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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTTGAGCCTGTACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAGgtagcctgcacattttttttgtaaatgcaatgtgcatgattttataccaagcaaataagttactcaatcgctttggcttctctagaaataacatatttat...

Basic information

species Zea mays
transcript GRMZM5G897073_T05
intron # 3
splice site 5'
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|88752874|gb|DY537015.1|DY537015
EST:     GTTGAGCCTGTACTTCGAGGAGTGCCTGCATCCGGGATTATCACACACAG                         TCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGG
genomic: GTTGAGCCTGTACT-CGAGGAGTGCCTGCATCCGGGATTATCACACACAGgtagcctgca ... ttgagtttagTCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGG
EST: gi|60345564|gb|DN212537.1|DN212537
EST:     TGTTGAGCCTGTACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAG                         TCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGG
genomic: TGTTGAGCCTGTACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAGgtagcctgca ... ttgagtttagTCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGG
EST: gi|211423204|gb|FL142523.1|FL142523
EST:     TGTTGAGCCTGTACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAG                         TCAATTTGTAGGARAGGGGACCGCCATACATCAAAGATGACTAAAGAAGAG
genomic: TGTTGAGCCTGTACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAGgtagcctgca ... ttgagtttagTCAATTTGTAGGAGAGGGGAC-GCCATACATCAAAGATGACTAAAGAAGAG
EST: gi|71446945|gb|DR827995.1|DR827995
EST:     TGTTGAGCCTGTACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAG                         TCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGG
genomic: TGTTGAGCCTGTACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAGgtagcctgca ... ttgagtttagTCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGG

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: 460

GATGTTGAGCCTGTACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAGgtagcctgca ... ttgagtttagTCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGGAAGATGAAGAATACCTCGAAGAGGAAGAAGATGCCCTTGCTGGTGCAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 85

GATGTTGAGCCTGTACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAGgtagcctgca ... ttgagtttagTCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGGAAGATGAAGAATACCTCGAAGAGGAAGAAGATGCCCTTGCTGGTGCAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65

GATGTTGAGCCTGTACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAGgtagcctgca ... ttgagtttagTCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGGAAGATGAAGAATACCTCGAAGAGGAAGAAGATGCCCTTGCTGGTGCAGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 191

GATGTTGAGCCTGTACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAGgtagcctgca ... ttgagtttagTCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGGAAGATGAAGAATACCTCGAAGAGGAAGAAGATGCCCTTGCTGGTGCAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGTTGAGCCTGTACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAGgtagcctgcacattttttttgtaaatgcaatgtgcatgattttataccaagcaaataagttactcaatcgctttggcttctctagaaataacatatttat

- - - - - - - - - GAGGAG