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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttttctcaccatgttatgtgtatttatgtatttgagtacatgacatggctactaagctggagttacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGTATGTCTCCCTTGTTTCGATTTGATTGGTTTGTGAAGTCCA

Basic information

species Zea mays
transcript GRMZM2G010085_T01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 22
gtatgtttt-tctcaccatgtta---tgtgtatttatgtatttgagtacatgacatggctactaagctggagttacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGTATGTCTCCCTTGTTTCGATTTGATTGGTTTGTGAAGTCCA
||||| | | ||  ||||| | |   | || |   || | |||    || ||||||| ||| | || ||   | ||||| ||||||||||||||||| || ||||| ||||||||||||||||||||||||||||||||||| ||||| || ||||| ||||||||||||||||| |||||||
gtatgctctatcataccatctcactttctgcacacatttgttttcaaacgtgacatgtctaattagttg---tcacatttcagCTTTGCATGGTGCATAAGCTTGGTTATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGCATGTCGCCTTTGTTCCGATTTGATTGGTTTGTCAAGTCCA

upper sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 22
gtatgtttttctcaccatgttatgtgta---tttatgtatttgagtacatgacatggctactaagctggagttacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGTATGTCTCCCTTGTTTCGATTTGATTGGTTTGTGAAGTCCA
||||| |   | ||| ||  |   || |   |||| |    |   |   |  |||    ||  |||| | ||   ||| ||| | ||||||||||||||||| ||||| ||||||||||||||||||||||| ||||| || ||||| |||||||| ||||||||||||||||||||||| |
gtatgctacac-cacaattgttcctgaacaatttaagcccctttcttttttgcattttaac--agcttgtgtc-tattacagTTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCAGCCTTTCGCATGTCGCCCTTGTTCCGATTTGATTGGTTTGTGAAGTCTA

upper sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 22
-----------------------------------------gtatgtttttctcaccatgtta-------tgtgtatttatgtattt---gagtacatgacatg-gctactaagctggagttaca--ttccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGTATGTCTCCCTTGTTTCGATTTGATTGGTTTGTGAAGTCCA
                                           || | ||| |   ||||||        ||| || |   || |||   ||  | |   | || | |      ||  | ||| |  || ||| | || ||| | ||||||||||| ||||| || ||||||||  |||| || || || || ||||| |||||||||||||||||||||||||| |||||  
gtgtgaattttatttccttttgtttttatttttgcccaaattcatttctttttgttcatgttcagttccttgtttagtctggtgttttccgaacagaattcttgtgttgtctgactttacttaaaacttgcagATATGTATGATTCACAAACTTGGCTATGGTAATTGGGATGAGTTGAAGGCAGCTTTTCGAATGTCGCCCTTGTTTCGATTTGATTGGTTTGTCAAGTCTC

upper sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 22
gtatgtttttctcaccatgttatgtgtatttatgtatttgagtacatgacatggctactaagctggagttacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGTATGTCTCCCTTGTTTCGATTTGATTGGTTTGTGAAGTCCA
|||   |||| |   |    || || ||  |   |   |   |  |||   |    |  ||  ||   | |  || ||| | |||||||||||||||||||| ||||| |||||||||||  | || || || || || |  || |||||||||||||||||||||||||| || ||  
gtacaatttttttttc----taggtctagctccat-catccttctatgggtttctaaaaaaattgctataaatttacagATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCAGCATTTCGAACATCACCCTTGTTTCGATTTGATTGGTTTGTCAAATCTC

upper sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 22
--gtatgtttt---tctcaccatgttatgtgtatttatgtatttgagtacatgacatggctact-----------aagctggagttacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGTATGTCTCCCTTGTTTCGATTTGATTGGTTTGTGAAGTCCA
    |  ||||   |||  | || || | | | ||| |   | |   | ||| |     |||             ||  ||   | |  || ||| | |||||||||||||||||||| ||||| |||||||||||  | || || || || || |  || |||||||||||||||||||||||||| || ||  
gtacaaattttatgtctttcaattttttttttctttctaggtctagctccatcatccttctatcggtttctaaaaaaattgctataaatttacagATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCAGCATTTCGAACATCACCCTTGTTTCGATTTGATTGGTTTGTCAAATCTC

upper sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 22
-----------------------------------------gtatgtttttctcaccatgtta-------tgtgtatttatgtattt---gagtacatgacatg-gctactaagctggagttaca--ttccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGTATGTCTCCCTTGTTTCGATTTGATTGGTTTGTGAAGTCCA
                                          ||| | |||     ||||||        ||| || |   || |||   ||  | |   | || | |      ||  | ||| |  || ||| |||| ||| | ||||||||||| ||||| || |||||||| ||||| || || || || ||||| |||||||||||||||||||||||||| |||||  
gtgtgaaatttatttccttttgtttttatttttgcccaaatttatttcttttcgttcatgttcagttccttgtttagtctggtgttttccgaacagaattcttgtgttttctgacttcacttaaaacttgcagATTTGTATGATTCACAAACTTGGCTATGGTAATTGGGATGAGCTGAAGGCAGCTTTTCGAATGTCGCCCTTGTTTCGATTTGATTGGTTTGTCAAGTCTC

upper sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 14
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 22
-----------------gtatgtttttctcaccatgttatgtgtatttatgtatttgagtacatgacatggctactaagctggagttacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGTATGTCTCCCTTGTTTCGATTTGATTGGTTTGTGAAGTCCA
                   |  | ||| |    || | ||   ||||  | ||||  | ||    |     |   | | || | | |   |  ||| | |||||||| || |||||||| ||||||||||||||||| || || || || || || |  || ||||||||| | ||||| |||||||| || ||| 
gtatgacatctatttatcaaactctttgttgagatttcattgttattgttttattctaatatgatattgacccgatgaacttgtgat---tatcagATATGCATGGTCCATAAACTTGGGTATGGAAACTGGGATGAGCTAAAGGCAGCGTTTCGGACATCCCCCTTGTTTAGGTTTGACTGGTTTGTAAAATCCC

upper sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 14
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 22
------------------------gtatgtttttctcaccatgttatgtgtatttatgtatttgagtacatgacatggctactaagctggagttacattcca----gCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGTATGTCTCCCTTGTTTCGATTTGATTGGTTTGTGAAGTCCA
                        || |||||    ||  |||||  |||| ||| ||| |     |  ||     |  |       ||     | | | ||    | | |||||||| ||||||||||||||||| ||||||||||| ||||| || || || || |  |||||||||||||| |||||||||||||| |||||  
gtgagaattgcaatcatctctctagtttgtttgatacaa-atgttg-gtgtgtttttgtttgacgattgatcttccgagtgtattcatgcctccatacttcatgtagATATGCATGGTTCACAAACTTGGATATGGGAACTGGGATGAGCTGAAGGCAGCATTTCGCACTTCTCCCTTGTTTCGTTTTGATTGGTTTGTAAAGTCTC

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|19057932|gb|BM736599.1|BM736599
EST:     ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATG                         CTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
genomic: ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatgttttt ... tacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
EST: gi|32943371|gb|CF048190.1|CF048190
EST:     ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATG                         CTTTGCATGGTGCACAAACTTGGATATGGAAACTGTTATTAACTGAAAGCT
genomic: ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatgttttt ... tacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
EST: gi|18648750|gb|BM497569.1|BM497569
EST:     ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATG                         C-TTGCATGG-GCACAAAC-TGGATATGGAAACTGGGATGAACTGAAAGCT
genomic: ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatgttttt ... tacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
EST: gi|5901273|gb|AW042373.1|AW042373
EST:     ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATG                         CTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
genomic: ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatgttttt ... tacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
EST: gi|67013537|gb|CO442286.1|CO442286
EST:     ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATG                         CTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
genomic: ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatgttttt ... tacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
EST: gi|60342830|gb|DN209803.1|DN209803
EST:     ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATG                         CTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAA-CT
genomic: ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatgttttt ... tacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
EST: gi|87153391|gb|DY398180.1|DY398180
EST:     ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATG                         CTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
genomic: ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatgttttt ... tacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
EST: gi|22489820|gb|BU049743.1|BU049743
EST:     ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATG                         CTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
genomic: ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatgttttt ... tacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
EST: gi|78022398|gb|DV490785.1|DV490785
EST:     ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATG                         CTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
genomic: ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatgttttt ... tacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
EST: gi|7216553|gb|AW562675.1|AW562675
EST:     ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATG                         CTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
genomic: ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatgttttt ... tacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
EST: gi|33098069|gb|CF058029.1|CF058029
EST:     ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATG                         CTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
genomic: ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatgttttt ... tacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
EST: gi|19855114|gb|BQ060166.1|BQ060166
EST:     CGGCCATATATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATG                         C-TTGCATGG-GCACAAAC-TGGATATGGAAACTGGGATGAACTGAAAGCT
genomic: CGGCCA-AAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatgttttt ... tacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
EST: gi|18648751|gb|BM497570.1|BM497570
EST:     ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATG                         CTTTGCATGG-GCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
genomic: ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatgttttt ... tacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
EST: gi|5915179|gb|AW052820.1|AW052820
EST:     ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGNCCGCTTTATG                         CTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT
genomic: ACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatgttttt ... tacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCT

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: 1520

GAAGAAGCTAGACCGCTACAAGAACCCATGGTTAGAGTTGAAAATTCAGTACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatgttttt ... tacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGTATGTCTCCCTTGTTTCGATTTGATTGGTTTGTGAAGTCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 430

GAAGAAGCTAGACCGCTACAAGAACCCATGGTTAGAGTTGAAAATTCAGTACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatgttttt ... tacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGTATGTCTCCCTTGTTTCGATTTGATTGGTTTGTGAAGTCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 524

GAAGAAGCTAGACCGCTACAAGAACCCATGGTTAGAGTTGAAAATTCAGTACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatgttttt ... tacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGTATGTCTCCCTTGTTTCGATTTGATTGGTTTGTGAAGTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 653

GAAGAAGCTAGACCGCTACAAGAACCCATGGTTAGAGTTGAAAATTCAGTACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatgttttt ... tacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGTATGTCTCCCTTGTTTCGATTTGATTGGTTTGTGAAGTCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatttatgtatttgagtacatgacatggctactaagctggagttacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGTATGTCTCCCTTGTTTCGATTTGATTGGTTTGTGAAGTCCA
     ttatgtattt  TA-rich tract