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

gtgcttagtttgtttggaattatttgttgaaaatatgtatcaccttcaaaatctcactatgtttatacattcagGATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAA

Basic information

species Zea mays
transcript GRMZM2G062416_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062416_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g17990.1 (Oryza sativa), 3'ss of exon 9
gtgcttagtttgtttggaattatttgttgaaaatatgtatcaccttcaaaatctcactatgtttatacatt-cagGATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAA
|| |  | | | ||    ||  ||||   |||| || | |||   || |||||| | |  || ||||| || ||||||||||| || ||||||||||| |||||||||||||| || |||||||| || |||
gtacgca-tctatt----atcttttggaaaaaaaatatttcaatatcgaaatcttattcagtgtatacttttcagGATTTTGGTGATAGCATACCTGGCCATGGTGGATTTACTGACAGGATGGATTGTCAA

upper sequence: GRMZM2G062416_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G02210.1 (Glycine max), 3'ss of exon 7
-------------------------------------gtgcttagtttgtttggaattatttgttgaaaatatgtatcaccttcaaaatctcactatgtttatacatt--cagGATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAA
                                      | | |  |   |||   |||   | |||||| |    | ||     | |   |   | | |||  |   |  ||||| ||||| || || |||||||| ||||||||||||||||| || ||||||||||| 
gtatgttcttgctctttatactagacatttattttgcatccatcatcctttttccattcact-ttgaaactcccaaacatagcaatagcattgatctctttgaatgattacagGACTTTGGTGATAGTATACCTGGACATGGTGGATTTACAGACAGAATGGACTGCCAG

upper sequence: GRMZM2G062416_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G46440.1 (Glycine max), 3'ss of exon 9
-----------------------------------gtgc---ttagtttgtttggaattatttgttgaaaat---atgtatcaccttcaaaatctcactatgtttatacattcagGATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAA
                                   || |   | |   | |||  | | | |  |||||| |   |   ||  | |  |  |||   || | |  ||   | ||||| ||||| ||||| |||||||| ||||||||||||||||| || ||||||||||| 
gtctgttcttgctctttatacaagacatttattttgtacccatcaccctttttccattcact--ttgaaactcccaaacatagcatatagcatcgatctctttcaatgattacagGACTTTGGTGACAGTATACCTGGACATGGTGGATTTACAGACAGAATGGACTGCCAG

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|71429076|gb|DR810126.1|DR810126
EST:     CATTTGGTGGCTTTTTTGCAAGTGGATTCAAGAGGGCATTCAAATTTAAG                         GATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
genomic: CATTTGGTGGCTTTTTTGCAAGTGGATTCAAGAGGGCATTCAAATTTAAGgtgcttagtt ... atacattcagGATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
EST: gi|211157823|gb|FL476882.1|FL476882
EST:     CATTTGGTGGCTTTTTTGCAAGTGGATTCAAGAGGGCATTCAAATTTAAG                         GATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
genomic: CATTTGGTGGCTTTTTTGCAAGTGGATTCAAGAGGGCATTCAAATTTAAGgtgcttagtt ... atacattcagGATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
EST: gi|71770625|gb|DR968562.1|DR968562
EST:     GGATTCAAGAGGGCATTCAAATTTAAG                         GATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
genomic: GGATTCAAGAGGGCATTCAAATTTAAGgtgcttagtt ... atacattcagGATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
EST: gi|211031482|gb|FL468605.1|FL468605
EST:     CATTTGGTGGCTTTTTTGCAAGTGGATTCAAGAGGGCATTCAAATTTAAG                         GATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
genomic: CATTTGGTGGCTTTTTTGCAAGTGGATTCAAGAGGGCATTCAAATTTAAGgtgcttagtt ... atacattcagGATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
EST: gi|24773898|gb|CA409152.1|CA409152
EST:     CATTTGGTGGCTTTTTTGCAAGTGGATTCAAGAGGGCATTCAAATTTAAG                         GATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
genomic: CATTTGGTGGCTTTTTTGCAAGTGGATTCAAGAGGGCATTCAAATTTAAGgtgcttagtt ... atacattcagGATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
EST: gi|32867266|gb|CF006948.1|CF006948
EST:     GAGGGCATTCAAATTTAAG                         GATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
genomic: GAGGGCATTCAAATTTAAGgtgcttagtt ... atacattcagGATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
EST: gi|32908945|gb|CF013758.1|CF013758
EST:     CATTTGGTGGCTTTTTTGCAAGTGGATTCAAGAGGGCATTCAAATTTAAG                         GATTTTGGGGACAGCATACCAGGTCATGGTGGATTTACAGATAGGATGGAC
genomic: CATTTGGTGGCTTTTTTGCAAGTGGATTCAAGAGGGCATTCAAATTTAAGgtgcttagtt ... atacattcagGATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
EST: gi|71770099|gb|DR968036.1|DR968036
EST:     CATTTGGTGGCTTTTTTGCAAGTGGATTCAAGAGGGCATTCAAATTTAAG                         GATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
genomic: CATTTGGTGGCTTTTTTGCAAGTGGATTCAAGAGGGCATTCAAATTTAAGgtgcttagtt ... atacattcagGATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
EST: gi|76913970|gb|DV165352.1|DV165352
EST:     ATTTGGGGGCTTTTTTGCAAGTGGATTCAAAGAGGGCATTCAAATTTAAG                         GATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
genomic: ATTTGGTGGCTTTTTTGCAAGTGGATTC-AAGAGGGCATTCAAATTTAAGgtgcttagtt ... atacattcagGATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
EST: gi|78074248|gb|DV502682.1|DV502682
EST:     CATTTGGTGGCTTTTTTGCAAGTGGATTCAAGAGGGCATTCAAATTTAAG                         GATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
genomic: CATTTGGTGGCTTTTTTGCAAGTGGATTCAAGAGGGCATTCAAATTTAAGgtgcttagtt ... atacattcagGATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
EST: gi|44900185|gb|CK826730.1|CK826730
EST:     CATTTGGTGGCTTTTTTGCAAGTGGATTCAAGAGGGCATTCAAATTTAAG                         GATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC
genomic: CATTTGGTGGCTTTTTTGCAAGTGGATTCAAGAGGGCATTCAAATTTAAGgtgcttagtt ... atacattcagGATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttgttgaaaatatgtatcaccttcaaaatctcactatgtttatacattcagGATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAA
                               atctcac  putative branch site (score: 3)
       ttgaaaatatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcttagtttgtttggaattatttgttgaaaatatgtatcaccttcaaaatctcactatgtttatacattcagGATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA