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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGTTAAATGAGAAGAGCGATGTCTACAGTTTTGGGGTGCTACTACTGGAAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatctgctattgtagtattgcctcgtgcatatgctgaagcaagaagtccatactatttacaatacgtttcacaacaaaacagcatctgcttggtt...

Basic information

species Zea mays
transcript GRMZM2G010953_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010953_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os10g35450.1 (Oryza sativa), 5'ss of exon 6
TCTGTTAAATGAGAAGAGCGATGTCTACAGTTTTGGGGTGCTACTACTGGAAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatctgctattgtagtat--tgcctcgtgcatatgctgaagcaagaagtccatactatttacaatacgtttcacaacaaaacagcatct--gcttggtt--
||||||||| |||||||| ||||||||||||||||| |||||| ||||||||||||||||||| || ||||||||||| ||||| ||||||||||||||||||||||| |     |  | | |  ||| |  |   |||| |  |     |||||| |||||||   |||   ||| ||  ||||| | | |||   || ||    
TCTGTTAAACGAGAAGAGTGATGTCTACAGTTTTGGTGTGCTATTACTGGAAGCAGTGACTGGTAGAGATCCAGTTGATTATGGCCGGCCTGCTAATGAGgtgagcatatatc-ctacaatctcatgcgtattatgtatgttacaa----aagtccgtactattggaaat-tattttacggcaaaataacgtctatactaggagag

upper sequence: GRMZM2G010953_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA02G45540.1 (Glycine max), 5'ss of exon 7
TCTGTTAAATGAGAAGAGCGATGTCTACAGTTTTGGGGTGCTACTACTGGAAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatctgctattgtagtattgcctcgtgcatatgctgaagcaagaagtcca-tactattta-caatacgtttcaca-acaaaacagcatctgcttggtt-------
| |||||||||||||||| ||  | ||||| ||||| || ||  ||||||||||||| ||||| |||||||| || |||||||  || |||||||||||||||   |  |  ||| | | | |  |  | |||   | || || ||     |||| |   | | | || |  |||||| | |    |    ||   |||  ||       
TTTGTTAAATGAGAAGAGTGACATTTACAGCTTTGGTGTCCTCTTACTGGAAGCAGTTACTGGAAGGGATCCTGTAGACTATGCGCGCCCTGCTAATGAGgtgcctaattcttat-gaactctgccagcttgccagttct-aaccatactttccactggaagtcatcactgtgtttcaaatagctgatgagataatcttcattatgacag

upper sequence: GRMZM2G010953_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA14G03290.1 (Glycine max), 5'ss of exon 5
TCTGTTAAATGAGAAGAGCGATGTCTACAGTTTTGGGGTGCTACTACTGGAAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatctgctattgtagtattgcctcgtgcatatgctgaagcaagaagtccatactattta--caatacgtttca--caacaaaacagcatctgcttggtt------------
| |||||||||||||||| ||  | ||||| ||||| || ||  | ||||||||||| ||||| ||||| || || |||||||  || |||||||||||||||   |  |  ||| | | | |  |  | |||   | || || || |   ||||    |  |   || | | |||||   | |  |  ||    || ||   |            
TTTGTTAAATGAGAAGAGTGACATTTACAGCTTTGGTGTCCTCTTGCTGGAAGCAGTTACTGGAAGGGACCCTGTAGACTATGCGCGTCCTGCTAATGAGgtggctaatttttat-gaactctacctgcttgccagttct-aaccatgctttccaccagaagtgatcactgcctttcaaatagctgatgagatattgtttatcttcattatgacag

upper sequence: GRMZM2G010953_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT2G42960.1 (Arabidopsis thaliana), 5'ss of exon 5
TCTGTTAAATGAGAAGAGCGATGTCTACAGTTTTGGGGTGCTACTACTGGAAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatctgctattgtagtattg-cctcgtgcatatgctgaagcaag--aagtccatactatttacaatacgtttcacaacaaaacagcatctgcttggtt
||| ||||| || ||||| ||| | || || ||||| ||  | || || |||||  | |||||  | ||||||||||| |||||||| |||||||||||||||||  |  | || | | || |||   | ||  || |   | |  |||  | |   ||  || || |   |   |    |||      | || |     |  
TCTTTTAAACGAAAAGAGTGATATATATAGCTTTGGTGTCTTGCTTCTTGAAGCTATAACTGGTCGAGATCCAGTTGATTATGGTCGTCCTGCTAATGAGgtgaggcttggttaat-tggtcttgattttgttaatgtatcggaaaaagttatgaatatgttaatttcctgaaactattgaacgggcttgtatattggcag--

upper sequence: GRMZM2G010953_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv12s0028g00310.t01 (Vitis vinifera), 5'ss of exon 7
TCTGTTAAATGAGAAGAGCGATGTCTACAGTTTTGGGGTGCTACTACTGGAAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatctg-ctattgtagt----attgcctcgtgcatatgctgaagcaagaa-gtccatactatttacaatacgtttcacaacaaaacag-catctgcttggtt-
  |||||||||||||||| ||| ||||||| ||||| || || || ||||||||||| ||||| |||||||||||||||||||| |||||||||||||||||     |||| | | || | |    | | | |  | | |  |  |||     ||  | ||  || | | ||| | |    |  | ||      |||   | |||   
CTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGATCCAGTTGACTATGGCCGGCCTGCTAATGAGgtatttctctgtccaatgcattggggacttctttctcctttcgtcgaaaggtaaatatacaggct-tgttcaagaagagctatgataagctgttcatgctcatggcag

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|60354736|gb|DN221709.1|DN221709
EST:     GCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAG                         GTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
genomic: GCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatct ... ggttgtgcagGTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
EST: gi|61118273|gb|DN559234.1|DN559234
EST:     AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAG                         GTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
genomic: AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatct ... ggttgtgcagGTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
EST: gi|88749325|gb|DY533466.1|DY533466
EST:     AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAG                         GTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
genomic: AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatct ... ggttgtgcagGTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
EST: gi|16746104|gb|BM032534.1|BM032534
EST:     AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAG                         GTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
genomic: AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatct ... ggttgtgcagGTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
EST: gi|18384770|gb|BM417969.1|BM417969
EST:     AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAG                         GTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
genomic: AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatct ... ggttgtgcagGTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
EST: gi|149079749|gb|EE168749.2|EE168749
EST:     AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAG                         GTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
genomic: AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatct ... ggttgtgcagGTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
EST: gi|33092310|gb|CF052304.1|CF052304
EST:     AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCCGCTAATGAG                         GTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
genomic: AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatct ... ggttgtgcagGTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
EST: gi|88752191|gb|DY536332.1|DY536332
EST:     AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAG                         GTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
genomic: AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatct ... ggttgtgcagGTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
EST: gi|148995005|gb|EE034340.2|EE034340
EST:     GGATCCAGTTGACTATGGTCGGCCTGCTAATGAG                         GTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
genomic: GGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatct ... ggttgtgcagGTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
EST: gi|78121330|gb|DV539714.1|DV539714
EST:     AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAG                         GTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
genomic: AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatct ... ggttgtgcagGTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
EST: gi|89759882|gb|DY688555.1|DY688555
EST:     AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAG                         GTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
genomic: AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatct ... ggttgtgcagGTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
EST: gi|18384771|gb|BM417970.1|BM417970
EST:     AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAG                         GTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
genomic: AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatct ... ggttgtgcagGTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
EST: gi|61118274|gb|DN559235.1|DN559235
EST:     AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAG                         GTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
genomic: AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatct ... ggttgtgcagGTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
EST: gi|31358946|gb|CD443303.1|CD443303
EST:     AAGCAGGGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAG                         GTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG
genomic: AAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatct ... ggttgtgcagGTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAG

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), 48 (downstream exon)
Score: 1070

TCTGTTAAATGAGAAGAGCGATGTCTACAGTTTTGGGGTGCTACTACTGGAAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatct ... ggttgtgcagGTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAGGAGGTGGTGGATCCTGACATGGAGTTGAAACCAGCGATTCGTGCTCTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 334

TCTGTTAAATGAGAAGAGCGATGTCTACAGTTTTGGGGTGCTACTACTGGAAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatct ... ggttgtgcagGTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAGGAGGTGGTGGATCCTGACATGGAGTTGAAACCAGCGATTCGTGCTCTGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 193

TCTGTTAAATGAGAAGAGCGATGTCTACAGTTTTGGGGTGCTACTACTGGAAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatct ... ggttgtgcagGTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAGGAGGTGGTGGATCCTGACATGGAGTTGAAACCAGCGATTCGTGCTCTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 391

TCTGTTAAATGAGAAGAGCGATGTCTACAGTTTTGGGGTGCTACTACTGGAAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatct ... ggttgtgcagGTTCATCTGGTGGAGTGGCTGAAAATGATGGTTGGCACTAGAAGAGCCGAGGAGGTGGTGGATCCTGACATGGAGTTGAAACCAGCGATTCGTGCTCTGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGTTAAATGAGAAGAGCGATGTCTACAGTTTTGGGGTGCTACTACTGGAAGCAGTGACTGGGAGGGATCCAGTTGACTATGGTCGGCCTGCTAATGAGgtgagcatctgctattgtagtattgcctcgtgcatatgctgaagcaagaagtccatactatttacaatacgtttcacaacaaaacagcatctgcttggtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaaaca