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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtagaaatgtttattttcaaacccgatactttgtttctgtactttgaagtggtttgttgcacactgcagCATGTGGAAGTTATCCCACATATGGAGAAATCAAGACGACTTGATCAGATCTTGCGTTCACAAGATCCTGGATCAAAAATCATAATATTTTGCTCCACCA

Basic information

species Zea mays
transcript GRMZM2G066440_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066440_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g07740.2 (Oryza sativa), 3'ss of exon 8
---gtgagtagaaatgtttattttcaaacccgatactttgtttctgtactttgaagtggtttgttgcacactgcagCATGTGGAAGTTATCCCACATATGGAGAAATCAAGACGACTTGATCAGATCTTGCGTTCACAAGATCCTGGATCAAAAATCATAATATTTTGCTCCACCA
    |||  |      ||| ||||        | ||||||||||  || |||||||  | |||||  |   ||||| ||||||| |||||| ||| |  ||||||||| || || |||||||| ||| |  | ||||| || |||||||| ||||||||||||||||||||||| |
gtaatgaaaatggtgctttctttttgttgatcagactttgtttcgttattttgaagcagattgttatatgttgcagTATGTGGATGTTATCACACCTCCGGAGAAATCGAGGCGGCTTGATCAAATCCTAAGGTCACAGGAACCTGGATCGAAAATCATAATATTTTGCTCCACAA
















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|13516058|gb|BG518334.1|BG518334
EST:     TTAACATTGGAAACACTGATCAGCTGGTTGCAAATAAATCAATTACTCAG                         CATGTGGAAGTTATCCCACATATGGAGAAATCAAGACGACTTGATCAGATC
genomic: TTAACATTGGAAACACTGATCAGCTGGTTGCAAATAAATCAATTACTCAGgtgagtagaa ... cacactgcagCATGTGGAAGTTATCCCACATATGGAGAAATCAAGACGACTTGATCAGATC
EST: gi|61118435|gb|DN559396.1|DN559396
EST:     TTAACATTGGAAACACTGATCAGCTGGTTGCAAATAAATCAATTACTCAG                         CATGTGGAAGTTATCCCACATATGGAGAAATCAAGACGACTTGATCAGATC
genomic: TTAACATTGGAAACACTGATCAGCTGGTTGCAAATAAATCAATTACTCAGgtgagtagaa ... cacactgcagCATGTGGAAGTTATCCCACATATGGAGAAATCAAGACGACTTGATCAGATC

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: 45 (upstream exon), 48 (downstream exon)
Score: 257

AAAAGAGGTTAGAAAAATAGCGTCGGATTTACTGAATAACCCAGTTCAAGTTAACATTGGAAACACTGATCAGCTGGTTGCAAATAAATCAATTACTCAGgtgagtagaa ... cacactgcagCATGTGGAAGTTATCCCACATATGGAGAAATCAAGACGACTTGATCAGATCTTGCGTTCACAAGATCCTGGATCAAAAATCATAATATTTTGCTCCACCA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 194

AAAAGAGGTTAGAAAAATAGCGTCGGATTTACTGAATAACCCAGTTCAAGTTAACATTGGAAACACTGATCAGCTGGTTGCAAATAAATCAATTACTCAGgtgagtagaa ... cacactgcagCATGTGGAAGTTATCCCACATATGGAGAAATCAAGACGACTTGATCAGATCTTGCGTTCACAAGATCCTGGATCAAAAATCATAATATTTTGCTCCACCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 180

AAAAGAGGTTAGAAAAATAGCGTCGGATTTACTGAATAACCCAGTTCAAGTTAACATTGGAAACACTGATCAGCTGGTTGCAAATAAATCAATTACTCAGgtgagtagaa ... cacactgcagCATGTGGAAGTTATCCCACATATGGAGAAATCAAGACGACTTGATCAGATCTTGCGTTCACAAGATCCTGGATCAAAAATCATAATATTTTGCTCCACCA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 129

AAAAGAGGTTAGAAAAATAGCGTCGGATTTACTGAATAACCCAGTTCAAGTTAACATTGGAAACACTGATCAGCTGGTTGCAAATAAATCAATTACTCAGgtgagtagaa ... cacactgcagCATGTGGAAGTTATCCCACATATGGAGAAATCAAGACGACTTGATCAGATCTTGCGTTCACAAGATCCTGGATCAAAAATCATAATATTTTGCTCCACCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcaaacccgatactttgtttctgtactttgaagtggtttgttgcacactgcagCATGTGGAAGTTATCCCACATATGGAGAAATCAAGACGACTTGATCAGATCTTGCGTTCACAAGATCCTGGATCAAAAATCATAATATTTTGCTCCACCA
           atacttt  TA-rich tract