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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATATCAGCATTTCTCTGGTACTAGGGTTGCTCTTGATGTGGCTGAAACCCCCTCAAACCTATTTGAgtatgtacgagcttttaggttttacatacgatgacagtttactttgtagcacatctaattttggtttgttcaaaaataaggtatttttattgtcaacccatttgagttgagtttcattcacattacag

Basic information

species Zea mays
transcript GRMZM2G450659_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G450659_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os06g47210.1 (Oryza sativa), 5'ss of exon 14
GAATATCAGCATTTCTCTGGTACTAGGGTTGCTCTTGATGTGGCTGAAACCCCCTCAAACCTATTTGAgtatgtacgagcttttaggttttacatacga---tgacagtttac---tttgtagcacatctaattttggtttgttcaaaaataaggtatttttattgtcaacccatttga------gttgagtttcattcacattacag
|| ||||| ||||||||||||||||| ||||||||||||||||||||||  || |||||||| |||||||| ||| ||  | ||  | |  | |||  |   |  |  || ||      | ||   |||||||| ||| || |  ||||   ||     ||| || |  |||   || |      ||||||||  ||||||||| |||
GAGTATCAACATTTCTCTGGTACTAGAGTTGCTCTTGATGTGGCTGAAATGCCATCAAACCTCTTTGAgtacgtatgacttgtt--gctaaaaataaaactttatccattaacactcccgcagggtatctaattctggcttatctaaaatacagcagcatttgttatttaccttctttatcagtagttgagttcaattcacattgcag

upper sequence: GRMZM2G450659_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv16s0022g01280.t01 (Vitis vinifera), 5'ss of exon 3
GAATATCAGCATTTCTCTGGTACTAGGGTTGCTCTTGATGTGGCTGAAACCCCCTCAAACCTATTTGAgtatgtacgagcttttaggttttacatacgatgacagtttactttgtagcacatctaattttggtttgttcaaaaataaggtatttttattgtcaacccatttgagttgagtttcattcacattacag
|| || || ||||| || ||||| ||||| | ||||||| |||||||||| || || |||||||||||||  |||    ||| |      || |    | |    |   | | |   |     | |  |   |   |  |  |||| |   ||||   ||     | |||||||   |||| ||            
GATTACCAACATTTTTCAGGTACAAGGGTGGTTCTTGATTTGGCTGAAACACCTTCGAACCTATTTGAgtgagta---acttctg----ctataactaaaggatttccccctcgactctgggattacctgcatgaatgtatgaatagg---ttttagctg-----ctatttgagc--agttacac-----------
















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|31354813|gb|CD439170.1|CD439170
EST:     GGTACTAGGGTTGCTCTTGATGTGGCTGAAACCCCCTCAAACCTATTTGA                         ATATTATGCCTGGGACTATCGTGTCTTGAAGACATTTGCTCTAGATGAAAC
genomic: GGTACTAGGGTTGCTCTTGATGTGGCTGAAACCCCCTCAAACCTATTTGAgtatgtacga ... cacattacagATATTATGCCTGGGACTATCGTGTCTTGAAGACATTTGCTCTAGATGAAAC




















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: 49 (upstream exon), 45 (downstream exon)
Score: 101

GAATATCAGCATTTCTCTGGTACTAGGGTTGCTCTTGATGTGGCTGAAACCCCCTCAAACCTATTTGAgtatgtacga ... cacattacagATATTATGCCTGGGACTATCGTGTCTTGAAGACATTTGCTCTAGATGAAACAACTGGAGATGCAATACCAGAAAAGCTGGTAAAGGCACTAAATGCTTCT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 56

GAATATCAGCATTTCTCTGGTACTAGGGTTGCTCTTGATGTGGCTGAAACCCCCTCAAACCTATTTGAgtatgtacga ... cacattacagATATTATGCCTGGGACTATCGTGTCTTGAAGACATTTGCTCTAGATGAAACAACTGGAGATGCAATACCAGAAAAGCTGGTAAAGGCACTAAATGCTTCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 57

GAATATCAGCATTTCTCTGGTACTAGGGTTGCTCTTGATGTGGCTGAAACCCCCTCAAACCTATTTGAgtatgtacga ... cacattacagATATTATGCCTGGGACTATCGTGTCTTGAAGACATTTGCTCTAGATGAAACAACTGGAGATGCAATACCAGAAAAGCTGGTAAAGGCACTAAATGCTTCT


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 40

GAATATCAGCATTTCTCTGGTACTAGGGTTGCTCTTGATGTGGCTGAAACCCCCTCAAACCTATTTGAgtatgtacga ... cacattacagATATTATGCCTGGGACTATCGTGTCTTGAAGACATTTGCTCTAGATGAAACAACTGGAGATGCAATACCAGAAAAGCTGGTAAAGGCACTAAATGCTTCT