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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctatatcagtatcctctgtcagaacctattctaagttttggtagatgagaactaaaacacagctaactgttacatccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCTCGTGAAGGAGAGGCTGCCCAGGTTCACTCCTGAGCAGGCTAAACTGGTG

Basic information

species Zea mays
transcript GRMZM2G118003_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118003_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g49600.1 (Oryza sativa), 3'ss of exon 7
-----------------------------------------gtaagctatatcagtatcctctgtcagaacctattcta---agttttggtagatgagaactaa-------aacacagctaactgttacatccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCTCGTGAAGGAGAGGCTGCCCAGGTTCACTCCTGAGCAGGCTAAACTGGTG
                                          ||    ||   ||  |  |   ||  |    ||||||   || ||   |  |  |||| ||        |  |  |||||| ||| ||   | | ||||| | |||||||||||||||| ||||| || || ||||||||||||||||| ||||| || |||||||||| |||||||||||| || |||| | |||| 
gtaagaccataaagaatatcctctcagaaagcctattttttttagataatggaagctttattaatctcagtaaattctatcgagcttcattgaaaaagaattatcattgttaggattgctaacggttgcaatggtc-cagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCTTGTGAAAGATAGGCTGCCCAAGTTCACTCCTGAACAAGCTAGATTGGTC
















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|22546685|gb|BU098996.1|BU098996
EST:     CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTG                         GTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAAT
genomic: CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAAT
EST: gi|87157163|gb|DY401952.1|DY401952
EST:     CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTG                         GTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
genomic: CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
EST: gi|32846693|gb|CD986374.1|CD986374
EST:     CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTG                         GTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
genomic: CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
EST: gi|31611947|gb|CD568569.1|CD568569
EST:     CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTG                         GTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
genomic: CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
EST: gi|32846787|gb|CD986468.1|CD986468
EST:     CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGGCTTCCACATTGGCTG                         GTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
genomic: CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
EST: gi|211416183|gb|FL300110.1|FL300110
EST:     CCTGATGACCAAGCAGCAGCCCAAASAGCCAGGGACTTCCACATTGGCTG                         GTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
genomic: CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
EST: gi|32829422|gb|CD969100.1|CD969100
EST:     CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTG                         GTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
genomic: CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
EST: gi|18659314|gb|BM500272.1|BM500272
EST:     CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTG                         GTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
genomic: CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
EST: gi|32793518|gb|CD945754.1|CD945754
EST:     CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTG                         GTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATC
genomic: CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATC
EST: gi|29543733|gb|CB604113.1|CB604113
EST:     CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTG                         GTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
genomic: CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
EST: gi|60350347|gb|DN217320.1|DN217320
EST:     CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTG                         GTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
genomic: CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
EST: gi|32847767|gb|CD987448.1|CD987448
EST:     CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTG                         GTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
genomic: CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
EST: gi|31359746|gb|CD444103.1|CD444103
EST:     CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTG                         GTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
genomic: CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
EST: gi|31353887|gb|CD438244.1|CD438244
EST:     CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTG                         GTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
genomic: CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
EST: gi|32847456|gb|CD987137.1|CD987137
EST:     CCTGATGACCAAGTAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTG                         GTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
genomic: CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
EST: gi|32847506|gb|CD987187.1|CD987187
EST:     CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTG                         GTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
genomic: CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
EST: gi|211416180|gb|FL300107.1|FL300107
EST:     CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTG                         GTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT
genomic: CCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCT

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: 855

AGGTCGGAATAGTCCTGGACTTCAACTGGTACGAGGCTCTTACAAACTCACCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCTCGTGAAGGAGAGGCTGCCCAGGTTCACTCCTGAGCAGGCTAAACTGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 779

AGGTCGGAATAGTCCTGGACTTCAACTGGTACGAGGCTCTTACAAACTCACCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCTCGTGAAGGAGAGGCTGCCCAGGTTCACTCCTGAGCAGGCTAAACTGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 183

AGGTCGGAATAGTCCTGGACTTCAACTGGTACGAGGCTCTTACAAACTCACCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCTCGTGAAGGAGAGGCTGCCCAGGTTCACTCCTGAGCAGGCTAAACTGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 502

AGGTCGGAATAGTCCTGGACTTCAACTGGTACGAGGCTCTTACAAACTCACCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaagctata ... tccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCTCGTGAAGGAGAGGCTGCCCAGGTTCACTCCTGAGCAGGCTAAACTGGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaagttttggtagatgagaactaaaacacagctaactgttacatccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCTCGTGAAGGAGAGGCTGCCCAGGTTCACTCCTGAGCAGGCTAAACTGGTG
                               agctaac  putative branch site (score: 502)
                    aactaaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctatatcagtatcctctgtcagaacctattctaagttttggtagatgagaactaaaacacagctaactgttacatccgacgcagGTTTGTTGATCCATTGATAAACGGACACTATCCACAGATAATGCAAGATCTCGTGAAGGAGAGGCTGCCCAGGTTCACTCCTGAGCAGGCTAAACTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG