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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttttttgcttgcctaacttcagtcatataatttcttaaagaactacatgttaaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG

Basic information

species Zea mays
transcript GRMZM2G005493_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 14
gtaatttttttgcttgcctaacttcagtcatataatttcttaaag----------aactacatgttaaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG
|| | ||| |||||| |||||| ||| |||    |  |   |  |          |||| ||||  ||| |||||||||||| ||||| || ||||||||| | |||||||| ||||||||||| |||||||| |||||||||||||| ||  | |
gttagtttcttgcttccctaacgtcattcaaggtagcttacagtggcagtgtcataactccatggaaaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG

upper sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 14
---------------------------------------------------------------gtaatttttttgcttgcctaacttcagtcatataatttcttaaagaactacatgttaaacttg-cagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG
                                                                || |  |    | |  || |     | ||  |  ||| |      | |   ||||  || ||  || || |||||||| || || |||||| | || |||||  |||| || || |||||||||||||||||||||||||||||||
gtgaatcgatcattgtatattgtgtttacatgggctgtccttgatctttcccttttaaatttgatattcataaatcataactgaaactggacacgttctttgtacttacaatttctgttgtacctggtagTTGTCATCATGAGCTCGAAACTGCAAGGATCAATGGATTGCTGGGTAATATTGATGCAAACACTGGTGATCCTCAAGTTG
















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|60337180|gb|DN204153.1|DN204153
EST:     AATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG                         CTGCCATCATGAACTGNAGACTGCACGCATTAATGGGCTGCTTGGAAACAT
genomic: AATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|211174464|gb|FL381682.1|FL381682
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|32836432|gb|CD976110.1|CD976110
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|211379703|gb|FL400539.1|FL400539
EST:     CAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
genomic: CAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|32844741|gb|CD984422.1|CD984422
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGGTTGGGAACAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|67027757|gb|CO456506.1|CO456506
EST:     GAGTTCAAGATTAATGTTGAGTGCA-CCATGCTACTCTATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|32838372|gb|CD978050.1|CD978050
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|60346929|gb|DN213902.1|DN213902
EST:     AGTGCAACCATGCTACTCTATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
genomic: AGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|32935034|gb|CF039846.1|CF039846
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|211459151|gb|FL411539.1|FL411539
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|211215524|gb|FL427999.1|FL427999
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCT--T-GGGAACAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|32844417|gb|CD984098.1|CD984098
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|67019408|gb|CO448157.1|CO448157
EST:     GAGTTCAAGAATAATGTNGAGTGCAACCATGCTACTCTATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|211214717|gb|FL394674.1|FL394674
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|60337495|gb|DN204468.1|DN204468
EST:     ATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
genomic: ATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|67037452|gb|CO464268.1|CO464268
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|6012630|gb|AW062067.1|AW062067
EST:     ATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
genomic: ATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|32838758|gb|CD978439.1|CD978439
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|60353702|gb|DN220675.1|DN220675
EST:     ATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
genomic: ATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|67010832|gb|CO439581.1|CO439581
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
EST: gi|32837235|gb|CD976913.1|CD976913
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGTTACTCTATCTGGACATAG                         CTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACAT

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: 358

GAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 388

GAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 363

GAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 651

GAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAGgtaatttttt ... aaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttgcctaacttcagtcatataatttcttaaagaactacatgttaaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG
    gcctaac  putative branch site (score: 651)
                  atataatttcttaaag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttttttgcttgcctaacttcagtcatataatttcttaaagaactacatgttaaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT