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

gttagcctggttgcatttccactacactcgagtgtcttctttaaaaatattcaagatttttcttttgttcgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCCGAAGGAGCAATGTATCTTTTCCCTCAGATTCTTCTGCCACAGAAGGCAA

Basic information

species Zea mays
transcript GRMZM2G088064_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088064_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g25130.1 (Oryza sativa), 3'ss of exon 13
gt-tagcctggttgcatttccactacact--cgagtgtcttctttaaaaatattcaagatttttcttttgttcgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCCGAAGGAGCAATGTATCTTTTCCCTCAGATTCTTCTGCCACAGAAGGCAA
|| || | | || || ||| || ||| | || ||| || | ||| ||| || | |||| | | | ||||| |||||| |||| ||||||| ||||||||| || |||| ||||| | |||||||||||||| || ||||||||| || ||||||||| |||||||
gtataccaggattccaattctcttatactgctaaatgatatctgggaacaaattgtagaattgtttttttcttgatg-gcagGCATTGGAGAATGCTTTCAACAGTCTTGAGGGAATTACATGCAACAAAACTGAAGGAGCAATGTACCTCTTCCCTCAGCTTAGTCTGCCACAAAAGGCAA

upper sequence: GRMZM2G088064_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT1G72330.3 (Arabidopsis thaliana), 3'ss of exon 12
gttagcct--ggttgcatttccactacactcgagtgtcttctttaaaaatattcaagatttttcttttgttcgt---tttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCCGAAGGAGCAATGTATCTTTTCCCTCAGATTCTTCTGCCACAGAAGGCAA
||||| | | || || | || || | | | | | ||| || | ||| | || ||| | ||||| || || |||||| | || || || ||||||||| |||||||||||||||||||| ||||| | ||| || || || ||||| |
gttagtcgaagattacaataccctctaacgacatttttcagtctctttgtatataatgtcacaagcttgaaaatgaacttgcagACTTTGGAAGACGCTCTCAACAGTTTAGAAGGTGTTACATGTAACAGAGCCGAAGGAGCAATGTATCTCTTCCCGCGAATTAACCTTCCTCAAAAGGCTA
















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|116816986|gb|EC859784.1|EC859784
EST:     ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|47962226|gb|CN844935.1|CN844935
EST:     ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|56538354|gb|CX054063.1|CX054063
EST:     ACAAGGCAGAGAAGGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|67018293|gb|CO447042.1|CO447042
EST:     ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|67014982|gb|CO443731.1|CO443731
EST:     ACAA-GCATAGAAAGA-GGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|24769730|gb|CA404859.1|CA404859
EST:     ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|6538906|gb|AW225045.1|AW225045
EST:     ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|62550335|gb|DN830755.1|DN830755
EST:     ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|113701726|gb|EE679230.1|EE679230
EST:     ACAAGGCAGAGAAGGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGATGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|5456278|gb|AI833968.1|AI833968
EST:     CCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: CCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|44681923|gb|CK786971.1|CK786971
EST:     ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|32856051|gb|CD995732.1|CD995732
EST:     ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|58029866|gb|CX725293.1|CX725293
EST:     ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|211264932|gb|FL212893.1|FL212893
EST:     ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|32838607|gb|CD978285.1|CD978285
EST:     ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|211267357|gb|FL212899.1|FL212899
EST:     ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|31355085|gb|CD439442.1|CD439442
EST:     ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|32907809|gb|CF012622.1|CF012622
EST:     ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|31359639|gb|CD443996.1|CD443996
EST:     ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|37381380|gb|CF627571.1|CF627571
EST:     ACAAGGCAGAGAAGGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|67024661|gb|CO453410.1|CO453410
EST:     ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
EST: gi|37384618|gb|CF629399.1|CF629399
EST:     ACAAGGCAGAGAAGGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAG                         GCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC
genomic: ACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCC

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), 41 (downstream exon)
Score: 10

GTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCCGAAGGAGCAATGTATCTTTTCCCTCAGATTCTTCTGCCACAGAAGGCAA


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 28

GTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCCGAAGGAGCAATGTATCTTTTCCCTCAGATTCTTCTGCCACAGAAGGCAA


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 23

GTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCCGAAGGAGCAATGTATCTTTTCCCTCAGATTCTTCTGCCACAGAAGGCAA


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 10

GTTGGAGACGAATCATATGCTTCCTACAAGGCAGAGAAAGATGGAATCCTTGAGTCTTTAGCTCGTCGTGCAAAGgttagcctgg ... cgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCCGAAGGAGCAATGTATCTTTTCCCTCAGATTCTTCTGCCACAGAAGGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactcgagtgtcttctttaaaaatattcaagatttttcttttgttcgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCCGAAGGAGCAATGTATCTTTTCCCTCAGATTCTTCTGCCACAGAAGGCAA
                                tttttcttttgttcgt  CT-rich tract
 ttctttaaaaatattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcctggttgcatttccactacactcgagtgtcttctttaaaaatattcaagatttttcttttgttcgttttacagGCGTTGGAGGATGCATTCAACAAGCTTGAGGGATTTTCATGTAACAAGGCCGAAGGAGCAATGTATCTTTTCCCTCAGATTCTTCTGCCACAGAAGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA