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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggtgatccatcttgctaatattggtgtatttatctattcattgattacatcattaatgttggttcagattactatgtatgcctgtacaagttccatttcaaacaattcatagttcgcctactgatcttattgttttaaatttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGCAATTGCGTCAAGCGTGTGGTGGTCATTGTGACCTCTGTTCTGTTCTTCA

Basic information

species Zea mays
transcript GRMZM2G047404_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047404_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os09g12600.1 (Oryza sativa), 3'ss of exon 7
------------------------gtggtgatccatcttgctaatattggtgtatttatctattcatt--gattacatcattaatgttggttcagattactatgtatgcctgtacaagttccatttcaaacaattcatagttcgcctactgatcttattgttttaaatttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGCAATTGCGTCAAGCGTGTGGTGGTCATTGTGACCTCTGTTCTGTTCTTCA
                            |       | |  | | ||   || ||     | ||||||     || ||  |   || ||  | | |||||  |   | | |  |  | |  |||   | |   | || ||  |   |  || |  | |    |  ||||| |||||||| || ||||||||||| || || || ||||| || || || || ||||| || || |||||||| ||||||||||||||||| || |||||||||||| 
gtcagccatctaattgattttctaaaaatagcttggccttttgaaatctctggatgcgcttgttcatttcagatagattctatgtgctgaat-acattacagttgttacattgatgaat--catcatacatg-tgcaaagcccatgtcttgctgatctcacat--aatttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGTAACTGTGTCAAGCGAGTGGTGGTCATTGTGACATCCGTTCTGTTCTTCC
















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|37395421|gb|CF634991.1|CF634991
EST:     TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG                         GTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
genomic: TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
EST: gi|8103136|gb|AW927794.1|AW927794
EST:     TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG                         GTATCATACATGATCCTCGCCAGCGGTATCCCCAGTCACACATTCAGTGGG
genomic: TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAG-GGTATCCCCAGTCACACATTCAGTGGG
EST: gi|40336776|gb|CK370846.1|CK370846
EST:     TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG                         GTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
genomic: TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
EST: gi|60395055|gb|DN227924.1|DN227924
EST:     TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG                         GTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
genomic: TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
EST: gi|116814527|gb|EC857099.1|EC857099
EST:     TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACCG                         GTGTCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATACAGTGGGC
genomic: TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
EST: gi|67026165|gb|CO454914.1|CO454914
EST:     TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG                         GTGTCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
genomic: TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
EST: gi|23199512|gb|BU582077.1|BU582077
EST:     TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG                         GTGTCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
genomic: TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
EST: gi|211071461|gb|FL174369.1|FL174369
EST:     TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG                         GTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
genomic: TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
EST: gi|23199513|gb|BU582078.1|BU582078
EST:     TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG                         GTGTCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
genomic: TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
EST: gi|14191027|gb|BG833257.1|BG833257
EST:     TATACTCAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG                         GTGTCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
genomic: TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
EST: gi|33103829|gb|CF063789.1|CF063789
EST:     TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG                         GTGTCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
genomic: TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
EST: gi|7844570|gb|AW787792.1|AW787792
EST:     TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG                         GTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
genomic: TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
EST: gi|37384374|gb|CF629256.1|CF629256
EST:     TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG                         GTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
genomic: TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
EST: gi|211145645|gb|FL480700.1|FL480700
EST:     TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG                         GTGTCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
genomic: TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
EST: gi|9028527|gb|BE238522.1|BE238522
EST:     TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG                         GTATCATGCATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
genomic: TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
EST: gi|12046824|gb|BF728963.1|BF728963
EST:     TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG                         GTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
genomic: TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
EST: gi|14191032|gb|BG833262.1|BG833262
EST:     TTGCTGCATTCTGCTTCCATGCATGCCAACAG                         GTGTCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
genomic: TTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
EST: gi|76281902|gb|DV021470.1|DV021470
EST:     TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG                         GTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
genomic: TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
EST: gi|110527946|gb|EE032130.1|EE032130
EST:     TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG                         GTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC
genomic: TATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGC

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: 49 (upstream exon), 49 (downstream exon)
Score: 336

GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGCAATTGCGTCAAGCGTGTGGTGGTCATTGTGACCTCTGTTCTGTTCTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGCAATTGCGTCAAGCGTGTGGTGGTCATTGTGACCTCTGTTCTGTTCTTCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 201

GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGCAATTGCGTCAAGCGTGTGGTGGTCATTGTGACCTCTGTTCTGTTCTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 649

GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAGgtggtgatcc ... tttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGCAATTGCGTCAAGCGTGTGGTGGTCATTGTGACCTCTGTTCTGTTCTTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcaaacaattcatagttcgcctactgatcttattgttttaaatttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGCAATTGCGTCAAGCGTGTGGTGGTCATTGTGACCTCTGTTCTGTTCTTCA
                        tactgat  putative branch site (score: 649)
                             atcttattgttttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggtgatccatcttgctaatattggtgtatttatctattcattgattacatcattaatgttggttcagattactatgtatgcctgtacaagttccatttcaaacaattcatagttcgcctactgatcttattgttttaaatttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGCAATTGCGTCAAGCGTGTGGTGGTCATTGTGACCTCTGTTCTGTTCTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG