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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAGTCATCTTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCTGGACAGgtacggaacttgccattgctgctgttgttgcttgtaacgtcttccgagtttggggcgcatgtgcag

Basic information

species Zea mays
transcript GRMZM5G879749_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G879749_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g55130.1 (Oryza sativa), 5'ss of exon 8
CACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAGTCATCTTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCTGGACAGgtacggaac--ttgccattgctgct-----gttgttgctt-----gtaacgt-----cttccgagtttggggcg-catgtgcag---------------------
||| ||||||||||| ||||| || || |||||||| ||  | || |||||||| |||||||  |||| ||||||||| || |||||||||||||||||||||  ||||  |  ||||||||| |     | ||  | ||     | ||  |     |||   ||| ||   |  ||| ||||                      
CACGGATTCAGTCGTTCCGGTTACTGCAACGAGGTTTGCGCTTAGCCATCTTGGACTGAAGACGAAGATCCGCTGGTACCCTTGGTACTCAGCTGGACAGgtagtgaacaatctccattgctgtttgtcagatgcagtttaagcagaaatcttgtcactttaaagtctgtaacttcatctgcaaatggtgcatctgtgtgtgcag

upper sequence: GRMZM5G879749_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA17G08090.1 (Glycine max), 5'ss of exon 10
CACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAGTCATCTTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCTGGACAGgtacggaacttgccattgctgctgttgttgcttgtaacgtcttccgagtttggggcgcatgtgcag----------------------------
||||||||| || || || || || || || |||||  |  |||  || |||   || |  ||||  || |||||||||||||||||||| | ||||||||||   || ||   |    ||       |   | |||| | || |  ||              | |                            
CACAGATTCTGTGGTTCCAGTTACTGCCACAAGGTTTTCTCTCAACCACCTTAACCTCAGCATCAGAACTCGCTGGTATCCATGGTACTCTGGTGGACAGgtatt-aatttattaaatttgaaagccatatatataacatattacatgtaccaatatttcacactgaggtttatgtatcttgtggttactttag
















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|93014933|gb|EB640453.1|EB640453
EST:     TTGGTTTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCTGGACAG                         GTAGGAGGATGGTCTGAGGTGTACGAAGGGCTCACGTTTGCGTCGGTGAGA
genomic: TTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCTGGACAGgtacggaact ... gcatgtgcagGTAGGAGGATGGTCTGAGGTGTACGAAGGGCTCACGTTTGCGTCGGTGAGA
EST: gi|76020008|gb|DT947178.1|DT947178
EST:     TTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCTGGACAG                         GTAGGAGGATGGTCTGAGGTGTACGAAGGGCTCACGTTTGCGTCGGTGAGA
genomic: TTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCTGGACAGgtacggaact ... gcatgtgcagGTAGGAGGATGGTCTGAGGTGTACGAAGGGCTCACGTTTGCGTCGGTGAGA
EST: gi|71775052|gb|DR972930.1|DR972930
EST:     TTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTATTCAGCTGGACAG                         GTAGGAGGATGGTTTGAGGTGTACGAAGGGCTCACGTTTGCGTCGGTGAGA
genomic: TTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCTGGACAGgtacggaact ... gcatgtgcagGTAGGAGGATGGTCTGAGGTGTACGAAGGGCTCACGTTTGCGTCGGTGAGA
EST: gi|211058977|gb|FL460151.1|FL460151
EST:     TCGGTCTGAAGATCAAGACCCGCTGGTATCCGTGGTACTCAGCTGGACAG                         GTAGGAGGATGGTCTGAGGTGTACGAAGGGCTCACGTTTGCGTCGGTGAGA
genomic: TTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCTGGACAGgtacggaact ... gcatgtgcagGTAGGAGGATGGTCTGAGGTGTACGAAGGGCTCACGTTTGCGTCGGTGAGA
EST: gi|91050417|gb|EB160835.1|EB160835
EST:     TTGGTTTGAAGATCAAGACCCGCTGGTATCCATGGTATTCAGCTGGACAG                         GTAGGAGGATGGTCTGAGGTGTACGAAGGGCTCACGTTTGCGTCGGTGAGA
genomic: TTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCTGGACAGgtacggaact ... gcatgtgcagGTAGGAGGATGGTCTGAGGTGTACGAAGGGCTCACGTTTGCGTCGGTGAGA
EST: gi|211181832|gb|FL473669.1|FL473669
EST:     TCGGTCTGAAGATCAAGACCCGCTGGTATCCGTGGTACTCAGCTGGACAG                         GTAGGAGGATGGTCTGAGGTGTACGAAGGGCTCACGTTTGCGTCGGTGAGA
genomic: TTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCTGGACAGgtacggaact ... gcatgtgcagGTAGGAGGATGGTCTGAGGTGTACGAAGGGCTCACGTTTGCGTCGGTGAGA

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), 47 (downstream exon)
Score: 75

CACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAGTCATCTTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCTGGACAGgtacggaact ... gcatgtgcagGTAGGAGGATGGTCTGAGGTGTACGAAGGGCTCACGTTTGCGTCGGTGAGAGGCGCAGGGCATGAGGTGCCGTTGTTCCAGCCCAGGAGGGCGTTCAGGA


Block sizes: 45 (upstream exon), 37 (downstream exon)
Score: 11

CACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAGTCATCTTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCTGGACAGgtacggaact ... gcatgtgcagGTAGGAGGATGGTCTGAGGTGTACGAAGGGCTCACGTTTGCGTCGGTGAGAGGCGCAGGGCATGAGGTGCCGTTGTTCCAGCCCAGGAGGGCGTTCAGGA


Block sizes: 47 (upstream exon), 39 (downstream exon)
Score: 5

CACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAGTCATCTTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCTGGACAGgtacggaact ... gcatgtgcagGTAGGAGGATGGTCTGAGGTGTACGAAGGGCTCACGTTTGCGTCGGTGAGAGGCGCAGGGCATGAGGTGCCGTTGTTCCAGCCCAGGAGGGCGTTCAGGA


Block sizes: 44 (upstream exon), 37 (downstream exon)
Score: 17

CACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAGTCATCTTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCTGGACAGgtacggaact ... gcatgtgcagGTAGGAGGATGGTCTGAGGTGTACGAAGGGCTCACGTTTGCGTCGGTGAGAGGCGCAGGGCATGAGGTGCCGTTGTTCCAGCCCAGGAGGGCGTTCAGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACAGATTCAGTCGTCCCGGTGACCGCGACGAGGTTCGCCATCAGTCATCTTGGTCTGAAGATCAAGACCCGCTGGTATCCATGGTACTCAGCTGGACAGgtacggaacttgccattgctgctgttgttgcttgtaacgtcttccgagtttggggcgcatgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA