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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgggactattatcagactattgtcacttgtcagcctggcttcagaatgttaagtagccattgcaatttcaatttattcaattcaacatggataacaattccatttatgttttttcgtttcagACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAACTACACCATCTAATTACTACTACATTTGTGAAAAGAATGGTGGCTCGTTG

Basic information

species Zea mays
transcript GRMZM2G130889_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130889_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 9
gtttgggactattatcagactattgtcacttgtcagcctggcttcagaatgttaagtagccattgcaatttcaatttattcaattcaacatggataacaattccatttatgttttttcgtttcagACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAACTACACCATCTAATTACTACTACATTTGTGAAAAGAATGGTGGCTCGTTG
||||| | |||| | |      ||    ||| |||   |  |||||     ||   |  |    | |||| ||     ||  ||| | ||||  | | || |   | |||| |||||   |  ||||||||||||||||||||||||||||| ||| |||| || ||||| ||||||||||| |||||||||||||||||||| || ||||||||||| || |||
gtttgagcctataagcctcacttttcaccttttcatattcccttcactgatttcttttactg--gaaattccatacagtttcatttagcatgt-tgataactgtttatatgatttttgact--agACAAATGTGGGAGACATCAATGGAAGGCCTACTAAGCTTGACCAAAAAAACTACACCCTCTAATTACTACTACATTTGCGAGAAGAATGGTGGTTCATTG

upper sequence: GRMZM2G130889_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv11s0052g00140.t01 (Vitis vinifera), 3'ss of exon 9
gtttgggactattatcagactattgtcacttgtcagcctggcttcagaatgttaagtagccattgcaatttcaatttattcaattcaacatggataacaattccatttatgttttttcgtttcagACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAACTACACCATCTAATTACTACTACATTTGTGAAAAGAATGGTGGCTCGTTG
       || ||  | |||  ||||  |   |  || |||       |||  |  | |     || |   | | |||  |  ||  ||  | || ||            ||  || |   | |||| ||||||||||||||||||||||||||||   ||| || |     |  || ||||||||    |     ||||| ||||| ||||||||  | |  |||
-------accatgttgagataattgaaaaa-gaaagtctgat----aaattgtgggaatttcctgaa---ttattttccttgatgaaattttgagaaag----------tggattctaaatccagAGAAATGTGGGAGACATCAATGGAAGGTCTCAAAAGCTTGATTCGTAGGACAACACCATCCTCCTTTGCATACATATGTGAGAAGAATGGGAGGTTCTTG
















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|67028781|gb|CO457530.1|CO457530
EST:     CTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAG                         ACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAAC
genomic: CTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAGgtttgggact ... ttcgtttcagACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAAC
EST: gi|60349712|gb|DN216685.1|DN216685
EST:     CTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAG                         ACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAAC
genomic: CTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAGgtttgggact ... ttcgtttcagACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAAC
EST: gi|22543150|gb|BU093588.1|BU093588
EST:     CTCAAGGNCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAG                         ACAAATGTGGGAGACATCCATGGA
genomic: CTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAGgtttgggact ... ttcgtttcagACAAATGTGGGAGACATCAATGGA
EST: gi|32849483|gb|CD989164.1|CD989164
EST:     CTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAG                         ACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAAC
genomic: CTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAGgtttgggact ... ttcgtttcagACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAAC
EST: gi|22935539|gb|BU571814.1|BU571814
EST:     CTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAG                         ACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAAC
genomic: CTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAGgtttgggact ... ttcgtttcagACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAAC
EST: gi|32801870|gb|CD954106.1|CD954106
EST:     GATCCGGGGGAATAAAACTGAGCATGTAAAACACTACAG                         ACAAATGTGGGAGACATCAATGGAAGGTCTATTA
genomic: GATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAGgtttgggact ... ttcgtttcagACAAATGTGGGAGACATCAATGGAAGGTCTATTA
EST: gi|60342116|gb|DN209089.1|DN209089
EST:     CTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAG                         ACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAAC
genomic: CTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAGgtttgggact ... ttcgtttcagACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAAC
EST: gi|32801642|gb|CD953878.1|CD953878
EST:     GATCCCGGGGAATAAAACTGAGCATGTAAAACACTACAG                         ACAAATGTGGGAGACATCAATGGAAGGTCTATTA
genomic: GATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAGgtttgggact ... ttcgtttcagACAAATGTGGGAGACATCAATGGAAGGTCTATTA
EST: gi|32941898|gb|CF046717.1|CF046717
EST:     CTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAG                         ACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAAC
genomic: CTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAGgtttgggact ... ttcgtttcagACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAAC
EST: gi|32801477|gb|CD953713.1|CD953713
EST:     GATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAG                         ACAAATGTGGGAGACATCAATGGAAGGTCTATTA
genomic: GATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAGgtttgggact ... ttcgtttcagACAAATGTGGGAGACATCAATGGAAGGTCTATTA

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: 48 (upstream exon), 46 (downstream exon)
Score: 103

CTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAGgtttgggact ... ttcgtttcagACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAACTACACCATCTAATTACTACTACATTTGTGAAAAGAATGGTGGCTCGTTG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 88

CTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAGgtttgggact ... ttcgtttcagACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAACTACACCATCTAATTACTACTACATTTGTGAAAAGAATGGTGGCTCGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

CTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAGgtttgggact ... ttcgtttcagACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAACTACACCATCTAATTACTACTACATTTGTGAAAAGAATGGTGGCTCGTTG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 223

CTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAGgtttgggact ... ttcgtttcagACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAACTACACCATCTAATTACTACTACATTTGTGAAAAGAATGGTGGCTCGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatttattcaattcaacatggataacaattccatttatgttttttcgtttcagACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAACTACACCATCTAATTACTACTACATTTGTGAAAAGAATGGTGGCTCGTTG
                     ggataac  putative branch site (score: 223)
                                       tgttttttcgtttc  putative PPT
                                  atttatgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgggactattatcagactattgtcacttgtcagcctggcttcagaatgttaagtagccattgcaatttcaatttattcaattcaacatggataacaattccatttatgttttttcgtttcagACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAACTACACCATCTAATTACTACTACATTTGTGAAAAGAATGGTGGCTCGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG