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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacaagcattttattcacttctgaatcacttatgtaattacacaatatccagtcatatgtacatgctctgatacggcttctgttgtccaaaatcaacagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATGAGATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTC

Basic information

species Zea mays
transcript GRMZM2G414496_T07
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G414496_T08 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os07g08729.1 (Oryza sativa), 3'ss of exon 16
--ttacaagcattttattcacttctgaatcacttatgtaattacacaatatccagtcatatgtacatgctctgatacggcttctgttgtccaaaatcaa-cagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATGAGATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTC
    | | |||||  |      |    | ||||    ||  | ||  |   |    | |||    ||  |     | |  |||| || ||||  || || |||| ||||||||||||||||||||||||||||||||||||||||| |||||||||||||| ||| | |||||||| ||||| ||||| ||||| |||||| |
gtcaataggcattaaagaagtattatgaacactccaata--tgcagtacgactgaac-tattctgatcattgttcatgttttctattttccaccatgaaacagCATTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGTGAAGATGAGATGCCAGATGTCAAGGATGAAACCCTTCCTGATGAAGAGGGCTTGGC
















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|32931709|gb|CF036521.1|CF036521
EST:     CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAG                         CTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
genomic: CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAGgtaaatagct ... aaatcaacagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
EST: gi|14245465|gb|BG874047.1|BG874047
EST:     CATGCCAATTTGCTAACCCAG                         CTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
genomic: CATGCCAATTTGCTAACCCAGgtaaatagct ... aaatcaacagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
EST: gi|76285513|gb|DV025081.1|DV025081
EST:     CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAG                         CTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
genomic: CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAGgtaaatagct ... aaatcaacagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
EST: gi|211402618|gb|FL252146.1|FL252146
EST:     CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAG                         CTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
genomic: CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAGgtaaatagct ... aaatcaacagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
EST: gi|78544440|gb|DV621938.1|DV621938
EST:     CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAG                         CTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
genomic: CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAGgtaaatagct ... aaatcaacagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
EST: gi|40334316|gb|CK368386.1|CK368386
EST:     CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAG                         CTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGGGAAGATG
genomic: CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAGgtaaatagct ... aaatcaacagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
EST: gi|71446738|gb|DR827788.1|DR827788
EST:     CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAG                         CTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
genomic: CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAGgtaaatagct ... aaatcaacagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
EST: gi|60338376|gb|DN205349.1|DN205349
EST:     GCATGCCAATTTGCTAACCCAG                         CTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
genomic: GCATGCCAATTTGCTAACCCAGgtaaatagct ... aaatcaacagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
EST: gi|101382023|gb|EB813067.1|EB813067
EST:     GCATGCCAATTTGCTAACCCAG                         C-TTGCAAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGAT
genomic: GCATGCCAATTTGCTAACCCAGgtaaatagct ... aaatcaacagCTTTGC-AAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGAT
EST: gi|33097000|gb|CF056960.1|CF056960
EST:     CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAG                         CTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
genomic: CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAGgtaaatagct ... aaatcaacagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
EST: gi|71761431|gb|DR959368.1|DR959368
EST:     CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAG                         CTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
genomic: CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAGgtaaatagct ... aaatcaacagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
EST: gi|24768047|gb|CA403179.1|CA403179
EST:     CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAG                         CTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
genomic: CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAGgtaaatagct ... aaatcaacagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
EST: gi|32935327|gb|CF040139.1|CF040139
EST:     CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAG                         CTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG
genomic: CAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAGgtaaatagct ... aaatcaacagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATG

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), 49 (downstream exon)
Score: 278

GATGCACCGCGTGCAACAGATGAACAAATCAAGAAAGCTTCGAACATATTCAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAGgtaaatagct ... aaatcaacagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATGAGATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTC


Block sizes: 40 (upstream exon), 47 (downstream exon)
Score: 32

GATGCACCGCGTGCAACAGATGAACAAATCAAGAAAGCTTCGAACATATTCAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAGgtaaatagct ... aaatcaacagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATGAGATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTC


Block sizes: 45 (upstream exon), 42 (downstream exon)
Score: 41

GATGCACCGCGTGCAACAGATGAACAAATCAAGAAAGCTTCGAACATATTCAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAGgtaaatagct ... aaatcaacagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATGAGATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTC


Block sizes: 40 (upstream exon), 42 (downstream exon)
Score: 35

GATGCACCGCGTGCAACAGATGAACAAATCAAGAAAGCTTCGAACATATTCAAACGTATTGATCTGATAAATTTCTCTGCATGCCAATTTGCTAACCCAGgtaaatagct ... aaatcaacagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATGAGATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatccagtcatatgtacatgctctgatacggcttctgttgtccaaaatcaacagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATGAGATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTC
                     ctctgat  putative branch site (score: 35)
                                            aaaatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttacaagcattttattcacttctgaatcacttatgtaattacacaatatccagtcatatgtacatgctctgatacggcttctgttgtccaaaatcaacagCTTTGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATGAGATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG