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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtatttagctatatattattgttatacatacatcatttttgagagcatggcttagcacacttttattgttatacatacatacctttgttatgtcaacagATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG

Basic information

species Zea mays
transcript GRMZM2G118316_T01
intron # 7
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|76922542|gb|DV169052.1|DV169052
EST:     GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGAT                         ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
genomic: GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGATgtaagaacca ... atgtcaacagATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
EST: gi|74237423|gb|DT645337.1|DT645337
EST:     AGGGCCGGGTTTTCCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGAT                         ATCTTTGATAATGCATACAGAGGTGG
genomic: AGGGCCGGGTTTTCC-TCGGGGTAACCCATTTGGTGACATCTTTGGTGATgtaagaacca ... atgtcaacagATCTTTGATAATGCATACAGAGGTGG
EST: gi|149101262|gb|EE187374.2|EE187374
EST:     GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGAT                         ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
genomic: GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGATgtaagaacca ... atgtcaacagATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
EST: gi|78088193|gb|DV516586.1|DV516586
EST:     GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGAT                         ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
genomic: GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGATgtaagaacca ... atgtcaacagATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
EST: gi|93017256|gb|EB642776.1|EB642776
EST:     GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGAT                         ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
genomic: GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGATgtaagaacca ... atgtcaacagATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
EST: gi|71757145|gb|DR955082.1|DR955082
EST:     GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGAT                         ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
genomic: GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGATgtaagaacca ... atgtcaacagATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
EST: gi|71771526|gb|DR969463.1|DR969463
EST:     GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGAT                         ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
genomic: GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGATgtaagaacca ... atgtcaacagATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
EST: gi|71427931|gb|DR808981.1|DR808981
EST:     GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGAT                         ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
genomic: GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGATgtaagaacca ... atgtcaacagATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
EST: gi|91049687|gb|EB160105.1|EB160105
EST:     GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGAT                         ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
genomic: GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGATgtaagaacca ... atgtcaacagATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
EST: gi|34391167|gb|CF384395.1|CF384395
EST:     GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGAT                         ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTTAAG
genomic: GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGATgtaagaacca ... atgtcaacagATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
EST: gi|211533908|gb|FL308317.1|FL308317
EST:     GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGAT                         ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTTAAG
genomic: GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGATgtaagaacca ... atgtcaacagATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
EST: gi|91049823|gb|EB160241.1|EB160241
EST:     GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGAT                         ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
genomic: GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGATgtaagaacca ... atgtcaacagATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
EST: gi|71769072|gb|DR967009.1|DR967009
EST:     GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGAT                         ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
genomic: GAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGATgtaagaacca ... atgtcaacagATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG

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), 39 (downstream exon)
Score: 215

CTTGGACCAGAAGCATACGAGCGTCAAGCGTCAGGTGGTGACCCTGGAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGATgtaagaacca ... atgtcaacagATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 143

CTTGGACCAGAAGCATACGAGCGTCAAGCGTCAGGTGGTGACCCTGGAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGATgtaagaacca ... atgtcaacagATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG


Block sizes: 46 (upstream exon), 39 (downstream exon)
Score: 108

CTTGGACCAGAAGCATACGAGCGTCAAGCGTCAGGTGGTGACCCTGGAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGATgtaagaacca ... atgtcaacagATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 241

CTTGGACCAGAAGCATACGAGCGTCAAGCGTCAGGTGGTGACCCTGGAGGGCCGGGTTTTCCTCGGGGTAACCCATTTGGTGACATCTTTGGTGATgtaagaacca ... atgtcaacagATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatggcttagcacacttttattgttatacatacatacctttgttatgtcaacagATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG
                ttttattgttatacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtatttagctatatattattgttatacatacatcatttttgagagcatggcttagcacacttttattgttatacatacatacctttgttatgtcaacagATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
tgtattt
- - - - - - - - - - - - - acataca
- - - - - - - - - - - - - - - - - - - - - -gagcatg