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

...tctaaactagattggctacttctgagtctgcatgtttcacttaattcattctcctgtttttgctaacaactaaactaatggtagtgtcatctcgttgcagCGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGTGATCCTGCTATG

Basic information

species Zea mays
transcript GRMZM2G171435_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171435_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 7
-----------tctaaactagattggctacttctgagtctgcat-gtttcacttaattcattctcctgtttttgctaacaactaaactaatggtagtgtcatctcgttgcagCGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGTGATCCTGCTATG
           |||   ||   ||  ||  | ||  || | ||| |   |||||  ||||| ||    | | ||  ||     || || |||  |||||||| |   ||||||| |||||||| ||||||||| | ||||||||  ||||| ||||||||||||| || |||||||||||||||||||||||||| || |||||  || ||
gttatataatttcttttcttattt--ctcttgctttgtttacattggagcacttttttcatccttggctctctgtgaa-----aagctgatgtcagtgtcatttttgtgcagCGTATCTTGAATGTTCAGTACTCAATTCCAGAAAACGTGGACATATCTCCAGAATGTAGGCATCTAATTTCGAGGATTTTTGTCGGGGATCCGTCTTTG

upper sequence: GRMZM2G171435_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA07G33120.1 (Glycine max), 3'ss of exon 7
tctaaactagattggctacttctgagtctgcatgtttcacttaattcattctcctgtttttgctaacaactaaactaatggtagtgtcatctcgttgcagCGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGTGATCCTGCTATG
    |||||      ||  || | |  |    || | |  || ||| | |     |||||         ||||| | |||  | |||    | ||||||| | || ||||| ||||||||| | ||||| ||||||||  |||||||| | |||||| | ||||| || || ||||||||||| | ||||||||| | |
--gtaactaatgacactttttttcaaccaatgtggtacttttgattgaatta---gttttc--------ctaaattgatg--aatgt----tggttgcagAGGATTTTGAATGTTCAGTACTCAATTCCTGACTACGTTCACATATCTTCCGAGTGCCGTCATCTGATATCAAGGATTTTTGTCGCTGATCCTGCAAGG

upper sequence: GRMZM2G171435_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 7
tctaaactagattggctacttctgagtctgcatgtttcacttaattcattctcctgtttttgct-aacaactaaactaatggtagtgtcatctcgttgcagCGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGTGATCCTGCTATG
                     || |   ||||  |||   | ||| || | |  |  |||   | ||  | |   |  |   |  ||    || ||||||| | || ||||| ||||||||| | ||||| ||||| ||  | |||||| | |||||| | ||||| || || ||||||||||||| ||||||||| | |
-----------------gtaactaa--ttgcacctttttttcaat-cagtgtgttactttgattgaattagttttcctaaactgatgcatgcttgttgcagAGGATTTTGAATGTTCAGTACTCAATTCCTGACTATGTTCATATATCTTCCGAGTGCCGTCATCTGATATCAAGGATTTTTGTTGCTGATCCTGCAAAG

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|148929921|gb|EE285697.2|EE285697
EST:     ATCCTTTTGAAGACCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAG                         CGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCA
genomic: ATCCTTTTGAAGACCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAGgttatttttt ... ctcgttgcagCGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCA
EST: gi|32859143|gb|CD998824.1|CD998824
EST:     ATCCTTTTGAAGACCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAG                         CGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCA
genomic: ATCCTTTTGAAGACCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAGgttatttttt ... ctcgttgcagCGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCA
EST: gi|6022633|gb|AW067445.1|AW067445
EST:     ATCCTTTTGAAGACCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAG                         CGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCA
genomic: ATCCTTTTGAAGACCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAGgttatttttt ... ctcgttgcagCGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCA
EST: gi|88749704|gb|DY533845.1|DY533845
EST:     TTCCGCAAGACAATTCAG                         CGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCA
genomic: TTCCGCAAGACAATTCAGgttatttttt ... ctcgttgcagCGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCA
EST: gi|78107855|gb|DV526273.1|DV526273
EST:     ATCCTTTTGAAGACCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAG                         CGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCA
genomic: ATCCTTTTGAAGACCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAGgttatttttt ... ctcgttgcagCGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCA
EST: gi|9028616|gb|BE238656.1|BE238656
EST:     ATCCTTTTGAAGACCCAGAAGATTCTAAGAACTTCCGCAAGACAATTCAG                         CGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCA
genomic: ATCCTTTTGAAGACCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAGgttatttttt ... ctcgttgcagCGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCA

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: 130

TGATGTTTGGTCATGTGGTGTAACCCTCTATGTAATGGCTGTTGGTGCATATCCTTTTGAAGACCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAGgttatttttt ... ctcgttgcagCGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGTGATCCTGCTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 77

TGATGTTTGGTCATGTGGTGTAACCCTCTATGTAATGGCTGTTGGTGCATATCCTTTTGAAGACCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAGgttatttttt ... ctcgttgcagCGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGTGATCCTGCTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

TGATGTTTGGTCATGTGGTGTAACCCTCTATGTAATGGCTGTTGGTGCATATCCTTTTGAAGACCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAGgttatttttt ... ctcgttgcagCGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGTGATCCTGCTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 78

TGATGTTTGGTCATGTGGTGTAACCCTCTATGTAATGGCTGTTGGTGCATATCCTTTTGAAGACCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAGgttatttttt ... ctcgttgcagCGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGTGATCCTGCTATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattctcctgtttttgctaacaactaaactaatggtagtgtcatctcgttgcagCGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGTGATCCTGCTATG
                                         tcatctc  CT-rich tract
                         taaactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctaaactagattggctacttctgagtctgcatgtttcacttaattcattctcctgtttttgctaacaactaaactaatggtagtgtcatctcgttgcagCGCATCTTGAACGTTCAGTACGCCATTCCAGACTACGTGAACATATCTCCAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGTGATCCTGCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT