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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtctgtctgctcaacccatgatgcatttctgctaaaatgtaactggtggtagtgtagcttaaaccggtttccttgtcctgatgtctgatcccatttgtatgtgtgcttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG

Basic information

species Zea mays
transcript GRMZM2G492252_T01
intron # 2
splice site 3'
intron type U2

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|211128948|gb|FL128226.1|FL128226
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|211128945|gb|FL128223.1|FL128223
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCANGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|149105940|gb|EE291566.2|EE291566
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|88758241|gb|DY542382.1|DY542382
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|71424496|gb|DR806334.1|DR806334
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|211129864|gb|FL128228.1|FL128228
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTT-CT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGC-AGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCT
EST: gi|211129863|gb|FL128227.1|FL128227
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|37417624|gb|CF646466.1|CF646466
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|50324565|gb|CO519691.1|CO519691
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|71774882|gb|DR972760.1|DR972760
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|91868647|gb|EB400100.1|EB400100
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|71426202|gb|DR807252.1|DR807252
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|211129866|gb|FL128230.1|FL128230
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|211128943|gb|FL128221.1|FL128221
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|211129865|gb|FL128229.1|FL128229
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|211039435|gb|FL384655.1|FL384655
EST:     ACATAGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|211252415|gb|FL420141.1|FL420141
EST:     ACATAGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|89760191|gb|DY688711.1|DY688711
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|211005956|gb|FL398095.1|FL398095
EST:     ACATAGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|148971543|gb|EE022249.2|EE022249
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|93014828|gb|EB640348.1|EB640348
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|211045933|gb|FL419469.1|FL419469
EST:     ACATAGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|211128939|gb|FL128217.1|FL128217
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|211128947|gb|FL128225.1|FL128225
EST:     ANATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|211128941|gb|FL128219.1|FL128219
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|211128940|gb|FL128218.1|FL128218
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
EST: gi|76936255|gb|DV174660.1|DV174660
EST:     ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATG                         CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT
genomic: ACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTT

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), 44 (downstream exon)
Score: 75

GCAGCGTCTGGTGGGAACCATGAGCTTCGTGTTCCGAGGAAGCAGGGCCGACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 26

GCAGCGTCTGGTGGGAACCATGAGCTTCGTGTTCCGAGGAAGCAGGGCCGACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 24

GCAGCGTCTGGTGGGAACCATGAGCTTCGTGTTCCGAGGAAGCAGGGCCGACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 22

GCAGCGTCTGGTGGGAACCATGAGCTTCGTGTTCCGAGGAAGCAGGGCCGACATCGAGGCCGGTGGCTTCACAGGGTTCGCCCCCGAGCGCCGCACCATGgtgagtgtct ... ttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccggtttccttgtcctgatgtctgatcccatttgtatgtgtgcttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG
                               atttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgtctgtctgctcaacccatgatgcatttctgctaaaatgtaactggtggtagtgtagcttaaaccggtttccttgtcctgatgtctgatcccatttgtatgtgtgcttgagtgtagCGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG