ATGCCTACCCAGCA-GCAGATGGGAGAAAAGTGGACA-CAAGAGGGTATTA
genomic: ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACA-AGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTA
EST: gi|91052321|gb|EB162739.1|EB162739
EST:     ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA                         ATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
genomic: ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
EST: gi|149072504|gb|EE160783.2|EE160783
EST:     ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA                         ATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
genomic: ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
EST: gi|30307225|gb|CD001898.1|CD001898
EST:     ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA                         ATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
genomic: ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
EST: gi|211227312|gb|FL251473.1|FL251473
EST:     TAGAGGATATGCATTCATTGGAGTATGTGCACACCACGAGACATGGAAAA                         ATGCCTACCAGGCAAGCCGATGGGGGAGAAAAAGTGGACAACAGGGAGGG
genomic: TAGAGGATATGCATTCATTG-AGTATGTGCACAC-ACGAGACATG-AAAAgtaagtttct ... ttctcaccagATGCCTACAAG-CAAGCAGATGGG--AGAAAA-GTGGACAACAGG-AGGG
EST: gi|211227315|gb|FL251476.1|FL251476
EST:     ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA                         ATGGCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGGAGGGTATTA
genomic: ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGG-AGGGTATTA
EST: gi|15313685|gb|BI478905.1|BI478905
EST:     ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA                         ATGCCTACAAGCAAGCAGATGGNGAGAAAAGTGGACAACAGGAGGGTATTA
genomic: ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACAAGCAAGCAGATGG-GAGAAAAGTGGACAACAGGAGGGTATTA
EST: gi|71310643|gb|DR791619.1|DR791619
EST:     ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA                         ATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
genomic: ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
EST: gi|16137392|gb|BI894257.1|BI894257
EST:     TCCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA                         ATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
genomic: ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
EST: gi|16137327|gb|BI894192.1|BI894192
EST:     ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA                         ATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG
genomic: ACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAG

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), 49 (downstream exon)
Score: 614

GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAGTTGATGTTGAGCGAGGCAGAACTGTTCCAAATTGGCGTCCTAGGAGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 314

GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAGTTGATGTTGAGCGAGGCAGAACTGTTCCAAATTGGCGTCCTAGGAGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 324

GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAGTTGATGTTGAGCGAGGCAGAACTGTTCCAAATTGGCGTCCTAGGAGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 472

GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttct ... ttctcaccagATGCCTACAAGCAAGCAGATGGGAGAAAAGTGGACAACAGGAGGGTATTAGTTGATGTTGAGCGAGGCAGAACTGTTCCAAATTGGCGTCCTAGGAGATT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAAgtaagtttctctttttgttgcaaattttccgtttggtttattctctttcataatagcttacattttctctgctaacttgggttctcaccag

- - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - -  GAGGAT