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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACCAGCTGTTCTAGCAATAAAGAGGGAAGGTTACAGCATTAAATGTAATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCTgtatgccactactttttagcatactttatctcagtaacttgaatgctttatattcttgtgctttaattttgcaataataatttagtttagttttaaccag...

Basic information

species Zea mays
transcript GRMZM2G036206_T01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036206_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os01g01800.1 (Oryza sativa), 5'ss of exon 18
GGAACCAGCTGTTCTAGCAATAAAGAGGGAAGGTTACAGCATTAAATGTAATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCTgtatgccactactttttagcatactttatctcagtaacttgaatgctttatattcttgtgctttaattttgcaataataatttagtttagtt---ttaaccag--
|||||||||| || | ||||||||||||||||| ||||| |||||||||| ||| |||||||||||| |  |||||||||| |||||||||| |||| ||||| | |  || |      | || | | |  |||||  |    ||  ||  |       | | | ||| |  |||  | |   |  |  |||   |    |||  
GGAACCAGCTATTTTGGCAATAAAGAGGGAAGGCTACAGTATTAAATGTACTGGTCAGCGTGGTGTTGTTCTCACAGAGAAATTTCAGCAAGCAACTTCTgtacgtccttattc-----cgtattctttagcagtacatcatttgaatttcaggaagtagatctcattctaaaattgtgagcaaactctgttggttccttcagta
















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|78180678|gb|DV551006.1|DV551006
EST:     ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCT                         ATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCG
genomic: ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCTgtatgccact ... ccctatccagATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCG
EST: gi|7844204|gb|AW787426.1|AW787426
EST:     ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCT                         ATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCG
genomic: ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCTgtatgccact ... ccctatccagATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCG
EST: gi|211089151|gb|FL459717.1|FL459717
EST:     ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCT                         ATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCA
genomic: ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCTgtatgccact ... ccctatccagATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCG
EST: gi|7844203|gb|AW787425.1|AW787425
EST:     ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCT                         ATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCG
genomic: ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCTgtatgccact ... ccctatccagATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCG
EST: gi|6020818|gb|AW065746.1|AW065746
EST:     ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGNTTCAGCAAGGAACTGCT                         ATTCATATTCCATATGGGCGTCCAACAGA
genomic: ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCTgtatgccact ... ccctatccagATTCATATTCCATATGGGCGTCCAACAGA
EST: gi|5762226|gb|AI967274.1|AI967274
EST:     ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCT                         ATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCG
genomic: ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCTgtatgccact ... ccctatccagATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCG
EST: gi|71772016|gb|DR969953.1|DR969953
EST:     ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCT                         ATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCG
genomic: ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCTgtatgccact ... ccctatccagATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCG
EST: gi|5871151|gb|AW017592.1|AW017592
EST:     ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCT                         ATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCG
genomic: ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCTgtatgccact ... ccctatccagATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCG
EST: gi|6020497|gb|AW065425.1|AW065425
EST:     ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCT                         ATTCATAGGGGATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCG
genomic: ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCTgtatgccact ... ccctatccagATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCG
EST: gi|7844205|gb|AW787427.1|AW787427
EST:     ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCT                         ATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCG
genomic: ATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCTgtatgccact ... ccctatccagATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCG

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: 36 (upstream exon), 49 (downstream exon)
Score: 85

GGAACCAGCTGTTCTAGCAATAAAGAGGGAAGGTTACAGCATTAAATGTAATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCTgtatgccact ... ccctatccagATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 61

GGAACCAGCTGTTCTAGCAATAAAGAGGGAAGGTTACAGCATTAAATGTAATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCTgtatgccact ... ccctatccagATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 52

GGAACCAGCTGTTCTAGCAATAAAGAGGGAAGGTTACAGCATTAAATGTAATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCTgtatgccact ... ccctatccagATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACT


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 54

GGAACCAGCTGTTCTAGCAATAAAGAGGGAAGGTTACAGCATTAAATGTAATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCTgtatgccact ... ccctatccagATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAACCAGCTGTTCTAGCAATAAAGAGGGAAGGTTACAGCATTAAATGTAATGGGCAGCGTGGTGTTCTAATCACAGAGAAGTTTCAGCAAGGAACTGCTgtatgccactactttttagcatactttatctcagtaacttgaatgctttatattcttgtgctttaattttgcaataataatttagtttagttttaaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA