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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGAAGACCTTGTTCTTCCCCTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGTgtaagaatctgagcagtgaaaatagtcatcaccttaactatgccaagtttttcttgtatagtaaactagtaatctgttagttacttaatttcaaccatgt...

Basic information

species Zea mays
transcript GRMZM2G027821_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027821_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g06120.3 (Oryza sativa), 5'ss of exon 5
GTTTGAAGACCTTGTTCTTCCCCTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGTgtaagaatctgagcagtgaaaatagtcatcaccttaactatgccaagtttttcttgtatagtaaactagtaatctgttagttacttaatttcaaccatgt--
||||||  || || || |||||||||||||| ||||| |  ||||||||||| || ||| ||||||| |||||||||||| |   |  ||| |||| ||||||  || |   |    | ||||| ||   |  ||   |  |  |   ||        |||    | |||||  
GTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGTgtaagaatatttccc-tgacaataatcatcatgttgagagttgataatttttgttcc-tcctagcatttttcttcatttccctgaaaatagtcatcatgtat
















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|6022374|gb|AW067302.1|AW067302
EST:     CTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGT                         CTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCT
genomic: CTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGTgtaagaatct ... ttgttttcagCTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCT
EST: gi|161587651|gb|EY960378.1|EY960378
EST:     CTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGT                         CTTCTGGAGAGGCTTGCAA
genomic: CTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGTgtaagaatct ... ttgttttcagCTTCTGGGGAGGCTTGCAA
EST: gi|211064881|gb|FL464879.1|FL464879
EST:     CTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGT                         CTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCT
genomic: CTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGTgtaagaatct ... ttgttttcagCTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCT
EST: gi|60357315|gb|DN224288.1|DN224288
EST:     CTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGT                         CTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCT
genomic: CTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGTgtaagaatct ... ttgttttcagCTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCT
EST: gi|211190398|gb|FL318556.1|FL318556
EST:     CTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGT                         CTTCTGGAGAGGCTTGCAATGATATTATGGCTTACTCCCTAATATTGTCCT
genomic: CTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGTgtaagaatct ... ttgttttcagCTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCT
EST: gi|211064880|gb|FL464878.1|FL464878
EST:     CTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGT                         CTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCT
genomic: CTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGTgtaagaatct ... ttgttttcagCTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCT
EST: gi|74235248|gb|DT643162.1|DT643162
EST:     CTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGT                         CTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCT
genomic: CTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGTgtaagaatct ... ttgttttcagCTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCT
EST: gi|32847753|gb|CD987434.1|CD987434
EST:     CTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGA                         CTTCTGGAGAGGCTTGCAATGATATTATGGCTTACTCCCTAATATTGTCCT
genomic: CTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGTgtaagaatct ... ttgttttcagCTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCT
EST: gi|71434265|gb|DR815315.1|DR815315
EST:     TGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGT                         CTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCT
genomic: TGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGTgtaagaatct ... ttgttttcagCTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCT
EST: gi|78078285|gb|DV506700.1|DV506700
EST:     CTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGT                         CTTTTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCT
genomic: CTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGTgtaagaatct ... ttgttttcagCTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCT
EST: gi|71328372|gb|DR800816.1|DR800816
EST:     GAGAATTGCTTCAATCGCCAAGGACAGGCCAATGT                         CTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCT
genomic: GAGAATTGCTTCAATCGCCAAGGACAGGCCAATGTgtaagaatct ... ttgttttcagCTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCT

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), 49 (downstream exon)
Score: 97

GTTTGAAGACCTTGTTCTTCCCCTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGTgtaagaatct ... ttgttttcagCTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCTGCTGCTGTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 50

GTTTGAAGACCTTGTTCTTCCCCTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGTgtaagaatct ... ttgttttcagCTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCTGCTGCTGTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 42

GTTTGAAGACCTTGTTCTTCCCCTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGTgtaagaatct ... ttgttttcagCTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCTGCTGCTGTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGA


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

GTTTGAAGACCTTGTTCTTCCCCTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGTgtaagaatct ... ttgttttcagCTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCTGCTGCTGTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGAAGACCTTGTTCTTCCCCTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGTgtaagaatctgagcagtgaaaatagtcatcaccttaactatgccaagtttttcttgtatagtaaactagtaatctgttagttacttaatttcaaccatgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatag