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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttcacttctgttttggttcatactagaatgtatagatgtacccatttgttgcactgtggcattactaaccgagatcatctaccaatgtcattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA

Basic information

species Zea mays
transcript GRMZM2G086805_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086805_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g43060.1 (Oryza sativa), 3'ss of exon 3
agttcacttctgttttggttcatactagaatgtatagatg--tacccatttgttgcactgtggcattactaaccgagatcatctaccaatgtcattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA
     || |   ||  | |   |  |  |  ||  |  ||  || |   | |    || |   || |   |   |  ||    | |   |  || | |||||| | |||||| |||||||||||||| || |||||| ||||||||||||| || ||||| |||
--aatacatgaattaagatgtgtgttcaacagttcaagtgtctagcttctagagcaaccgaaacaatctcatttgtcatgtgttccttttcgcaatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGGAGGAGTACCAA
















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|7844125|gb|AW787328.1|AW787328
EST:     CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATCCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|29129751|gb|CB380455.1|CB380455
EST:     CTCTCTGATGGACCCCAGTAGGAG-NGGGCAGCCCGTTGGTTGAG-ATTG                         GCAGGTTCATTCCTGGG-GCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|32930934|gb|CF035746.1|CF035746
EST:     CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGGGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|211373132|gb|FL346967.1|FL346967
EST:     CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|28986940|gb|CB351384.1|CB351384
EST:     CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|211388869|gb|FL452911.1|FL452911
EST:     CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|37378989|gb|CF626218.1|CF626218
EST:     CTCTCTGATGGACCCCAGTTGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         G----TTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|4730597|gb|AI649763.1|AI649763
EST:     CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|32943412|gb|CF048231.1|CF048231
EST:     CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|26557678|gb|CA829913.1|CA829913
EST:     CTGATGGGCCCCCGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATTCCTGGGTGCTATACCCTTGCTGTCTCGGGGGAGCTTCCAG
genomic: CTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|37375940|gb|CF624458.1|CF624458
EST:     CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|91869839|gb|EB400567.1|EB400567
EST:     CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|45847108|gb|CN071051.1|CN071051
EST:     CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|30087685|gb|CB885891.1|CB885891
EST:     CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|93015254|gb|EB640774.1|EB640774
EST:     CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|60339603|gb|DN206576.1|DN206576
EST:     CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|211528033|gb|FL311002.1|FL311002
EST:     CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|60398153|gb|DN230969.1|DN230969
EST:     CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|26557679|gb|CA829914.1|CA829914
EST:     CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATTCCTGGG-GCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|60351934|gb|DN218907.1|DN218907
EST:     CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|32857871|gb|CD997552.1|CD997552
EST:     CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATTCCTGGGTGCTATACACTTGCTGGCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
EST: gi|7844126|gb|AW787329.1|AW787329
EST:     CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTG                         GCAGGTTCATCCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG
genomic: CTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAG

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: 475

AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 248

AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 260

AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 205

AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttg ... cattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgttgcactgtggcattactaaccgagatcatctaccaatgtcattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA
                   tactaac  putative branch site (score: 205)
                 attactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttcacttctgttttggttcatactagaatgtatagatgtacccatttgttgcactgtggcattactaaccgagatcatctaccaatgtcattatgcagGCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - -gttgcac