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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgttcggcaattcatcctgctgatcgtacttttggttttgtacttccgtagtatatcatcacgtgaatcttttttctgttctttctgtcatactgccagGACTCGTTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATCGAGTGGAGCCCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACC

Basic information

species Zea mays
transcript GRMZM2G458888_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G458888_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G28040.2 (Glycine max), 3'ss of exon 10
---gtgttcggcaa--ttcatcctgctgatcgtacttttggttttgtacttccgtagtatatcatcacgtgaatcttttttctgttctttctgtca-tactgccagGACTCGTTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATCGAGTGGAGCCCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACC
    |     | ||  ||||   ||       |  || || || |  | || | |    ||| |   |    ||      |   || ||| |||    |       || ||  ||||||||||||| || || |||||| |  |||| |||||||| |||||||| ||||| ||||| || |||||||| ||  | ||        
gatttagaaagtaactttcacattgtctgatttttttctgcttattaatttacttttgttattaaagctgatatgacaagtgcattatttttgtgggcagGAAGGAGATTCTGTGGTAGCACATTTCGAATATCACAAGCACCCAATCACATCCATTGAGTGGAGTCCACATGAAGCCTCTTCATTAGCAGTTTCTTCAT------
















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|211433222|gb|FL465175.1|FL465175
EST:     CTGGGTGCGACGATGGCAGTTTCTCAGTTCATGATCTTAGATCAATTCAG                         GACTCGTTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATC
genomic: CTGGGTGCGACGATGGCAGTTTCTCAGTTCATGATCTTAGATCAATTCAGgtatttcttt ... atactgccagGACTCGTTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATC
EST: gi|37393369|gb|CF633947.1|CF633947
EST:     GGCAGTTTCTCAGTTCATGATCTTAGATCAATTCAG                         GACTCATTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATC
genomic: GGCAGTTTCTCAGTTCATGATCTTAGATCAATTCAGgtatttcttt ... atactgccagGACTCGTTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATC
EST: gi|211433223|gb|FL465176.1|FL465176
EST:     TTCATGATCTTAGATCAATTCAG                         GACTCGTTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATC
genomic: TTCATGATCTTAGATCAATTCAGgtatttcttt ... atactgccagGACTCGTTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATC
EST: gi|87156090|gb|DY400879.1|DY400879
EST:     CTGGGTGCGACGATGGCAGTTTCTCAGTTCATGATCTTAGATCAATTCAG                         GACTCATTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATC
genomic: CTGGGTGCGACGATGGCAGTTTCTCAGTTCATGATCTTAGATCAATTCAGgtatttcttt ... atactgccagGACTCGTTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATC
EST: gi|26558492|gb|CA830727.1|CA830727
EST:     CTGGG-GCGACGATGGCAGTTTCTCAGTTCATGATCTTAGATCAATTCAG                         GACTCATTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATC
genomic: CTGGGTGCGACGATGGCAGTTTCTCAGTTCATGATCTTAGATCAATTCAGgtatttcttt ... atactgccagGACTCGTTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATC
EST: gi|40336456|gb|CK370526.1|CK370526
EST:     GGCAGTTTCTCAGTTCATGATCTTAGATCAATTCAG                         GACTCATTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATC
genomic: GGCAGTTTCTCAGTTCATGATCTTAGATCAATTCAGgtatttcttt ... atactgccagGACTCGTTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATC
EST: gi|22472647|gb|BU037127.1|BU037127
EST:     CTGGG-GCGACGATGGCAGTTTCTCAGTTCATGATCTTAGATCAATTCAG                         GACTCATTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATC
genomic: CTGGGTGCGACGATGGCAGTTTCTCAGTTCATGATCTTAGATCAATTCAGgtatttcttt ... atactgccagGACTCGTTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATC

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), 41 (downstream exon)
Score: 82

GCTTGCTAGCTGCATGATAGCTTCTGGGTGCGACGATGGCAGTTTCTCAGTTCATGATCTTAGATCAATTCAGgtatttcttt ... atactgccagGACTCGTTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATCGAGTGGAGCCCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACC


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 36

GCTTGCTAGCTGCATGATAGCTTCTGGGTGCGACGATGGCAGTTTCTCAGTTCATGATCTTAGATCAATTCAGgtatttcttt ... atactgccagGACTCGTTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATCGAGTGGAGCCCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 58

GCTTGCTAGCTGCATGATAGCTTCTGGGTGCGACGATGGCAGTTTCTCAGTTCATGATCTTAGATCAATTCAGgtatttcttt ... atactgccagGACTCGTTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATCGAGTGGAGCCCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 45

GCTTGCTAGCTGCATGATAGCTTCTGGGTGCGACGATGGCAGTTTCTCAGTTCATGATCTTAGATCAATTCAGgtatttcttt ... atactgccagGACTCGTTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATCGAGTGGAGCCCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgtagtatatcatcacgtgaatcttttttctgttctttctgtcatactgccagGACTCGTTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATCGAGTGGAGCCCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACC
                       tcttttttctgttctt  CT-rich tract
                     aatctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttcggcaattcatcctgctgatcgtacttttggttttgtacttccgtagtatatcatcacgtgaatcttttttctgttctttctgtcatactgccagGACTCGTTGGTAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATCGAGTGGAGCCCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - cctgctg
- - - - - - - - - - - - - - - ttttggt