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

...ttataatgccacttgtttgcagattcctagttctagtcgtatttacttctgattttagccatgctgttctataagtttgtacatttttatgttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGCTGTGACATTTGTAACCGATGATGATAGATGCCTCTTGAAAGCAATT

Basic information

species Zea mays
transcript GRMZM2G420865_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G420865_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os12g29660.1 (Oryza sativa), 3'ss of exon 11
-ttataatgccacttgtttgcagattcctagttctagtcgtatttacttctgattttagccatgctgttctataagtttgtacatttttatgttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGCTGTGACATTTGTAACCGATGATGATAGATGCCTCTTGAAAGCAATT
 || |    |   |||| |     |    ||    | |  |      |  | || ||        | ||  |||| | | | | | || ||| | ||| |||||||| ||||||||||| |||||||| || ||||| |||||||| ||||||||||||||||| || || |||||||| | |||||||||||| |||
cttttgcccctttttgtcttgcagtcataaggaagaattatgccatttaattatgttctttgacttctttcataaatgttt-cttgttcatgctgttgcagTTATCTACATCGTGTTGGACGCACTGCTCGTGCAGGCAGAGAAGGATATGCTGTGACATTTGTTACTGACGATGATAGGTCCCTCTTGAAAGCTATT

upper sequence: GRMZM2G420865_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv18s0001g14540.t01 (Vitis vinifera), 3'ss of exon 11
ttataatgccacttgtttgcagattcctagt-tctagtcgtatttacttctg-attttagccatgct---gttctataagtttgtacattt--ttatgttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGCTGTGACATTTGTAACCGATGATGATAGATGCCTCTTGAAAGCAATT
       ||     | ||  | | |   ||| |  | | ||  |    | || |||| ||   | ||    ||   | | ||| | | |||  |    || ||| |||||  ||||||||||||| || || ||  |||| || |||||||| |||||||| ||||||||||| ||| |||||||||  ||||||||| | || 
-------gctttcagcttatataataagagtgttcaatggtcatactctgtgcatttgagtggttcttatatttctttatttttttcttttgttctcatttttgcagTTACGTTCATCGTGTTGGTCGTACAGCAAGGGCTGGTAGAGAAGGATATGCTGTTACATTTGTAACTGATAATGATAGATCTCTCTTGAAATCTATA
















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|78027541|gb|DV495928.1|DV495928
EST:     GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAAC                         TTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
genomic: GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAACgtaagtgata ... gttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
EST: gi|211352888|gb|FL146172.1|FL146172
EST:     GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAAC                         TTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
genomic: GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAACgtaagtgata ... gttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
EST: gi|67031210|gb|CO459959.1|CO459959
EST:     GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAAC                         TTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAG-CTATGC
genomic: GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAACgtaagtgata ... gttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
EST: gi|211352883|gb|FL146167.1|FL146167
EST:     GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAAC                         TTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
genomic: GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAACgtaagtgata ... gttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
EST: gi|4887454|gb|AI677553.1|AI677553
EST:     GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAAC                         TTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
genomic: GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAACgtaagtgata ... gttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
EST: gi|211352882|gb|FL146166.1|FL146166
EST:     GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAAC                         TTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
genomic: GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAACgtaagtgata ... gttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
EST: gi|31349040|gb|CD433397.1|CD433397
EST:     GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAAC                         TTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
genomic: GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAACgtaagtgata ... gttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
EST: gi|211352886|gb|FL146170.1|FL146170
EST:     GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAAC                         TTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
genomic: GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAACgtaagtgata ... gttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
EST: gi|211352887|gb|FL146171.1|FL146171
EST:     GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAAC                         TTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
genomic: GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAACgtaagtgata ... gttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
EST: gi|211352885|gb|FL146169.1|FL146169
EST:     GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAAC                         TTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
genomic: GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAACgtaagtgata ... gttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
EST: gi|4887453|gb|AI677552.1|AI677552
EST:     GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAAC                         TTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
genomic: GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAACgtaagtgata ... gttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
EST: gi|78090029|gb|DV518403.1|DV518403
EST:     GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAAC                         TTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
genomic: GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAACgtaagtgata ... gttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGC
EST: gi|166430507|gb|EG124353.1|EG124353
EST:     GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAAC                         TTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTA
genomic: GTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAACgtaagtgata ... gttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTA

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: 112

GGGATTGATATTGTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAACgtaagtgata ... gttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGCTGTGACATTTGTAACCGATGATGATAGATGCCTCTTGAAAGCAATT


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

GGGATTGATATTGTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAACgtaagtgata ... gttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGCTGTGACATTTGTAACCGATGATGATAGATGCCTCTTGAAAGCAATT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 78

GGGATTGATATTGTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAACgtaagtgata ... gttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGCTGTGACATTTGTAACCGATGATGATAGATGCCTCTTGAAAGCAATT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 68

GGGATTGATATTGTTGGTGTTCAGACTGTAATAAATTTCGCATGCCCAAGAGATGTGAAAACgtaagtgata ... gttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGCTGTGACATTTGTAACCGATGATGATAGATGCCTCTTGAAAGCAATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctgattttagccatgctgttctataagtttgtacatttttatgttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGCTGTGACATTTGTAACCGATGATGATAGATGCCTCTTGAAAGCAATT
 ttctgat  putative branch site (score: 68)
                        tataagtttgtacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttataatgccacttgtttgcagattcctagttctagtcgtatttacttctgattttagccatgctgttctataagtttgtacatttttatgttattgtagTTATCTTCATCGTGTTGGCCGCACTGCGCGGGCAGGAAGAGAAGGCTATGCTGTGACATTTGTAACCGATGATGATAGATGCCTCTTGAAAGCAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA