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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttgcaacggttatttcgtagtgttcttcgtatattgccttgcatctatgtttttatgatgctcttctctag

Basic information

species Zea mays
transcript GRMZM5G856436_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G856436_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g49150.1 (Oryza sativa), 5'ss of exon 3
GACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttgcaacggttatttcgtagtgttcttcgtatattgccttgcatctatgtttttatgatgctctt-ctctag
|||||||||||||||||| |||||||||||||| || |||||||||||||| ||||||||||||||||||||||| |||||||| |||||||||||||||||||||||||  |   || | |  |    |   |  | |||||| | ||||||| ||||| ||| ||| | | ||||||
GACTTCTGGAGTAAAAGAGGATCGCATGATGATAACCGGAATGCATACTGTGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATATgtaagatttgtgattattttatgttgtcatatatgttgtattgcgtagcatctaagtttt-atggtgcccctactctag

upper sequence: GRMZM5G856436_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv08s0007g02170.t01 (Vitis vinifera), 5'ss of exon 4
GACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttgcaacggttatttcgtagtgttcttcgtatatt--gccttgcatctatgtttttatgatgctctt--ctctag-------------------
 ||    ||||  || ||||||||  |||||||||| |||||||| ||||||  ||| || ||||||||||| ||||| ||||| |||||||||||||||||||||| ||   | |  |||  || |  ||  | |  | ||   | |||   || |   || ||   | |      | ||                    
CACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAATGCACACTGTTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGATGGAAATATgtaagatctggttcagaaattctgttgcattgcttgagtttttaactttgtgcctgttacttgatctagtttgggattttaattttgattatcgaaattag
















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|211161884|gb|FL207305.1|FL207305
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|26558493|gb|CA830728.1|CA830728
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCACATGAGAAGAGCCAAAGATACAAGGAAGGAAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|211161885|gb|FL207306.1|FL207306
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTT-ATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|22472703|gb|BU037183.1|BU037183
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCACATGAGAAGAGCCAAAGATACAAGGAAGGAAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|211161891|gb|FL207312.1|FL207312
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|211161881|gb|FL207302.1|FL207302
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|16927653|gb|BM080722.1|BM080722
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|211160284|gb|FL207292.1|FL207292
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCTCATGAGAAGAGC-AGAGATACAAGGAAGGAAAGTTT
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTT
EST: gi|211458337|gb|FL363659.1|FL363659
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|14243210|gb|BG840951.2|BG840951
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|67017876|gb|CO446625.1|CO446625
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|113701952|gb|EE679456.1|EE679456
EST:     TTCTGATATCTTCTGTCGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
genomic: TTCTGATATCTTCTGT-GTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|16917041|gb|BM073101.1|BM073101
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGATCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|21389991|gb|BQ528040.1|BQ528040
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCACATGAGAAGAGCCAAAGATACAAGGAAGGAAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|60341900|gb|DN208873.1|DN208873
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|31352331|gb|CD436688.1|CD436688
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTTTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|211161892|gb|FL207313.1|FL207313
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCTCAT
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCAT
EST: gi|211161889|gb|FL207310.1|FL207310
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTAT-CTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|37376556|gb|CF624817.1|CF624817
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|31352347|gb|CD436704.1|CD436704
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|16925094|gb|BM078162.1|BM078162
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|31351127|gb|CD435484.1|CD435484
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTG
EST: gi|14242748|gb|BG840532.2|BG840532
EST:     CTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCT
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGC-TGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCT
EST: gi|211161883|gb|FL207304.1|FL207304
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATAT                         GAGGCTGCTCATGAG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAG

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: 47 (upstream exon), 48 (downstream exon)
Score: 73

GACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 42

GACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 29

GACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 69

GACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttg ... tcttctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttgcaacggttatttcgtagtgttcttcgtatattgccttgcatctatgtttttatgatgctcttctctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA