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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAAGCGAAGGACCCTTCTCAGAAGTTGACTAAACAGCATTCAGCTGTTGGTATCGTTGAAGAGATATTTGAAGAAGGTTCAGCGATGCTATCAGAAAGgtcagttgtaccctttctctaaatgttttcttgatcagaattttctagtgttttcccactagttcactgttgatgtatgcaaggagcatggtctattttg...

Basic information

species Zea mays
transcript GRMZM2G173734_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G173734_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g32964.1 (Oryza sativa), 5'ss of exon 7
AGAAAGCGAAGGACCCTTCTCAGAAGTTGACTAAACAGCATTCAGCTGTTGGTATCGTTGAAGAGATATTTGAAGAAGGTTCAGCGATGCTATCAGAAAGgtcagttgtaccctttctctaaatgttttcttgatcagaattttctagtgttttcccactagttcactgttgatgtatgcaaggagcatggtctattttg----
| ||  | || |||| | || | ||  ||||||| ||||  ||||| |  ||||| || |||||| |||| |||||||||||||| ||||||||||| |||||||||||| |  | ||||||  || ||  ||| |    |||   |||||||  |  |||| || |||||  ||  || ||| |||  | |  ||  |     
AAAAGACAAAAGACCATCCTAATAAACTGACTAAGCAGCTGTCAGCAGCGGGTATGGTGGAAGAGTTATTCGAAGAAGGTTCAGCAATGCTATCAGAGAGgtcagttgtagctctcctctaagagtgtttatgaac----tttctaagtgtttcactgctagctccctgttcttgggtgtaagcagctggattcatagtcaacc
















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|78180869|gb|DV551242.1|DV551242
EST:     GGTATCGTTGAAGAGATATTTGAAGAAGGTTCAGCGATGCTATCAGAAAA                         ACCTTTAACAAGACCCCTTATGTTATC
genomic: GGTATCGTTGAAGAGATATTTGAAGAAGGTTCAGCGATGCTATCAGAAAGgtcagttgta ... cataggacagACCTTTAACAAGACCCCTTATGTTATC
EST: gi|93014755|gb|EB640275.1|EB640275
EST:     GGTATCGTTGAAGAGATATTTGAAGAAGGTTCAGCGATGCTATCAGAAAG                         ACCTTTAACAAGACCCCTTATGTTATTTTTGCATTGTGGTCCTGAAAGCCT
genomic: GGTATCGTTGAAGAGATATTTGAAGAAGGTTCAGCGATGCTATCAGAAAGgtcagttgta ... cataggacagACCTTTAACAAGACCCCTTATGTTATCTTCGCATTGTGGTCCTGAAAGCCT
EST: gi|93014756|gb|EB640276.1|EB640276
EST:     GGTATCGTTGAAGAGATATTTGAAGAAGGTTCAGCGATGCTATCAGAAAG                         ACCTTTAACAAGACCCCTTATGTTATCTTCGCATTGTGGTCCTGAAAGCCT
genomic: GGTATCGTTGAAGAGATATTTGAAGAAGGTTCAGCGATGCTATCAGAAAGgtcagttgta ... cataggacagACCTTTAACAAGACCCCTTATGTTATCTTCGCATTGTGGTCCTGAAAGCCT

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: 39 (upstream exon), 49 (downstream exon)
Score: 41

AGAAAGCGAAGGACCCTTCTCAGAAGTTGACTAAACAGCATTCAGCTGTTGGTATCGTTGAAGAGATATTTGAAGAAGGTTCAGCGATGCTATCAGAAAGgtcagttgta ... cataggacagACCTTTAACAAGACCCCTTATGTTATCTTCGCATTGTGGTCCTGAAAGCCTGCTTGAAACTTGATTTCCAGTTCGAATATTACCTGCTTGAAAAAGGGCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 66

AGAAAGCGAAGGACCCTTCTCAGAAGTTGACTAAACAGCATTCAGCTGTTGGTATCGTTGAAGAGATATTTGAAGAAGGTTCAGCGATGCTATCAGAAAGgtcagttgta ... cataggacagACCTTTAACAAGACCCCTTATGTTATCTTCGCATTGTGGTCCTGAAAGCCTGCTTGAAACTTGATTTCCAGTTCGAATATTACCTGCTTGAAAAAGGGCC


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

AGAAAGCGAAGGACCCTTCTCAGAAGTTGACTAAACAGCATTCAGCTGTTGGTATCGTTGAAGAGATATTTGAAGAAGGTTCAGCGATGCTATCAGAAAGgtcagttgta ... cataggacagACCTTTAACAAGACCCCTTATGTTATCTTCGCATTGTGGTCCTGAAAGCCTGCTTGAAACTTGATTTCCAGTTCGAATATTACCTGCTTGAAAAAGGGCC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 64

AGAAAGCGAAGGACCCTTCTCAGAAGTTGACTAAACAGCATTCAGCTGTTGGTATCGTTGAAGAGATATTTGAAGAAGGTTCAGCGATGCTATCAGAAAGgtcagttgta ... cataggacagACCTTTAACAAGACCCCTTATGTTATCTTCGCATTGTGGTCCTGAAAGCCTGCTTGAAACTTGATTTCCAGTTCGAATATTACCTGCTTGAAAAAGGGCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAAGCGAAGGACCCTTCTCAGAAGTTGACTAAACAGCATTCAGCTGTTGGTATCGTTGAAGAGATATTTGAAGAAGGTTCAGCGATGCTATCAGAAAGgtcagttgtaccctttctctaaatgttttcttgatcagaattttctagtgttttcccactagttcactgttgatgtatgcaaggagcatggtctattttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG