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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagataccagtgcttcatttatgcataaattcctgttcctggtaatctggcatgaactattatgtgatatagttagtaaatccattagttatgatt...

Basic information

species Zea mays
transcript GRMZM2G134747_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134747_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g33270.1 (Oryza sativa), 5'ss of exon 2
ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagat--accagtgcttcatttatgcataaattcctgttcctggtaatctggcatgaactattatgtgatatagttagtaaatccatta-gttatgatt
||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| ||   ||  |||||||||  |   | | || |  || |    | | |  | |||  |  | |      ||  | | | ||  |  | |||| |  |
ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGTGATGGAATgtaagatatctgcctatgcttcattc-tatttgattttcatttaccc-cagtatttcttgacttcctgttcctggtaact-gcacatggacgaagttaaggat

upper sequence: GRMZM2G134747_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA10G00790.1 (Glycine max), 5'ss of exon 2
ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaag----agatac-cagtgcttcatttatgcataaattcctgttcctggtaatctggcatgaactattatgtgatatagttagtaaatccattagttatgatt-
 |||||||||||||||||||||||||| ||||||||||| ||||| ||||||||||||||||||||||| |||||||    |  |||  | || |  |||| | ||| |||    | ||  | | |  | |  ||   | ||     ||||   | | |  |   |   | ||| || 
GTTGAATGAAGCTGTTATGCATTTTGGGGAGAGCATCAAAGAAATAATCAATGAGGAGTTTGGTGATGGGATgtaagtttcaattacataatgatatatttct-catgaat----gctcaagatgaagttgtttggtgtttttctatatatgacttg-agttgagtgtatcatgtttt

upper sequence: GRMZM2G134747_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT3G23490.1 (Arabidopsis thaliana), 5'ss of exon 2
ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagataccagtgcttcatttatgcataaattcctgttcctggtaat--ctggcatgaactattat--gtgatatagtta-gtaaatccattagttatgatt
 ||||||||||| || ||||||||||| ||||| || ||||| || |||||||| || ||||| ||||| |||||||   |  |  || |   |   |   |||| |     |  || |  |  ||   | |    ||| |  ||   ||| ||  || | ||  || |||   |  
GTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCATgtaag---tttctatgttctttaagtatgtaaagtttgagttgtgatcgttgctttaaagggtcattgttagtagcatacttgtgtgattcattttgttcata--

upper sequence: GRMZM2G134747_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv05s0049g01520.t01 (Vitis vinifera), 5'ss of exon 2
ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagataccagtgcttcatttatgcataaattcctgttcctggtaatctggcatgaactattatgtgatatagttagtaaatccattagttatgatt--
|||||||||||| || ||||||||||| ||||||||||||||||| ||||||||||||||||| ||||| |||||||   |    ||    || || |   |   | | ||   |   |   ||        || ||     |     |  | |||    ||    |   ||  
ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGCGATGGCATgtaagtctttttggtctcccaatt-tctctgtttgcttgccacacatgtacttttg-agcctgtttgacaacggtttctgaaaacaggtttcccaaatttca

upper sequence: GRMZM2G134747_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S272_13V6.5 (Physcomitrella patens), 5'ss of exon 4
ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaag-agatacca------gtgcttcatttatgcataaattcctgt-tcctggtaatctggcatgaactattatg-tgatatagttagtaaatccattagttatgatt----------------------------------------------------------------------
  || | |||||   | | ||||  || || ||||||||||| ||||||||||| ||||||||||| || ||||||| | ||  ||      | || |  ||      |   || || | | |    | || |   |  || | | |  |||    ||     ||    |  |   ||||                                                                       
GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaatctcatcttaagagcatagttcgaatgttggtttctatgtacatacagtcagaagttcacaaatgtaatgacgctgtactgcaacgtgtctggcttgatgctgtcacagcctgtaaaattgctggaaacggataatcccactaatatatgtttcaactggcgatctgcag

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|7844018|gb|AW787345.1|AW787345
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
EST: gi|211047251|gb|FL125325.1|FL125325
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTG
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTG
EST: gi|211044297|gb|FL125320.1|FL125320
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTG
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTG
EST: gi|60400889|gb|DN233696.1|DN233696
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
EST: gi|211469684|gb|FL432027.1|FL432027
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
EST: gi|211044290|gb|FL125313.1|FL125313
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTG
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTG
EST: gi|31441069|gb|CD510500.1|CD510500
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
EST: gi|22542458|gb|BU092896.1|BU092896
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
EST: gi|211191597|gb|FL255435.1|FL255435
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
EST: gi|78544325|gb|DV621823.1|DV621823
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
EST: gi|211047250|gb|FL125324.1|FL125324
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACT
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACT
EST: gi|26457359|gb|CA828942.1|CA828942
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
EST: gi|31405717|gb|CD484449.1|CD484449
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
EST: gi|60399029|gb|DN231845.1|DN231845
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
EST: gi|211044293|gb|FL125316.1|FL125316
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
EST: gi|12046752|gb|BF728891.1|BF728891
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
EST: gi|31611770|gb|CD568392.1|CD568392
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
EST: gi|30032230|gb|CB834081.1|CB834081
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
EST: gi|211044299|gb|FL125322.1|FL125322
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTG
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTG
EST: gi|31406273|gb|CD485005.1|CD485005
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
EST: gi|7844445|gb|AW787667.1|AW787667
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
EST: gi|149011217|gb|EE042296.2|EE042296
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
EST: gi|7844017|gb|AW787344.1|AW787344
EST:     TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT                         CATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA
genomic: TTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGA

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), 49 (downstream exon)
Score: 51

ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGACGGAAAAGATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGACGGAAAAGATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 126

ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGACGGAAAAGATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 86

ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagata ... cttattgcagCATGTCAGCCATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGACGGAAAAGATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagataccagtgcttcatttatgcataaattcctgttcctggtaatctggcatgaactattatgtgatatagttagtaaatccattagttatgatt

- - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA