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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaatggatctccgcctaaattaaactacttgctttcagtcttggctgtgcctgtaccatccattttgcaagtgatagatgtctagctgccgtttctgacctggtccatgttatccaacagTGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAACCAGATCGCGATCGGCATGAGCGACGGCAAGGTCCATGTGGTGGAGCCA

Basic information

species Zea mays
transcript GRMZM2G042992_T01
intron # 24
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|19057897|gb|BM736564.1|BM736564
EST:     CGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTG                         TGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCACACCCCATGGAGCCTAA
genomic: CGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTGgtatgaatgg ... tatccaacagTGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA
EST: gi|60357392|gb|DN224365.1|DN224365
EST:     CGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTG                         TGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA
genomic: CGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTGgtatgaatgg ... tatccaacagTGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA
EST: gi|211011031|gb|FL029056.1|FL029056
EST:     CGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTG                         TGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCACACCCCATGGAGCCTAA
genomic: CGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTGgtatgaatgg ... tatccaacagTGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA
EST: gi|60337113|gb|DN204086.1|DN204086
EST:     TCCACCTTCAATACTAGCCTG                         TGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA
genomic: TCCACCTTCAATACTAGCCTGgtatgaatgg ... tatccaacagTGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA
EST: gi|87152612|gb|DY397401.1|DY397401
EST:     CGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTG                         TGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCACACCCCATGGAGCCTAA
genomic: CGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTGgtatgaatgg ... tatccaacagTGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA
EST: gi|89761150|gb|DY689280.1|DY689280
EST:     CGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTG                         TGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA
genomic: CGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTGgtatgaatgg ... tatccaacagTGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA
EST: gi|67011448|gb|CO440197.1|CO440197
EST:     CGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTG                         TGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA
genomic: CGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTGgtatgaatgg ... tatccaacagTGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA
EST: gi|60394881|gb|DN227750.1|DN227750
EST:     ATTCCACCTTCAATACTAGCCTG                         TGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA
genomic: ATTCCACCTTCAATACTAGCCTGgtatgaatgg ... tatccaacagTGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA
EST: gi|78073590|gb|DV502024.1|DV502024
EST:     GCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTG                         TGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA
genomic: GCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTGgtatgaatgg ... tatccaacagTGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA
EST: gi|166618638|gb|EG278491.1|EG278491
EST:     CGCTTACATTCCACCTTCAATACTAGCCTG                         TGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCACACCCCATGGAGCCTAA
genomic: CGCTTACATTCCACCTTCAATACTAGCCTGgtatgaatgg ... tatccaacagTGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA
EST: gi|60349882|gb|DN216855.1|DN216855
EST:     CGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTG                         TGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA
genomic: CGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTGgtatgaatgg ... tatccaacagTGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA
EST: gi|71432286|gb|DR813336.1|DR813336
EST:     CGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTG                         TGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA
genomic: CGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTGgtatgaatgg ... tatccaacagTGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAA

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: 1288

GGTTCTGCGATGGTGCTATCGGAGTCTTCGAAGCAGAATCTCTTAGGCTGCGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTGgtatgaatgg ... tatccaacagTGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAACCAGATCGCGATCGGCATGAGCGACGGCAAGGTCCATGTGGTGGAGCCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 199

GGTTCTGCGATGGTGCTATCGGAGTCTTCGAAGCAGAATCTCTTAGGCTGCGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTGgtatgaatgg ... tatccaacagTGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAACCAGATCGCGATCGGCATGAGCGACGGCAAGGTCCATGTGGTGGAGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

GGTTCTGCGATGGTGCTATCGGAGTCTTCGAAGCAGAATCTCTTAGGCTGCGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTGgtatgaatgg ... tatccaacagTGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAACCAGATCGCGATCGGCATGAGCGACGGCAAGGTCCATGTGGTGGAGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 471

GGTTCTGCGATGGTGCTATCGGAGTCTTCGAAGCAGAATCTCTTAGGCTGCGCTGCCGGATTGCTCCTTCCGCTTACATTCCACCTTCAATACTAGCCTGgtatgaatgg ... tatccaacagTGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAACCAGATCGCGATCGGCATGAGCGACGGCAAGGTCCATGTGGTGGAGCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaagtgatagatgtctagctgccgtttctgacctggtccatgttatccaacagTGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAACCAGATCGCGATCGGCATGAGCGACGGCAAGGTCCATGTGGTGGAGCCA
                           ttctgac  putative branch site (score: 471)
 atgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaatggatctccgcctaaattaaactacttgctttcagtcttggctgtgcctgtaccatccattttgcaagtgatagatgtctagctgccgtttctgacctggtccatgttatccaacagTGCTGGACGGGTCTACCCGTTGGTAGTCGCTGCGCACCCCATGGAGCCTAACCAGATCGCGATCGGCATGAGCGACGGCAAGGTCCATGTGGTGGAGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG