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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatacatttataatcaggagtatgtgagttgatacttgtttctagatatttatatgaggctaccctggatcatggctgtcaaaactataattatg...

Basic information

species Zea mays
transcript GRMZM5G802854_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G802854_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g66730.2 (Oryza sativa), 5'ss of exon 5
TATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatacatttataatcaggagtatgtgagttgatacttgtttct-agatatttatatgaggctaccctggatcatggctgtcaaaactataattatg--
|||| |||||||||||||||||| ||||||||| ||||||| |||||||||||||| |||||| |||||||||    |    ||||| | || || ||| | | | |   |||| |  |    |   |   |   |   ||  | ||  |   || ||  
TATATACCTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGTTGACACCAAACCAGATgtaagtgtacatttatgtgtatt--tatgtaaattaattcttctatatgatgcattttttagtatgtggacctaactgtt-ttgatataatcactgttctgta

upper sequence: GRMZM5G802854_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g47256.2 (Oryza sativa), 5'ss of exon 4
TATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatacatttataatcaggagtatgtgagttgatacttgtttctag-atatttatatgaggctaccctggatcatggctgtcaaaactataattatg----
|||| |||||||||||||||||| ||||||||| ||||||| |||||||||||||| |||||||  |||||||    |    ||||| | || || ||| | | | |   |||| |  |    |   |   ||  |   ||  | ||  |   || ||    
TATATACCTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGTTGACACCAAACCAGATgtaagta--catttatg--tatatttatgtaaattaattcttctatatggtgcattttttagtatgtggacctaattgtt-ttgatacaatcactgttctgtaca
















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|71756425|gb|DR954362.1|DR954362
EST:     CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC                         AACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
genomic: CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
EST: gi|71434798|gb|DR815848.1|DR815848
EST:     CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC                         AACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTTCTAC-AGTACT
genomic: CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTT-CTACCAGTACT
EST: gi|211385471|gb|FL080437.1|FL080437
EST:     CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC                         AACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
genomic: CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT

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: 70

TATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 40

TATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 42

TATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 51

TATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCAAG