Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttacttctgtccatatctgacggtgatgtttgtttatgtataatttactatggtaacatccatgctgcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTG

Basic information

species Zea mays
transcript GRMZM5G804382_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 28
gtaacttacttctgtccatatctgacggtgatgtttgtttatgtataatttactatggtaacatc-catgctgcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTG
||| |||  ||| || ||| | |   ||   | ||  |||| | | | ||| | ||   ||||   | |||| |||||||||||||| || || ||||| |||||||| |||||  ||||||||||||| ||||| ||||||||||||| ||| |  ||||||||||| || ||||||||||
gtatcttgtttccgttcatgtgtt-tgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 28
gtaacttacttctgtccatatctgacggtgatgtttgtttatgtataatttactatggtaacatc-catgctgcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTG
||| |||  ||| || ||| | |   ||   | ||  |||| ||| | ||| | ||   ||||   | |||| | |||||||||||| || || ||||| |||||||| |||||  ||||||||||||| ||||| ||||||||||||| ||| |  ||||||||||| || ||||||||||
gtatcttgtttccgttcatgtgtt-tgggactattcatttacgtacagttttccataacaacaaagcttgcttcatgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
















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|211137943|gb|FL090180.1|FL090180
EST:     CCTTCCCATACCTGTTGCAG                         TTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT
genomic: CCTTCCCATACCTGTTGCAGgtaacttact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT
EST: gi|33093317|gb|CF053311.1|CF053311
EST:     TTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAG                         TTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT
genomic: TTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAGgtaacttact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT
EST: gi|166573060|gb|EG189009.1|EG189009
EST:     ATACCTGTTGCAG                         TTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT
genomic: ATACCTGTTGCAGgtaacttact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT
EST: gi|32945927|gb|CF050746.1|CF050746
EST:     TTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAG                         TTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT
genomic: TTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAGgtaacttact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT
EST: gi|24934286|gb|CA452504.1|CA452504
EST:     TTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAG                         TTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT
genomic: TTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAGgtaacttact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT
EST: gi|60355880|gb|DN222853.1|DN222853
EST:     TGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAG                         TTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT
genomic: TGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAGgtaacttact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT
EST: gi|32846561|gb|CD986242.1|CD986242
EST:     TTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAG                         TTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT
genomic: TTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAGgtaacttact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT
EST: gi|32846264|gb|CD985945.1|CD985945
EST:     TTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAG                         TTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT
genomic: TTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAGgtaacttact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT
EST: gi|32847239|gb|CD986920.1|CD986920
EST:     TTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAG                         TTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT
genomic: TTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAGgtaacttact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT
EST: gi|71765800|gb|DR963737.1|DR963737
EST:     TTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAG                         TTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT
genomic: TTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAGgtaacttact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATT

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: 656

TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAGgtaacttact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 530

TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAGgtaacttact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 641

TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAGgtaacttact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 601

TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAGgtaacttact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgatgtttgtttatgtataatttactatggtaacatccatgctgcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTG
                             tggtaac  putative branch site (score: 601)
       tttgtttatgtataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttacttctgtccatatctgacggtgatgtttgtttatgtataatttactatggtaacatccatgctgcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA