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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttcgaagtacttttttgtgtgccatgtgcacctatatatatcaaccctctttttaatactactacaaatactgatgctttagtattgactgaacaaagGATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCTTGTGTTGAAAGAAAAGAAGATAACTATTTCTTTGCCTTGTCAAAGTACC

Basic information

species Zea mays
transcript GRMZM2G029055_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029055_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g11120.1 (Oryza sativa), 3'ss of exon 3
--tgttcgaagtacttttttgtgtgccatgtgcacctatatatatcaaccctctttttaatactactacaaatactgatgctttagtattgactgaa-caaagGATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCTTGTGTTGAAAGAAAAGAAGATAACTATTTCTTTGCCTTGTCAAAGTACC
  | |||    |      |||| |||||| | ||| |||| ||       || |||  || | |  ||    | |  ||  | | || |||  ||||  | |||| |||||||||||   ||| ||||| |||||||| |||||||| |||||||||||   |||||| ||||| ||||||||||||||||||||||| ||||
tcttttcatgctttacagttgt-tgccatattcacttatagatcatccttctttttccaacattggtaattgtgcaaat--tctggttttgtttgaagtacagGACGAAAAAGAGCTTGGGGAAAACAAATGTTGCCCAGTGCATCTAAAGCCTTGTGTACCAAGAAAGGAAGACAACTATTTCTTTGCCTTGTCAAAATACC

upper sequence: GRMZM2G029055_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT3G55400.1 (Arabidopsis thaliana), 3'ss of exon 2
tgttcgaagtacttttttgtgtgccatgtgcacctatatatatcaaccctctttttaatactactacaaatactgat--gctttagtattgactgaacaaagGATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCTTGTGTTGAAAGAAAAGAAGATAACTATTTCTTTGCCTTGTCAAAGTACC
             |||   | ||  || || |    |||||||  ||  ||||     | | || |    ||  | |  |||||  | |||| |      ||||||| |||||| |  | || ||||||||||||||||| ||||  | ||| ||||||| ||| |||||||||||||| |||||||| ||||| || || |
------------gtttgattttgaaatttggaaaggtatatat--actttcttgcctgtgccacaagctttatgggtctgctttgtttttgaattc-tgtagGATGAGAAAGAGTTGCTTGAAAACAATTGTTGCCCTGTCCATCAAATGCCATGTGTTGCAAGGAAAGAAGATAACTACTTCTTTGCTTTGTCGAAATATC

upper sequence: GRMZM2G029055_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0019g00810.t01 (Vitis vinifera), 3'ss of exon 3
tgttcgaagtacttttt-tgtgtgccatgtgcacctatatatatcaaccctctttttaatactactacaaatactgatgctttagtattgactgaacaaa------gGATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCTTGTGTTGAAAGAAAAGAAGATAACTATTTCTTTGCCTTGTCAAAGTACC
      || || | | |   ||     | |||  ||        |  ||| |    |  | | | |  || ||||  |    || | || | |  | |||      |||||| || ||  |  |||| || || ||||||||| ||||  | ||||| ||||||   || |||||||||||||| ||||||||| |||||||||| |
------aaatagtgtatgcatgcatggtttgcttctcccccctccccccccccccctttttcaaatg-aagtacttgtctaatattgttaattcgaaaaaactgcagGATGAGAAGGAATTGCTGGAAAATAACTGTTGCCCTATGCACTTAAAGCCATGTGTTTTGAGGAAAGAAGATAACTACTTCTTTGCCCTGTCAAAGTATC

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|148964149|gb|EE015315.2|EE015315
EST:     ATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAG                         GATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCT
genomic: ATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAGgtaagctttc ... ctgaacaaagGATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCT
EST: gi|211024980|gb|FL404649.1|FL404649
EST:     ATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAG                         GATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCAT
genomic: ATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAGgtaagctttc ... ctgaacaaagGATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCAT
EST: gi|211284183|gb|FL388287.1|FL388287
EST:     ATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAG                         GA-GAAAAGGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTG
genomic: ATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAGgtaagctttc ... ctgaacaaagGATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTG
EST: gi|148957317|gb|EC903360.2|EC903360
EST:     ATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAG                         GATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCT
genomic: ATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAGgtaagctttc ... ctgaacaaagGATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCT
EST: gi|149076722|gb|EE165367.2|EE165367
EST:     ATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAG                         GATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCT
genomic: ATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAGgtaagctttc ... ctgaacaaagGATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCT
EST: gi|78110212|gb|DV528627.1|DV528627
EST:     ATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAG                         GATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCT
genomic: ATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAGgtaagctttc ... ctgaacaaagGATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCT
EST: gi|78086927|gb|DV515320.1|DV515320
EST:     ATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAG                         GATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCT
genomic: ATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAGgtaagctttc ... ctgaacaaagGATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCT
EST: gi|211351239|gb|FL411973.1|FL411973
EST:     TAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTTGTGAAGAGTACACG                         CATGAAAAAGAGCTTTTGGAAAACA
genomic: TAGAGCTGATTATGAAGGACTTTATTGTGTGAGCT-GTGAAGAGTACAAGgtaagctttc ... ctgaacaaagGATGAAAAAGAGCTATTGGAGAACA

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), 48 (downstream exon)
Score: 76

GGCTGTTGTGAACGAATTCTATTCCAGAGTGTTAAACAATGGCGACATATATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAGgtaagctttc ... ctgaacaaagGATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCTTGTGTTGAAAGAAAAGAAGATAACTATTTCTTTGCCTTGTCAAAGTACC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 105

GGCTGTTGTGAACGAATTCTATTCCAGAGTGTTAAACAATGGCGACATATATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAGgtaagctttc ... ctgaacaaagGATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCTTGTGTTGAAAGAAAAGAAGATAACTATTTCTTTGCCTTGTCAAAGTACC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 27

GGCTGTTGTGAACGAATTCTATTCCAGAGTGTTAAACAATGGCGACATATATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAGgtaagctttc ... ctgaacaaagGATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCTTGTGTTGAAAGAAAAGAAGATAACTATTTCTTTGCCTTGTCAAAGTACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 91

GGCTGTTGTGAACGAATTCTATTCCAGAGTGTTAAACAATGGCGACATATATAGAGCTGATTATGAAGGACTTTATTGTGTGAGCTGTGAAGAGTACAAGgtaagctttc ... ctgaacaaagGATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCTTGTGTTGAAAGAAAAGAAGATAACTATTTCTTTGCCTTGTCAAAGTACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accctctttttaatactactacaaatactgatgctttagtattgactgaacaaagGATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCTTGTGTTGAAAGAAAAGAAGATAACTATTTCTTTGCCTTGTCAAAGTACC
                                       tattgac  putative branch site (score: 91)
      tttttaatactactac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttcgaagtacttttttgtgtgccatgtgcacctatatatatcaaccctctttttaatactactacaaatactgatgctttagtattgactgaacaaagGATGAAAAAGAGCTATTGGAGAACAATTGTTGCCCTGTGCATCTGAAGCCTTGTGTTGAAAGAAAAGAAGATAACTATTTCTTTGCCTTGTCAAAGTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - gccatgt
- - - - - - - - - - - - - - -gcaccta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgc