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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtactaactattccctccatatatatttatatttcttcgtccttatctttatttgttcccgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTT

Basic information

species Zea mays
transcript GRMZM2G164265_T03
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 11
gtctgtacta---actattc------cctccatatat-atttatattt-cttcgtccttatcttta---tttgttcccgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTT------
|||||||| |   || |||       | ||||||| |  ||||  | | || | |   | ||  |      |  ||    | |||||||||| |||||||||||||||   |||| |      |||||||| ||||| || ||||| ||||||||||| |||||||| |||||||||||||| ||||      
gtctgtaccacccaccattttactcacttccatattttgtttaggtctgctccatatctgtccatgaacccttctcttaaattatagGTTGGGCAGAAACGTGGAAGAAACCATGAA------GAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACG
















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|32912903|gb|CF017715.1|CF017715
EST:     TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAG                         GTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
genomic: TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtacta ... cgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
EST: gi|211391059|gb|FL093738.1|FL093738
EST:     TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAG                         GTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
genomic: TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtacta ... cgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
EST: gi|37423723|gb|CF649590.1|CF649590
EST:     TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAG                         GTTGGACAGAAACGGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACC
genomic: TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtacta ... cgtactatagGTTGGACAGAAAC-GTGGAAGATTGCATGCAAATCTAGAAGATGAACAACC
EST: gi|32913238|gb|CF018050.1|CF018050
EST:     TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAG                         GTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
genomic: TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtacta ... cgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
EST: gi|71430775|gb|DR811825.1|DR811825
EST:     TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAG                         GTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
genomic: TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtacta ... cgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
EST: gi|67043197|gb|CO469452.1|CO469452
EST:     TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAG                         GTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT
genomic: TGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtacta ... cgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCT

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: 631

ATTTGATGAAGAGCCAAATTATGCCAAGCTTATCTCTATTTTTGATGGTTTGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtacta ... cgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 459

ATTTGATGAAGAGCCAAATTATGCCAAGCTTATCTCTATTTTTGATGGTTTGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtacta ... cgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 494

ATTTGATGAAGAGCCAAATTATGCCAAGCTTATCTCTATTTTTGATGGTTTGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtacta ... cgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 464

ATTTGATGAAGAGCCAAATTATGCCAAGCTTATCTCTATTTTTGATGGTTTGATTGAAGCACCTGCGTCGAGACCAGTCAGAATTGATGGGGCCCTCAAGgtctgtacta ... cgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccatatatatttatatttcttcgtccttatctttatttgttcccgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTT
                 tttcttcgtccttatc  CT-rich tract
     tatatatttatatttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtactaactattccctccatatatatttatatttcttcgtccttatctttatttgttcccgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG