Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaagattttaattaatagatagccgtacaccactgatttgccagccttgctaataattgtcataccttatctgaatttttattttatgacctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGGTAAAGTTGTTTTGGGTGTATTGGCTTGTCCAAATCTTCCATTGTCATCA

Basic information

species Zea mays
transcript GRMZM2G152757_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152757_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g08280.1 (Oryza sativa), 3'ss of exon 4
tcaagattttaattaatagatagccgtacaccactgatttgccagccttgctaataattgtcataccttatctgaatt----tttattttatgacctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGGTAAAGTTGTTTTGGGTGTATTGGCTTGTCCAAATCTTCCATTGTCATCA
   | |    |  ||| ||  | ||   ||  | |  |   |  |   ||   |||  |   |   || | |  ||||    ||| |||||  || | | |||||||||| ||||| ||||||||||| |||||  |||||||||||||||| |||||||||||||||||||||||||||||||| || ||| | |||  ||||
---aaaagccatgtaaaaggcatcctgtcaa-attagtactcttgtgatgtgcatatctcaaacttctgacccaaattcacattttttttacaacgttactcagTTTCTTAAGGGGAGACCAATATGCTATTGCCCTGGCTCTGCTTGATGAGGGTAAAGTTGTTTTGGGTGTATTGGCTTGTCCCAACCTTTCTTTGGGATCA

upper sequence: GRMZM2G152757_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G09180.1 (Glycine max), 3'ss of exon 4
------tcaagattttaattaatagatagccgtacaccactgatttgccagccttgctaataattgtcataccttatctgaatttttattttatgacctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGGTAAAGTTGTTTTGGGTGTATTGGCTTGTCCAAATCTTCCATTGTCATCA
      || | ||| || ||  |   |  |  | ||    |  | ||| | | |||   ||   ||||||    || || | |  || |   ||||| | |   || ||  | || || || |||||||| || || || ||| | || |||||||| |||||||| |||||||| |||||||||||||| |||||| || |||| 
ttacagtctatattatactttttgtttcact-tgcatggttactgtgctatcattgtgtatg--tgtcattgagtagctca-tggttgtgagatgacatta--tagGTTTGTAAGAGGAGATCAATATGCTATAGCGTTAGCTTTACTAGATGAAGGCAAAGTTGTATTGGGTGTCTTGGCTTGTCCAAACCTTCCACTGGCATCC

upper sequence: GRMZM2G152757_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G26250.1 (Glycine max), 3'ss of exon 4
tcaagattttaattaatag-atagccgt-acaccactgatttgccagccttgctaataattgtcataccttatctgaatttttatt-ttatgacctga-atca--gTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGGTAAAGTTGTTTTGGGTGTATTGGCTTGTCCAAATCTTCCATTGTCATCA
      ||  | |  |||| ||||   |     ||||    ||    || |||||  | ||   ||   | ||        | ||  || |||   || || |  | ||  | || || || |||||||| || ||||| ||| || |  ||||||| ||| |||| |||||||| ||||||||||||||||||||| || |||| 
------ttacagtctatagtatagtttttgtttcacttgcatggtcaccgtgctatcattttgtatgtgtcattgagtagctcatggttgtgagaggacattatagGTTTGTAAGAGGAGATCAATATGCTATAGCATTAGCTTTGTTACATGAAGGCAAAATTGTATTGGGTGTCTTGGCTTGTCCAAATCTTCCACTGGCATCC

upper sequence: GRMZM2G152757_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0044g01480.t01 (Vitis vinifera), 3'ss of exon 4
--tcaagattttaattaatagatagccgtacaccactgatttgccagccttgctaataattgtcataccttatctgaatttttattttatgacctgaat-cagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGGTAAAGTTGTTTTGGGTGTATTGGCTTGTCCAAATCTTCCATTGTCATCA
  | |   |||| |  | ||  |    |      | ||||||      ||| | |         ||   | |  |   || |  || |  |   | |||  |||||  | || || ||||| ||||| || ||||| || ||||| |||||||| ||||| || ||||||||  | ||||||||||||||||| ||| |||| 
tttgagtcttttgaccactaattgagtgctttatattgattttaagtacttaccagc--ccacaatga-tgaaatagcttgtgtttgtgagtttttaatgtagTTTTCTAAGAGGAGACCAGTATGCAATAGCATTAGCACTGCTAGATGAAGGAAAAGTGGTGTTGGGTGTCCTCGCTTGTCCAAATCTTCCCTTGGCATCC

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|211140497|gb|FL400397.1|FL400397
EST:     GGTCCATCTGGACGACATTGGGTGCTTAATCCGATTGACGGTACTAAAGG                         TTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
genomic: GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
EST: gi|50326445|gb|CO521571.1|CO521571
EST:     GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGG                         TTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
genomic: GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
EST: gi|211426998|gb|FL426768.1|FL426768
EST:     GGTCCATCTGGACGACATTGGGTGCTTAATCCGATTGACGGTACTAAAGG                         TTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
genomic: GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
EST: gi|71435796|gb|DR816846.1|DR816846
EST:     GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGG                         TTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
genomic: GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
EST: gi|93012264|gb|EB637784.1|EB637784
EST:     GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGG                         TTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
genomic: GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
EST: gi|13316247|gb|BG410694.1|BG410694
EST:     GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGG                         TTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
genomic: GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
EST: gi|15208795|gb|BI430679.1|BI430679
EST:     GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGG                         TTTCTTGAGGGGCGACCAATATGCCATT
genomic: GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATT
EST: gi|211027069|gb|FL381517.1|FL381517
EST:     GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGG                         TTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
genomic: GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
EST: gi|76016036|gb|DT943206.1|DT943206
EST:     GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGG                         TTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
genomic: GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
EST: gi|32841437|gb|CD981118.1|CD981118
EST:     GGTACT-AAGG                         TTTCTTGAGGGGCGACCAATATGCCA-TGCCATTGGCTCTGCTTGATGAAG
genomic: GGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTG-CATTGGCTCTGCTTGATGAAG
EST: gi|211217102|gb|FL383485.1|FL383485
EST:     GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGG                         TTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAANG
genomic: GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
EST: gi|211084814|gb|FL392700.1|FL392700
EST:     GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGG                         TTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
genomic: GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
EST: gi|211131362|gb|FL428332.1|FL428332
EST:     GGTCCATCTGGACGACATTGGGTGCTTAATCCGATTGACGGTACTAAAGG                         TTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
genomic: GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
EST: gi|32842117|gb|CD981798.1|CD981798
EST:     GGTACTAAAGG                         TTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
genomic: GGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
EST: gi|13316248|gb|BG410695.1|BG410695
EST:     GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGG                         TTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
genomic: GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
EST: gi|149037768|gb|EE155430.2|EE155430
EST:     GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGG                         TTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
genomic: GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG
EST: gi|211225357|gb|FL370946.1|FL370946
EST:     GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGG                         TTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAANG
genomic: GGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGG

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), 44 (downstream exon)
Score: 93

TTACAAAGGAAGGTATACTCTCTGCAATTGATGATGGGAAGTCTGAGGGAGGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGGTAAAGTTGTTTTGGGTGTATTGGCTTGTCCAAATCTTCCATTGTCATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 357

TTACAAAGGAAGGTATACTCTCTGCAATTGATGATGGGAAGTCTGAGGGAGGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGGTAAAGTTGTTTTGGGTGTATTGGCTTGTCCAAATCTTCCATTGTCATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

TTACAAAGGAAGGTATACTCTCTGCAATTGATGATGGGAAGTCTGAGGGAGGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGGTAAAGTTGTTTTGGGTGTATTGGCTTGTCCAAATCTTCCATTGTCATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

TTACAAAGGAAGGTATACTCTCTGCAATTGATGATGGGAAGTCTGAGGGAGGTCCATCTGGACGACATTGGGTGCTTGATCCGATTGACGGTACTAAAGGgtgagtttgg ... cctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGGTAAAGTTGTTTTGGGTGTATTGGCTTGTCCAAATCTTCCATTGTCATCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgctaataattgtcataccttatctgaatttttattttatgacctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGGTAAAGTTGTTTTGGGTGTATTGGCTTGTCCAAATCTTCCATTGTCATCA
   tgctaat  putative branch site (score: 155)
                      ttatctgaatttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaagattttaattaatagatagccgtacaccactgatttgccagccttgctaataattgtcataccttatctgaatttttattttatgacctgaatcagTTTCTTGAGGGGCGACCAATATGCCATTGCATTGGCTCTGCTTGATGAAGGTAAAGTTGTTTTGGGTGTATTGGCTTGTCCAAATCTTCCATTGTCATCA

- - - - - - - - - - - - - - caccact
- - - - - - - - - - - - - - - - - - - -tgccagc
- - - - - - - - - - - - - - - - - - - - - - - -ttgctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catacct