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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggctttttactgcataggagttgctgtagcttttaatcgaattaattttgttatggtatcagactaatcatatggttcactgatgttcactccgacagAGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCTGGGAGTGAGCAACTAAGATCTATGCTGCCGACTCGCGTACTCCCACAAC

Basic information

species Zea mays
transcript GRMZM2G320949_T01
intron # 2
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|13250022|gb|BG360925.1|BG360925
EST:     AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAG                         AGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
genomic: AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAGgtatgcccat ... actccgacagAGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
EST: gi|94478468|gb|EB707426.1|EB707426
EST:     AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAG                         AGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
genomic: AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAGgtatgcccat ... actccgacagAGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
EST: gi|78108486|gb|DV526904.1|DV526904
EST:     AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAG                         AGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
genomic: AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAGgtatgcccat ... actccgacagAGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
EST: gi|19769519|gb|BQ034240.1|BQ034240
EST:     AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAG                         AGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
genomic: AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAGgtatgcccat ... actccgacagAGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
EST: gi|18177418|gb|BM378621.1|BM378621
EST:     AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAG                         AGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
genomic: AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAGgtatgcccat ... actccgacagAGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
EST: gi|16378634|gb|BI992528.1|BI992528
EST:     AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAG                         AGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
genomic: AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAGgtatgcccat ... actccgacagAGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
EST: gi|211103895|gb|FL455676.1|FL455676
EST:     AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAG                         AGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
genomic: AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAGgtatgcccat ... actccgacagAGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
EST: gi|19770039|gb|BQ034760.1|BQ034760
EST:     AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAG                         AGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
genomic: AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAGgtatgcccat ... actccgacagAGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
EST: gi|211093414|gb|FL432118.1|FL432118
EST:     AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAG                         AGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
genomic: AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAGgtatgcccat ... actccgacagAGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
EST: gi|33100705|gb|CF060665.1|CF060665
EST:     AGCAGGACCATTGGCACCTTCATCAATTTAAGCTCAGTGTCAGCGGTGAG                         AGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
genomic: AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAGgtatgcccat ... actccgacagAGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
EST: gi|78108487|gb|DV526905.1|DV526905
EST:     AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAG                         AGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
genomic: AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAGgtatgcccat ... actccgacagAGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
EST: gi|18650405|gb|BM499224.1|BM499224
EST:     AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAG                         AGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT
genomic: AGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAGgtatgcccat ... actccgacagAGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCT

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: 48 (upstream exon), 39 (downstream exon)
Score: 38

TGTGGCAGCTGGTGCTGTTGTTGGTTTTGTTGTAATGGGTCAGAGGTGGCAGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAGgtatgcccat ... actccgacagAGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCTGGGAGTGAGCAACTAAGATCTATGCTGCCGACTCGCGTACTCCCACAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 50

TGTGGCAGCTGGTGCTGTTGTTGGTTTTGTTGTAATGGGTCAGAGGTGGCAGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAGgtatgcccat ... actccgacagAGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCTGGGAGTGAGCAACTAAGATCTATGCTGCCGACTCGCGTACTCCCACAAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 55

TGTGGCAGCTGGTGCTGTTGTTGGTTTTGTTGTAATGGGTCAGAGGTGGCAGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAGgtatgcccat ... actccgacagAGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCTGGGAGTGAGCAACTAAGATCTATGCTGCCGACTCGCGTACTCCCACAAC


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 24

TGTGGCAGCTGGTGCTGTTGTTGGTTTTGTTGTAATGGGTCAGAGGTGGCAGCAGGACCATTGGCACCTTCATCAATTTAAGTTCAGTGTCAGCGGTGAGgtatgcccat ... actccgacagAGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCTGGGAGTGAGCAACTAAGATCTATGCTGCCGACTCGCGTACTCCCACAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattttgttatggtatcagactaatcatatggttcactgatgttcactccgacagAGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCTGGGAGTGAGCAACTAAGATCTATGCTGCCGACTCGCGTACTCCCACAAC
                                          ttcactcc  CT-rich tract
                     taatcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggctttttactgcataggagttgctgtagcttttaatcgaattaattttgttatggtatcagactaatcatatggttcactgatgttcactccgacagAGCATGAATCGAGTCATTGGAGCATTCAGTCGTTTGAAGGATGGGCTTCCTGGGAGTGAGCAACTAAGATCTATGCTGCCGACTCGCGTACTCCCACAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - -ctgcata
- - - - - - - - - - -gttgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtt