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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCGAGCTGGCGAAGAAGAGGGGTAAGATGGTTGATGTGGGACACAAGGAAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcatggctcaaccgatttcctcaaccagagaatgctcattgttctgtggtctgcgatgatggtatgattatattgttccttgcag

Basic information

species Zea mays
transcript GRMZM2G015902_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015902_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g25720.1 (Oryza sativa), 5'ss of exon 3
GACCGAGCTGGCGAAGAAGAGGGGTAAGATGGTTGATGTGGGACACAAGGAAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcatggctcaa---ccgatttcctcaaccagagaatgctcattgttctg-------tggtctgcgatgatggtat-gattatattgttccttgcag
|| |||||||  |||||||||||| |||| ||||||||||    ||||||| ||||  ||||| || || |||||||| || ||||||||||||||||||||| |     |     |    ||||   |||    |  ||    |||| ||| ||       ||   ||  ||||||||    || |  || || |||  ||
GAACGAGCTGTTGAAGAAGAGGGGCAAGAAGGTTGATGTGAAGGACAAGGAGGAGAAAGACCAGGTCGATGAGCTCTACACTGTGCCAGACCACCTCAAGgttggtagccgaacagagcttcgatgcactcctgaaaggatatttcatggttttgatatgtgtgcattgtaatgatggtgccaatcaattttttgcttatag
















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|91048276|gb|EB158694.1|EB158694
EST:     AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
EST: gi|76935876|gb|DV174501.1|DV174501
EST:     AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
EST: gi|149014683|gb|EE044352.2|EE044352
EST:     AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
EST: gi|211001836|gb|FL114782.1|FL114782
EST:     AAGAGATGGACCATGTGGACGAGCTCTACACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
EST: gi|211001838|gb|FL114784.1|FL114784
EST:     AAGAGATGGACCATGTGGACGAGCTCTACACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
EST: gi|71332986|gb|DR803518.1|DR803518
EST:     AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
EST: gi|76018908|gb|DT946078.1|DT946078
EST:     AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
EST: gi|211469324|gb|FL299243.1|FL299243
EST:     AAGAGATGGACCATGTGGACGAGCTCTACACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
EST: gi|20802771|gb|BQ293821.1|BQ293821
EST:     ACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAA-GGACAACTGGCATT
genomic: ACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
EST: gi|211001837|gb|FL114783.1|FL114783
EST:     AAGAGATGGACCATGTGGACGAGCTCTACACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
EST: gi|211001833|gb|FL114779.1|FL114779
EST:     AAGAGATGGACCATGTGGACGAGCTCTACACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
EST: gi|78116755|gb|DV535142.1|DV535142
EST:     AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
EST: gi|91870478|gb|EB400898.1|EB400898
EST:     AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
EST: gi|148960852|gb|EE011528.2|EE011528
EST:     AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
EST: gi|211469326|gb|FL299245.1|FL299245
EST:     AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAG
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAG
EST: gi|71446263|gb|DR827313.1|DR827313
EST:     AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
EST: gi|71437898|gb|DR818948.1|DR818948
EST:     AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
EST: gi|211466800|gb|FL299231.1|FL299231
EST:     AAGAGATGGACCATGTGGACGAGCTCTACACCGTGCCAGACCACCTCAAG                         GTAAAGAA-AAGAACTCAGAGGAGAGCT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCT
EST: gi|211469331|gb|FL299250.1|FL299250
EST:     AAGAGATGGACCATGTGGACGAGCTCTACACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
EST: gi|211471856|gb|FL299263.1|FL299263
EST:     AAGAGATGGACCATGTGGACGAGCTCTACACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGC
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGC
EST: gi|71770078|gb|DR968015.1|DR968015
EST:     AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
EST: gi|71323571|gb|DR798454.1|DR798454
EST:     AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATT
EST: gi|211469318|gb|FL299237.1|FL299237
EST:     AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAG                         GTAAAGAAGAAGAACT
genomic: AAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACT

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), 45 (downstream exon)
Score: 69

GACCGAGCTGGCGAAGAAGAGGGGTAAGATGGTTGATGTGGGACACAAGGAAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 42

GACCGAGCTGGCGAAGAAGAGGGGTAAGATGGTTGATGTGGGACACAAGGAAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 67

GACCGAGCTGGCGAAGAAGAGGGGTAAGATGGTTGATGTGGGACACAAGGAAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 25

GACCGAGCTGGCGAAGAAGAGGGGTAAGATGGTTGATGTGGGACACAAGGAAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcat ... ttccttgcagGTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCGAGCTGGCGAAGAAGAGGGGTAAGATGGTTGATGTGGGACACAAGGAAGAGATGGACCATGTGGACGAGCTCTATACCGTGCCAGACCACCTCAAGgtttgctcatggctcaaccgatttcctcaaccagagaatgctcattgttctgtggtctgcgatgatggtatgattatattgttccttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA