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

...gaaagtttgaccctctacctgtaaggctgtaatgatcgaggacactgctagtgttatcttactagcttctaaacttagtttgctcatgtgttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTGCTGTCTTGACACACAAGGGAAGAAGTGCAGACTCTGGCCACTATGTTGG

Basic information

species Zea mays
transcript GRMZM2G017086_T03
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017086_T03 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 15
--------------------------------------------------------------------------------------------------gaaagtttgaccctctacctgtaaggc-tgtaatgatcgaggacactgctagtgttatcttactagcttctaaacttagtttgctcatgtgttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTGCTGTCTTGACACACAAGGGAAGAAGTGCAGACTCTGGCCACTATGTTGG
| | | |||| || || || | | | | |||| |||||| || ||||| | | |||||| | |||||| || |||||| | ||||||||||| || |||||| |||||||||| ||||||| ||||| ||||| || |||||||||||||| ||||| ||||||||
gcaagtagttggcttctgttcttatttagagaaatagctcagatacttgtactctttgtttgtcaaatggtggggtttttctgcctcttattatgttagggttctagtgtatctattcaagtagcatgctgcgacccatacttcaatactttcaatctggttagctt-tatgcttagctgtgttgtgtgtttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTGCTGTTTTGACGCACAAAGGGAGAAGTGCAGACTCAGGCCATTATGTTGG

upper sequence: GRMZM2G017086_T03 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA08G20900.1 (Glycine max), 3'ss of exon 15
gaaagtttgaccctctacctgtaaggctgtaatgatcgaggacactgctagtgttatcttactagcttctaaacttagtttgctcatgtgttaaatgcagCTGAGTCT-TCTCTACCAAAGAAACA--ATTAACTGGCGTCTATGATTTGGTTGCTGTCTTGACACACAAGGGAAGAAGTGCAGACTCTGGCCACTATGTTGG---------
|| | ||| | | || | || | | || | | | | || | || | |||| || ||| | ||| || |||| | | || |||||| | ||||| | ||||||||||||||||| || || |||||||| |||||||| || || || || ||||||||
----gtaaaaacctgcaacattatgcct--actcatttatt-tattttattttttgtttttttgttttctcaatccgcttt--ctgctttttactccattctctgtctatagGTGAAAAGGAAACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGCAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAA

upper sequence: GRMZM2G017086_T03 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA07G01480.1 (Glycine max), 3'ss of exon 15
gaaagtttgaccctctacctgtaaggctgtaatgatcgaggacactgctagtgttatcttactagcttctaaacttagtttgctc-atgtgttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTGCTGTCTTGACACACAAGGGAAGAAGTGCAGACTCTGGCCACTATGTTGG---------
|| | ||| | | || | | || | | || | |||| ||| | | | | ||| ||| ||| || | | || ||| | | | ||| | ||||| | ||||||||||||||||| || || |||||||| |||||||| || || || || ||||||||
----gtaaaaacctgcaacattatgctactcatatttatttattttgtttttgttttctcaatccactttctgctt--tttactccattctctgtctatagGTGA---------AAAGGAAACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGTAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAA

upper sequence: GRMZM2G017086_T03 (Zea mays), 3'ss of exon 15
lower sequence: AT1G51710.1 (Arabidopsis thaliana), 3'ss of exon 14
-------------------------------------------------------------------------------gaaagtttgaccctctacctgtaaggct------gtaatgatcgaggacactgctagtgttatcttactagcttctaaacttagtttgctcatgtgttaaatgcagCTGAGT--CTTCTCTACCAAAGAAAC--AATTAACTGGCGTCTATGATTTGGTTGCTGTCTTGACACACAAGGGAAGAAGTGCAGACTCTGGCCACTATGTTGG
| | ||| |||| || || || | ||| || || || || | || || || || || | || | | | | || | ||| || ||||| | | ||||| ||||||| ||||| ||||| ||||| |||||||| || |||||||||||||| || |||||||
gtacattatctaagacccccttttcaacatttttcttttctggcttggaaagagcggtaattggtttgtgtaaatactttgatgattgtttgtctatctatagatctcatttcaaagcaatcaagaaccttgtcagagcctaattgtgag-----gaatctaattctgttatataatggaactttttagGTACTTCTTCTGAGAAGGAAACTCACATGACTGGAATCTATGACTTGGTCGCTGTGTTGACCCACAAGGGCAGGAGTGCAGACTCTGGTCATTATGTTGC

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|5901176|gb|AW042276.1|AW042276
EST:     GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG                         CTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTG
genomic: GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAGgcaagttgtt ... ttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTG
EST: gi|12968043|gb|BG264990.1|BG264990
EST:     GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG                         CTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCG
genomic: GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAGgcaagttgtt ... ttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCG
EST: gi|5296339|gb|AI783109.1|AI783109
EST:     GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG                         CTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTG
genomic: GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAGgcaagttgtt ... ttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTG
EST: gi|5932702|gb|AW057063.1|AW057063
EST:     GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG                         CTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTG
genomic: GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAGgcaagttgtt ... ttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctagtgttatcttactagcttctaaacttagtttgctcatgtgttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTGCTGTCTTGACACACAAGGGAAGAAGTGCAGACTCTGGCCACTATGTTGG
                     ttctaaa  putative branch site (score: 2)
 ttatctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaagtttgaccctctacctgtaaggctgtaatgatcgaggacactgctagtgttatcttactagcttctaaacttagtttgctcatgtgttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTGCTGTCTTGACACACAAGGGAAGAAGTGCAGACTCTGGCCACTATGTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT