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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTCTTCATGTGGGCCTGAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAGgtacaaaattcaactattcagcttttgtcgttatatgacagattttctaaaatttgaattattgtcacacataactattcagctcttggatgcatttgca...

Basic information

species Zea mays
transcript GRMZM2G050484_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050484_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g10230.1 (Oryza sativa), 5'ss of exon 7
GGTCTTCATGTGGGCCTGAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAGgtacaaaattcaactattcagcttttgtcgttatatgacagattttctaaaatttgaattattgtcacacataactattcagctcttggatgcat-ttgca---
|| |||| |||||| |||||||||||| |||||||||| ||||| || |||||||||||| | || |||||| ||||| ||| | || |||| | |||| || | || ||| || || ||| | || || | ||| |
GGCCTTCGTGTGGGACTGAACTTGGCTATTGCTATTGCTTTACACAATATACCAGAGgtagataaatcaacttatcagcatttctggtc-catgagaa---ttcttaactacagtttgatgttgcatattgctaattaggataccctagcttgttgtatgt
















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|88749903|gb|DY534044.1|DY534044
EST:     TGTGGGCCTG-ACTTTGGCTGTTGCTATTGCCTTACATAACATACCAGAG                         GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
genomic: TGTGGGCCTGAAC-TTGGCTGTTGCTATTGCCTTACATAACATACCAGAGgtacaaaatt ... accttttcagGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
EST: gi|101385255|gb|EB814673.1|EB814673
EST:     ATGTGGGCCTGAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAG                         GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
genomic: ATGTGGGCCTGAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAGgtacaaaatt ... accttttcagGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
EST: gi|71308419|gb|DR790442.1|DR790442
EST:     ATGTGGGCCTGAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAG                         GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
genomic: ATGTGGGCCTGAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAGgtacaaaatt ... accttttcagGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
EST: gi|76288875|gb|DV028443.1|DV028443
EST:     CTTACATAACATACCAGAG                         GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
genomic: CTTACATAACATACCAGAGgtacaaaatt ... accttttcagGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
EST: gi|50324963|gb|CO520089.1|CO520089
EST:     ATTGCCTTACATAACATACCAGAG                         GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
genomic: ATTGCCTTACATAACATACCAGAGgtacaaaatt ... accttttcagGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
EST: gi|71300310|gb|DR786224.1|DR786224
EST:     ATGTGGGCCTGAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAG                         GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
genomic: ATGTGGGCCTGAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAGgtacaaaatt ... accttttcagGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
EST: gi|89762575|gb|DY690101.1|DY690101
EST:     ATGTGGGCCTGAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAG                         GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
genomic: ATGTGGGCCTGAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAGgtacaaaatt ... accttttcagGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
EST: gi|71446246|gb|DR827296.1|DR827296
EST:     GAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAG                         GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
genomic: GAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAGgtacaaaatt ... accttttcagGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
EST: gi|91052253|gb|EB162671.1|EB162671
EST:     CCTGAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAG                         GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
genomic: CCTGAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAGgtacaaaatt ... accttttcagGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG
EST: gi|211448870|gb|FL218800.1|FL218800
EST:     ATGTGGGCCTGAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAG                         GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAGC
genomic: ATGTGGGCCTGAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAGgtacaaaatt ... accttttcagGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAGC

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: 47 (upstream exon), 49 (downstream exon)
Score: 46

GGTCTTCATGTGGGCCTGAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAGgtacaaaatt ... accttttcagGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 67

GGTCTTCATGTGGGCCTGAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAGgtacaaaatt ... accttttcagGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 144

GGTCTTCATGTGGGCCTGAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAGgtacaaaatt ... accttttcagGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 121

GGTCTTCATGTGGGCCTGAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAGgtacaaaatt ... accttttcagGGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTCTTCATGTGGGCCTGAACTTGGCTGTTGCTATTGCCTTACATAACATACCAGAGgtacaaaattcaactattcagcttttgtcgttatatgacagattttctaaaatttgaattattgtcacacataactattcagctcttggatgcatttgca

- - - - - - - - - - - - GCTGTT