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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtattattattaaactaatgacatacatgtacatttttagccgttgctttattaatttattggaccttttttatgtgtgaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG

Basic information

species Zea mays
transcript GRMZM2G165926_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165926_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g13970.2 (Oryza sativa), 3'ss of exon 8
gtatgtattattattaaactaatgacatac--atgtacatttttagccgttgctttattaatttattggaccttttttatgtgtgaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG
||| |||||  | |  ||| |||||||| |  || || |  | |   | |||| | || | |   |    |  ||||      | ||||  ||||| ||||||||||| |||||||| || ||||| ||||||||||||||||| |||||  | ||||| |||
gtaagtatttgtttagaaccaatgacatgctaatctatagatattttcattgcgt-atgactgactcttgctgttttcccccttcaaattgtagCTCCCTGGTGTTGACCCCAATGACCCCTCTGTGAAAGATTTGCTGGCATCATTGCATGGGCAGGGCGAG

upper sequence: GRMZM2G165926_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA02G05250.2 (Glycine max), 3'ss of exon 8
gtatgtattattattaaactaatgacatacatgtacatttttagc-cgttgctttattaatttattggacctttttta-tgtgtgaaata----------atagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG
    ||||   ||| || | | | |  |     |    ||| |     ||  |  | | ||| |    |  || || | ||  | | ||             |||||||||| ||||| || ||||| |||||||| |||||||||||||| ||  |||| |  |||   |||
----gtatgtctataaatccagtaaattttccatgttctttaaatgtattaatagaatgattgacaatatgttcttaactgaataatattcattgcttctgcagCTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCCATGCAAAATCAGTCTGAG

upper sequence: GRMZM2G165926_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA16G23590.1 (Glycine max), 3'ss of exon 8
gtatgtattattattaaactaatgacatacatgtacatttttagc-cgttgctttattaatttattggacctttttta-tgtgtgaaata----------atagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG
    ||||   ||| || | | | |       ||    ||| |     ||| |  | | ||| |    |  || |  | ||  | | ||             |||||||||| ||||| || |||||||||||||| |||||||||||||| || ||||| |  |||   |||
----gtatgtctataaatccagtaaatgttccgtgttctttaaatgtattgatagaatgattgacaatatgttctgcactgaataatattcgttgcttctgcagCTTCCTGGGGTTGACCCAAATGATCCATCTGTCAAAGATTTGCTGGCTTCCTTGCAAAATCAGTCTGAG

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|37380959|gb|CF627330.1|CF627330
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|18162870|gb|BM332709.1|BM332709
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|5525732|gb|AI861625.1|AI861625
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|71419000|gb|DR804613.1|DR804613
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|37398277|gb|CF636450.1|CF636450
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|60337128|gb|DN204101.1|DN204101
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|60353359|gb|DN220332.1|DN220332
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|60347266|gb|DN214239.1|DN214239
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|37383110|gb|CF628537.1|CF628537
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|31664308|gb|CD573033.1|CD573033
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|261490449|gb|GO359940.1|GO359940
EST:     TGAGTAAGGTGTTTGAAAACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGNTGTTGATCCCAATGATCCATCTGTTAAAAATTTGCTGGCTTCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|60349443|gb|DN216416.1|DN216416
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|60346958|gb|DN213931.1|DN213931
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|33097806|gb|CF057766.1|CF057766
EST:     AGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: AGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|18174967|gb|BM350355.1|BM350355
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|211072583|gb|FL217264.1|FL217264
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|60357544|gb|DN224517.1|DN224517
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|211442872|gb|FL468446.1|FL468446
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|60354620|gb|DN221593.1|DN221593
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|5847367|gb|AW000446.1|AW000446
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|5706125|gb|AI941901.1|AI941901
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|44901350|gb|CK827895.1|CK827895
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|60399456|gb|DN232268.1|DN232268
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|37383796|gb|CF628931.1|CF628931
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
EST: gi|38502551|gb|CF972411.1|CF972411
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGGGGTGATCCCAATGGTCCCTCTGGTAAAAAATTTGCTGGCATC
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGA-TTTGCTGGCATC
EST: gi|32930239|gb|CF035051.1|CF035051
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCG

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: 262

CTCTTCAAATGTCTGTCCAGGATGCAAACATGTCCAGTGACACTGATATGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 327

CTCTTCAAATGTCTGTCCAGGATGCAAACATGTCCAGTGACACTGATATGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 297

CTCTTCAAATGTCTGTCCAGGATGCAAACATGTCCAGTGACACTGATATGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG


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

CTCTTCAAATGTCTGTCCAGGATGCAAACATGTCCAGTGACACTGATATGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... gaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttagccgttgctttattaatttattggaccttttttatgtgtgaaataatagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG
                tattaat  putative branch site (score: 357)
              tttattaatttattgg  TA-rich tract