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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatgtagcctaatctcgatttcttttgttgttgttgttgttgttgttgttgttgttgttgcagaccatttgtgtggactggttttctaattgctattttttcttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAGATGTATCTCACCGAAAAAAAGATGAGGATGGAATCATCTGTCTTTGGTG

Basic information

species Zea mays
transcript GRMZM2G170326_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170326_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g44150.1 (Oryza sativa), 3'ss of exon 2
gtaaaatgtagcctaatctcgatttcttttgttgttgttgttgttgttgttgttgttgttgttgcagaccatttgtgtggactggttttctaattgctattttttcttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAGATGTATCTCACCGAAAAAAAGATGAGGATGGAATCATCTGTCTTTGGTG
                      | || | |    ||    ||  | | | |  | || |  || |||| |||   | || |     | |||||| |  ||| | |||| ||||||||||| ||||||||||| ||  |||||||||| || || |||||||| |||||||||||||  || || ||| |||| | |||  ||||  ||| ||| |
---------------------gtatcatattgcattacgatttatat-gctact-ttctactttcagatcatc-atttgaagca-ctgtctaatcggcattatgtctttcaatagGTCAGGGATGAAATAGAGCAGCTAATGGATGACGACGGAGATATGGCCGAGATGTATCTCAGTGAGAAGAAGTTGAGAACGGAGGCATCCTTCTATGGCG

upper sequence: GRMZM2G170326_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G00510.1 (Glycine max), 3'ss of exon 3
gtaaaatgtagcc-taatctcgatttcttttgttgttgttgttgt-tgttgttgttgttgttgttgcagaccatttgtgtggactggttttctaattgctattttttcttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAGATGTATCTCACCGAAAAAAAGATGAGGATGGAATCATCTGTCTTTGGTG
|| |     |    || | ||   ||  ||| |  |||    ||  ||    |     | || ||  || |   || |    | | | |||  || ||| || | |||       |||| |||||||||||||| ||  | ||||| ||||||||||||||||| || |||||||| || || || || | | | ||||| |  ||  | | ||| |
gtgatgctcatttatattttcttctttctttatgattgcaagtgagtgccagttaccatatttttttagtcttattattactattagctttgcaaatgc-atatattc-------agGTTAGAGATGAAATAGAGCAGCTTATGGACGATGATGGTGATATGGCCGAAATGTATCTTACTGAGAAGAAAAGGCGAATGGAGTTGTCATTTTATGGAG

upper sequence: GRMZM2G170326_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G44820.1 (Glycine max), 3'ss of exon 3
gtaaaatgtagcctaatctcgatttcttttgttgttgttgttgttgttgttgttgttgttgttgcagaccatttgtgtggactggttttctaattgctattttttcttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAGATGTATCTCACCGAAAAAAAGATGAGGATGGAATCATCTGTCTTTGGTG
|| | |||     | || |    ||||||  || |  |||    |||   |     | || ||  || |   || |    | | |||||  || ||| || | |||       |||| |||||||||||||| ||  | |||||||||||||| |||||||| || |||||||| ||||| || || | | | ||||| |  ||  | | ||| |
gtgatatgctcatttatattttattctttctttatgattgcaagtgtcagttaccatattttttgagtcttattattactatttgttttgcaaatgc-atatattc-------agGTTAGAGATGAAATAGAGCAGCTTATGGATGATGATGGAGATATGGCCGAAATGTATCTTACCGAGAAGAAAAGGCGAATGGAGTTGTCATTTTATGGAG

upper sequence: GRMZM2G170326_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv09s0018g00570.t01 (Vitis vinifera), 3'ss of exon 2
gtaaaatgtagcctaatctcgatttcttttgttgttgttgttgttgttgttgttgttgttgttgcagaccatttgtgtggactggttttctaattgctattttttcttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAGATGTATCTCACCGAAAAAAAGATGAGGATGGAATCATCTGTCTTTGGTG
                                                               | |   ||| |            ||  |     ||   |||| |    |||||| || ||||| ||||| |||||||||||||||||||| || |||||||| |||||||||||||| || || | | |||||||||||||  ||| |||||
---------------------------------------------------------------gtaatacatctccacatttcatgttctt-----ctggattttataggtatagGTTAGGGATGAGATAGAGCAATTAATGGATGATGATGGAGACATGGCTGAAATGTATCTCACCGAGAAGAAAAGGCGGATGGAATCATCATTCTATGGTG

upper sequence: GRMZM2G170326_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv09s0018g00600.t01 (Vitis vinifera), 3'ss of exon 2
gtaaaatgtagcctaatctcgatttcttttgttgttgttgttgttgttgttgttgttgttgttgcagaccatttgtgtggactggttttctaattgctattttttcttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAGATGTATCTCACCGAAAAAAAGATGAGGATGGAATCATCTGTCTTTGGTG
                        |  |   |        ||  | || ||  |||  |    | | |   || |     |     ||||   || ||   |||| ||   |||||| || ||||| ||||| |||||||||||||||||||| || |||||||| |||||||||||||| || || | | |||||||||||||  ||| |||||
-----------------------gtaatacatctccacatttcatcttctttgtgtcatcaaagtaaatggtt-gccaaaatcaaatttc---tttctggattttattggtatagGTTAGGGATGAGATAGAGCAATTAATGGATGATGATGGAGACATGGCTGAAATGTATCTCACCGAGAAGAAAAGGCGGATGGAATCATCATTCTATGGTG

upper sequence: GRMZM2G170326_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S493_8V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaaaatgtagcctaatctcgatttcttttgttgttgttgttgtt------gttgttgttgttgttgt-tgcagac----catttgtgtg---gactggt--tttctaattgctattttttcttccaata----------------gGTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAGATGTATCTCACCGAAAAAAAGATGAGGATGGAATCATCTGTCTTTGGTG
||||    |    || | || |||||   |||   | ||    ||      | ||| | |||||   | ||||||     | || | ||     | |||   |||  ||  ||   || ||| |  | ||                |||  |||||||||| |||||| |||||||||||||  | |||||||| ||||||||| | || || || |||  |  |  ||     | |   |||  ||
gtaagtcttga--tagtttctatttcaagtgtcagtattagcatttgtcaagctgtggatgttgcgatgtgcagaagcagctttcgcgtatcaaattggacatttacaagcgcggattattcctgaattacctgcatgcatgtccagGTGCGAGATGAAATCGAACAACTAATGGATGATGACAGCGATATGGCAGAGATGTATTTAACGGAGAAGAAGGAGCAGCAGGCCGACTTTTCTTTTTTTG

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|78076627|gb|DV505061.1|DV505061
EST:     TCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAG                         GTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAG
genomic: TCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAGgtaaaatgta ... cttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAG
EST: gi|78104709|gb|DV523127.1|DV523127
EST:     TCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAG                         GTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAG
genomic: TCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAGgtaaaatgta ... cttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAG
EST: gi|78076278|gb|DV504712.1|DV504712
EST:     TCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAG                         GTCAGAGATGAAATAGAACAATTAATGGATGATGATGG
genomic: TCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAGgtaaaatgta ... cttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATGG
EST: gi|78089038|gb|DV517431.1|DV517431
EST:     TCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAG                         GTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAG
genomic: TCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAGgtaaaatgta ... cttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAG
EST: gi|5847172|gb|AW000251.1|AW000251
EST:     TCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAG                         GTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAG
genomic: TCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAGgtaaaatgta ... cttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAG
EST: gi|78076448|gb|DV504882.1|DV504882
EST:     TCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAG                         GTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATA
genomic: TCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAGgtaaaatgta ... cttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATA
EST: gi|91872270|gb|EB402227.1|EB402227
EST:     TCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAG                         GTCAGAGATGAAATAGAACAATTAATGGATGATGATG
genomic: TCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAGgtaaaatgta ... cttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATG
EST: gi|74233302|gb|DT641216.1|DT641216
EST:     TCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAG                         GTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAG
genomic: TCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAGgtaaaatgta ... cttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAG

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: 27

ATTATTGGATGAGCTGACATCCAAAATCAGTACTCTCAATTTGGAACGTGTCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAGgtaaaatgta ... cttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAGATGTATCTCACCGAAAAAAAGATGAGGATGGAATCATCTGTCTTTGGTG


Block sizes: 45 (upstream exon), 43 (downstream exon)
Score: 17

ATTATTGGATGAGCTGACATCCAAAATCAGTACTCTCAATTTGGAACGTGTCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAGgtaaaatgta ... cttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAGATGTATCTCACCGAAAAAAAGATGAGGATGGAATCATCTGTCTTTGGTG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 28

ATTATTGGATGAGCTGACATCCAAAATCAGTACTCTCAATTTGGAACGTGTCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAGgtaaaatgta ... cttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAGATGTATCTCACCGAAAAAAAGATGAGGATGGAATCATCTGTCTTTGGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 56

ATTATTGGATGAGCTGACATCCAAAATCAGTACTCTCAATTTGGAACGTGTCCGGCGATTAAAAAGTAGACTAGTTGCATTGACCAGAAGAGTTCAAAAGgtaaaatgta ... cttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAGATGTATCTCACCGAAAAAAAGATGAGGATGGAATCATCTGTCTTTGGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgcagaccatttgtgtggactggttttctaattgctattttttcttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAGATGTATCTCACCGAAAAAAAGATGAGGATGGAATCATCTGTCTTTGGTG
                           ttctaat  putative branch site (score: 56)
                                 ttgctattttttcttc  CT-rich tract
                              taattgctatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatgtagcctaatctcgatttcttttgttgttgttgttgttgttgttgttgttgttgttgcagaccatttgtgtggactggttttctaattgctattttttcttccaatagGTCAGAGATGAAATAGAACAATTAATGGATGATGATGGTGATATGGCTGAGATGTATCTCACCGAAAAAAAGATGAGGATGGAATCATCTGTCTTTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA