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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggcttataaactgagtgcatgcatataatggcatgatgttcacgtagttgtggtagcaatttaggtatttcttctaagcttctgtaactttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCATGATCTTGTAGAGCTTTTCCGAATTGGTGGGAAG

Basic information

species Zea mays
transcript GRMZM2G112793_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112793_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g07150.1 (Oryza sativa), 3'ss of exon 2
tggcttataaactgagtgcatgc---atataatggcatgatgttcacgtagttgtggtagcaatttaggtatttcttctaagcttctgtaactttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCATGATCTTGTAGAGCTTTTCCGAATTGGTGGGAAG
  | |   ||| |   ||||||     |   |||| |   || | | |||| ||  |||    |||     |||   ||    || | |    ||   ||||||||||||| || ||||| || || ||||||||||| || ||||||||||||||||||||||| ||||| || || |||||||||
acgttctcaaaatatttgcatgttctgttccatggtaatttggtaaggtagatg-agtactggttttaaggttttgccttttttttttttgggtta--tgcagCCTGTCAAAAGCCCAGTAACGATTTGTGGTGATATTCACGGACAATTCCATGATCTTGTAGAACTTTTTCGGATCGGTGGGAAG

upper sequence: GRMZM2G112793_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S81_198V6.3 (Physcomitrella patens), 3'ss of exon 3
---tggcttataa-actgagtgcatgcatataatggcatgatgttcacgtagttgtggtagcaatttaggtatttcttctaagcttctgtaactt-tgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCATGATCTTGTAGAGCTTTTCCGAATTGGTGGGAAG
    |||   | |  ||  ||    |||| ||  | |||| |  |     |    |   ||  |||||  | ||  || |  | |  |||      || || ||||| || ||| ||||||| ||||| ||||||||||| ||||| || || ||||||||||  || || ||||||||||| || | |
attgggcaggtcatgcttggtcagcgcatttag-gacatgcttctgtttcaaaactctgag--atttacctgttgttttt--gttgttgtggtggatgattacagCCAGTGAAGTGTCCAGTCACAATTTGTGGTGATATTCATGGCCAGTTTCATGATCTTGCTGAACTCTTCCGAATTGGAGGAATG

upper sequence: GRMZM2G112793_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
tggcttataaactgagtgcatgc-atataatggcatgat--gttcacgtagttgtggtagcaatttaggtatttcttctaa-gcttctgtaactttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCATGATCTTGTAGAGCTTTTCCGAATTGGTGGGAAG
|   ||||| | |   | || || ||      ||| | |  |    ||||  ||    |  | | | |  ||||  | |   | |  ||  |    | |  ||||| || ||| | || || ||||| ||||||||||| ||||| ||||||||||||||||  || || |||||||| || || | |
taaattatatattatattcacgctatggttcagcacgctcaggatgcgtatctgacccaaaactctggaaattttctgtggtggtgatggga----gataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG

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|22818811|gb|BU498901.1|BU498901
EST:     CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG                         CCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
genomic: CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
EST: gi|22490124|gb|BU050047.1|BU050047
EST:     CCCTGTGCGAGAAGGCCAAGGAGTTATTGATGGAGGAAAGCAACGTTCAG                         CCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
genomic: CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
EST: gi|211046221|gb|FL204514.1|FL204514
EST:     CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG                         CCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
genomic: CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
EST: gi|211043271|gb|FL204511.1|FL204511
EST:     CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG                         CCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
genomic: CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
EST: gi|211046223|gb|FL204516.1|FL204516
EST:     CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG                         CCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
genomic: CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
EST: gi|211046224|gb|FL204517.1|FL204517
EST:     CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG                         CCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
genomic: CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
EST: gi|211043272|gb|FL204512.1|FL204512
EST:     CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG                         CCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
genomic: CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
EST: gi|78118757|gb|DV537141.1|DV537141
EST:     CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG                         CCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
genomic: CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
EST: gi|26559743|gb|CA831978.1|CA831978
EST:     CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG                         CCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
genomic: CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
EST: gi|211043270|gb|FL204510.1|FL204510
EST:     CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG                         CCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
genomic: CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
EST: gi|211046225|gb|FL204518.1|FL204518
EST:     CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG                         CCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
genomic: CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
EST: gi|18655213|gb|BM500018.1|BM500018
EST:     CCTGTGCGAGAAGGCCAAGGAGATATTGATGGCAGGAAAGCAACGTTCAG                         CCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
genomic: CCTGTGCGAGAAGGCCAAGGAGATATTGATGG-AGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
EST: gi|6021718|gb|AW066646.1|AW066646
EST:     CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG                         CCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
genomic: CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
EST: gi|31360213|gb|CD444570.1|CD444570
EST:     CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG                         CCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
genomic: CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
EST: gi|211043273|gb|FL204513.1|FL204513
EST:     CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG                         CCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
genomic: CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
EST: gi|87153205|gb|DY397994.1|DY397994
EST:     CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG                         CCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
genomic: CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
EST: gi|22541924|gb|BU092362.1|BU092362
EST:     CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG                         CCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
genomic: CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
EST: gi|211046226|gb|FL204519.1|FL204519
EST:     CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG                         CCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT
genomic: CCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCAT

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: 46 (upstream exon), 46 (downstream exon)
Score: 98

GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCATGATCTTGTAGAGCTTTTCCGAATTGGTGGGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 84

GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCATGATCTTGTAGAGCTTTTCCGAATTGGTGGGAAG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 87

GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCATGATCTTGTAGAGCTTTTCCGAATTGGTGGGAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 71

GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAGgtaagctgtg ... ttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCATGATCTTGTAGAGCTTTTCCGAATTGGTGGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttgtggtagcaatttaggtatttcttctaagcttctgtaactttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCATGATCTTGTAGAGCTTTTCCGAATTGGTGGGAAG
                                     ctgtaac  putative branch site (score: 71)
                                           ctttgctt  CT-rich tract
                     tatttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggcttataaactgagtgcatgcatataatggcatgatgttcacgtagttgtggtagcaatttaggtatttcttctaagcttctgtaactttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCATGATCTTGTAGAGCTTTTCCGAATTGGTGGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - tgcatgc
- - - - - - - - - - - - - - - - - tgatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttctg