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'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgcctttaagttttgtagctttattataggacttaagtatgcacattctatttaatcagacatggctaaggtgctaattttttatgtactgtctgctggatgaacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG

Basic information

species Zea mays
transcript GRMZM2G037683_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 7
--------------------------------gtatgtgcctttaagttttgtagctttattataggacttaagtatg----------cacattctatttaatcag----------acatggctaaggtgctaatttt---ttatgtactgtctgc--------tggatgaacactt--cagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG
                                | |       ||||||| | || |   ||||  | |||   | |||          ||  ||| | || | |||          |||||  || | |  |  ||||   |||  ||     | |        |  |  | |||||  ||||||||||| ||||||||||| ||  | ||||| | ||||||||| ||||| |||||||| ||||||||||||||||||||||||||||||||||||
gtaaggccataggattgatgttttctcaaattgaacaacgaattaagttat-taacacgattactgtactggtgcatgtggaaagcaacatcttcaagttcagcagctttatggggacatgcatatgttcttttttttagtttaaatataaatttcaataattttcaaaaaccactttacagGAAAGCTTCATGATGCACGATGATGCGGTGCTTTCTGTTGATTTCAGTAGAGATTCTGAGATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG

upper sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 8
-gtatgtgcctttaagttttgtagctttatt-ataggacttaagtatgcacattctatttaatcagacatggctaaggtgctaattttttatgtactgtctgctggatgaacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG
 |||||    | | |   |  | |||| ||| ||      |||| ||  | ||  |||  | |     ||| || ||     |||||| |             |  ||||||  | ||||||   || |||||||| || ||  ||||||| ||||| || ||||| || ||||| |||||||| |||||||| || || |||||||||||||| 
tgtatgaagttatgaacatatttgcttgatttatgctgtctaagaatttaaatattatcgatt----tatgccttaga----aattttctg----------attctatgaac-ttgcagGAAGTGTTCATGATGCATGATGATGCTGTGCTTTGTGTAGACTTTAGCAGAGATTCAGAAATGCTTGCATCTGGGTCTCAAGATGGAAAGATTAAA

upper sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 8
gtatgtgcctttaagttttgtagctttattataggacttaagtatgcacattctatttaatcagacatggctaaggtgctaattttttatgtactgtctgctggatgaacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG
 ||||    | ||||  || ||    || ||| |   | ||| |      || || || ||||         || ||  |  |   |||   | |      |  ||||||  | ||||||   || |||||||| || ||  ||||||| ||||| || ||||| || ||||| |||||||| |||||||| || || |||||||||||||| 
-tatgc-tgtctaagaattttaa---tactattgatttaaaggaaatttcttatagtttatca---------aaagtctt--tgccttagacatttctgattctatgaac-ttgcagGAAGTGTTCATGATGCATGATGATGCTGTGCTTTGTGTAGACTTTAGCAGAGATTCAGAAATGCTTGCATCTGGGTCTCAAGATGGAAAGATTAAA

upper sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatgtgcctttaagttttgtagctttattataggacttaagtatgcacattctatttaatcagacatggctaaggtgctaattttttatgtactgt--ctgctg-gatgaacactt--cagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG
                   ||| ||    |           |||| || | |       |||||   ||| ||| | | |    ||  ||   || |   | ||  ||| ||    |  ||||||   || |||||||| || || ||||| || ||  | || ||||| || ||||| || ||||| |||||||| ||||| |||||||||||||| 
---------------ccaagtatctcgtctgagacttcctggtatacaaaat-------atcagttttggataaagagttcccattccatcctctttacttactatgattaatttctgacagGAATCTTTCATGATGCATGATGATCCTGTCCTCTGCATAGACTTTAGCAGAGATTCAGAGATGCTTGCATCTGGGTCACAAGATGGAAAGATTAAA

upper sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 8
gtatgtgcctttaagttttgtagctttattataggacttaagtatgcacattctatttaatcagacatggctaaggtgctaattttttatgtactgtc-tgctggatgaacactt-cagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG
           ||  ||| ||  ||  |    |  |   || | |   || | ||| |  |      ||||  ||  ||    | |  || | ||| | ||||  ||||||  || ||||||| |||||||||||| || ||  |||| || |||||||||||||| || ||||| || ||||| |||||||||||||| |||||||| || || 
---------cctatttttggttcctacaaagcacaaagaaacttttagcaatttatctttt------tggc--agaggcctcctatgaatttgctgacatgct--atgaacttttacagGAAACCTTTATGATGCATGATGATGCTGTCCTTTGTGTTGATTTTAGCAGAGATTCGGAGATGCTTGCATCTGGATCACAAGATGGAAAAATCAAA

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|211525027|gb|FL310982.1|FL310982
EST:     GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATRTCAAGCCGAT                         GAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG
genomic: GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGATgtatgtgcct ... aacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG
EST: gi|211475898|gb|FL358552.1|FL358552
EST:     GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGAT                         GAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG
genomic: GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGATgtatgtgcct ... aacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG
EST: gi|76010783|gb|DT937953.1|DT937953
EST:     GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCTATATCAAGCCGAT                         GAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG
genomic: GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGATgtatgtgcct ... aacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG
EST: gi|67019283|gb|CO448032.1|CO448032
EST:     GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGAT                         GAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG
genomic: GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGATgtatgtgcct ... aacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG
EST: gi|23357683|gb|BU645332.1|BU645332
EST:     GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGAT                         GAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG
genomic: GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGATgtatgtgcct ... aacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG
EST: gi|111433444|gb|EE297761.1|EE297761
EST:     GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGAT                         GAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG
genomic: GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGATgtatgtgcct ... aacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG
EST: gi|22521028|gb|BU079839.1|BU079839
EST:     GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGAT                         GAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG
genomic: GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGATgtatgtgcct ... aacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG
EST: gi|211160334|gb|FL327726.1|FL327726
EST:     GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGAT                         GAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG
genomic: GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGATgtatgtgcct ... aacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG
EST: gi|26457208|gb|CA828791.1|CA828791
EST:     GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGAT                         GAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG
genomic: GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGATgtatgtgcct ... aacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG
EST: gi|91873183|gb|EB403140.1|EB403140
EST:     GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGAT                         GAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG
genomic: GGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGATgtatgtgcct ... aacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGG

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: 47 (upstream exon), 49 (downstream exon)
Score: 290

GTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGATgtatgtgcct ... aacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

GTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGATgtatgtgcct ... aacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 117

GTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGATgtatgtgcct ... aacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

GTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGATgtatgtgcct ... aacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacatggctaaggtgctaattttttatgtactgtctgctggatgaacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG
              tgctaat  putative branch site (score: 94)
                 taattttttatgtact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgcctttaagttttgtagctttattataggacttaagtatgcacattctatttaatcagacatggctaaggtgctaattttttatgtactgtctgctggatgaacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA