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

...tgtcagaatttaatgccagttacataattcagtttatggtactctcaagtaaaaccttccgagttgacgccgccttggcaccctttgcttccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTTCCCACATGATGCTTTGGAGGCTACTGCATGGACTGAAGATGGACTTATC

Basic information

species Zea mays
transcript GRMZM2G325131_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G325131_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g38950.1 (Oryza sativa), 3'ss of exon 6
---------tgtcagaatttaatgccagttacataattcagtttatggtactctcaagtaaaaccttccgagttgacgccgccttggcaccctttgcttccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTTCCCACATGATGCTTTGGAGGCTACTGCATGGACTGAAGATGGACTTATC
         ||  | ||    ||||  ||| |  | || || | ||   ||| | |   |  |  |||  | |     | | | ||     | |  |||||||| ||||||| ||||| || || || ||||| |||||||| || ||||| || |||||||| ||||| ||| |||| || || || |||||||||||||| ||||||
cttggagcatggaaaaaaaatatgctcgtttc-catttgagatcatacaacttttatcaagtagtttctcaat-----ctgacatgat---cctcacttccatgaacagCCCATTTACCGCTGCAAGATACCATAGCTTGGTGATCGAGCAGGAGACCTTCCCCCATGACGCTCTGGAAGCCACCGCGTGGACTGAAGATGGCCTTATC
















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|78105962|gb|DV524380.1|DV524380
EST:     AAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
genomic: AAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|16920775|gb|BM074824.1|BM074824
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACCACATCTTGGTCATTGAGCAAGAAACCTT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|31354238|gb|CD438595.1|CD438595
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|44901120|gb|CK827665.1|CK827665
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|211331403|gb|FL462816.1|FL462816
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|18163922|gb|BM333761.1|BM333761
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|5740708|gb|AI948398.1|AI948398
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|211412150|gb|FL109914.1|FL109914
EST:     TACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCTGCGAGGTACCACAGSTTGGTCATTGAGCAAGAAACCTT
genomic: TACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|33099441|gb|CF059401.1|CF059401
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGT
EST: gi|149102824|gb|EE288168.2|EE288168
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|211435759|gb|FL463295.1|FL463295
EST:     GGCATTGTTCAATGGCTTGGCCAAA                         CCCTTTTTCTGCCCGCGGGGTACCACAGCTTGGTCATTGAGCAAGAAACC
genomic: GGCATTGTTCAATGGCTT-GCCAAAgtatggttta ... ccatggacagCCCTTTTACTG-CCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACC
EST: gi|18660207|gb|BM500741.1|BM500741
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|33099920|gb|CF059880.1|CF059880
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCCTTTACTGCCGCGAGGTACC
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACC
EST: gi|110202087|gb|EC883984.1|EC883984
EST:     TTTATTCCGATGAGGAATTAGGAAAGGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTTCTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
genomic: TTTATTACGATGAGGAATTAGGAAA-GGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|33099846|gb|CF059806.1|CF059806
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACC
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACC
EST: gi|24769166|gb|CA404295.1|CA404295
EST:     GTTTATTCCGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|37389434|gb|CF631937.1|CF631937
EST:     GTTTATTACGATGAGGAATTAGGATAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|33099031|gb|CF058991.1|CF058991
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTA
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTA
EST: gi|211412147|gb|FL109911.1|FL109911
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|18173984|gb|BM349372.1|BM349372
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|33099524|gb|CF059484.1|CF059484
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGT
EST: gi|18168211|gb|BM338057.1|BM338057
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|33099508|gb|CF059468.1|CF059468
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGT
EST: gi|86469587|gb|DY235957.1|DY235957
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|33100076|gb|CF060036.1|CF060036
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGT
EST: gi|110215812|gb|EC897710.1|EC897710
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|211399741|gb|FL461917.1|FL461917
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCGAGAAACCTT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|113701050|gb|EE678554.1|EE678554
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|44901121|gb|CK827666.1|CK827666
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|211412146|gb|FL109910.1|FL109910
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCTGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTT
EST: gi|33100338|gb|CF060298.1|CF060298
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGT
EST: gi|33099759|gb|CF059719.1|CF059719
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGTACC
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGTACC
EST: gi|33099556|gb|CF059516.1|CF059516
EST:     GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAA                         CCCTTTTACTGCCGCGAGGT
genomic: GTTTATTACGATGAGGAATTAGGAAAGGCATTGTTCAATGGCTTGCCAAAgtatggttta ... ccatggacagCCCTTTTACTGCCGCGAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagtaaaaccttccgagttgacgccgccttggcaccctttgcttccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTTCCCACATGATGCTTTGGAGGCTACTGCATGGACTGAAGATGGACTTATC
                agttgac  putative branch site (score: 4)
                                 caccctttgcttcc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcagaatttaatgccagttacataattcagtttatggtactctcaagtaaaaccttccgagttgacgccgccttggcaccctttgcttccatggacagCCCTTTTACTGCCGCGAGGTACCACAGCTTGGTCATTGAGCAAGAAACCTTCCCACATGATGCTTTGGAGGCTACTGCATGGACTGAAGATGGACTTATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA