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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatttgtctaaattgtcttaaaatctacctgttctatgtttctttcctatgattcacatgatgctgatttttctcctatcactagAATGTCGTTGTGTTCCCTTCTCGCTCTGTGGCAATAGAGAATGCTCTTCAATTGTTCTCACCGGCGCTTGCAATTGTTGATGAACATTTAACCAGACACT

Basic information

species Zea mays
transcript GRMZM2G098039_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098039_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 7
gtaagatttgtctaaattgtcttaaaatctacctgttctatgtttctttcctatgattcacatgatgctgatttttctcctatcactagAATGTCGTTGTGTTCCCTTCTCGCTCTGTGGCAATAGAGAATGCTCTTCAATTGTTCTCACCGGCGCTTGCAATTGTTGATGAACATTTAACCAGACACT
|||||| |||       |||||   |   |    |||  || |  ||        ||| | || ||    ||||||   |   | | ||||||| ||||| |||||||| ||  ||||||||||||| |||||||||| ||| |||||||| |||||||| || |||||||||||| | ||||||||||
gtaagacttgg------tgtctgttatagttatagttacat-tcactcattagaaattaaaataattgatattttttatcgtcctccagAATGTTGTTGTTTTCCCTTCCCGTGCTGTGGCAATAGAAAATGCTCTTCGATTATTCTCACCAGCGCTTGCGATCGTTGATGAACATCTGACCAGACACT

upper sequence: GRMZM2G098039_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv12s0035g01920.t01 (Vitis vinifera), 3'ss of exon 8
-gtaagatttgtctaaattgtct--taaaatctacctgttctatgtttctttcct----atgattcacatgatgctgatttttctc----ctatcactagAATGTCGTTGTGTTCCCTTCTCGCTCTGTGGCAATAGAGAATGCTCTTCAATTGTTCTCACCGGCGCTTGCAATTGTTGATGAACATTTAACCAGACACT
 ||   |    |||  ||| |||  ||  ||  |  | || | |  | || |  |    | | || |  |    ||  ||||||||    ||  | | ||||||| ||  | || |||||  |  |||||||||| ||||||||||||| ||| ||||||||    |||||||||||||||||| || | ||  ||||  
agttctaaaaatcttcattatctgttagtattgattttttttttcatactgtgttgagcaagttttatttctgacttgtttttctcaattcttgcgcaagAATGTTGTCATATTTCCTTCAAGGGCTGTGGCAATTGAGAATGCTCTTCGATTATTCTCACCCCGTCTTGCAATTGTTGATGAAGATCTGACTCGACATC
















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|87155600|gb|DY400389.1|DY400389
EST:     CCATCACATTCCTCTAACTCCTGAT                         AATGTCGTTGTGTTCCCTTCTCGCTCTGTGGCAATAGAGAATGCTCTTCAA
genomic: CCATCACATTCCTCTAACTCCTGATgtaagatttg ... ctatcactagAATGTCGTTGTGTTCCCTTCTCGCTCTGTGGCAATAGAGAATGCTCTTCAA




















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), 49 (downstream exon)
Score: 89

CAAGTCAAATCCCTGTGAGCCACCAGCTGGATGTCTAAACTTTAGGAAACTTGTTGCTGGATTTATGAAGAGCTACCATCACATTCCTCTAACTCCTGATgtaagatttg ... ctatcactagAATGTCGTTGTGTTCCCTTCTCGCTCTGTGGCAATAGAGAATGCTCTTCAATTGTTCTCACCGGCGCTTGCAATTGTTGATGAACATTTAACCAGACACT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 155

CAAGTCAAATCCCTGTGAGCCACCAGCTGGATGTCTAAACTTTAGGAAACTTGTTGCTGGATTTATGAAGAGCTACCATCACATTCCTCTAACTCCTGATgtaagatttg ... ctatcactagAATGTCGTTGTGTTCCCTTCTCGCTCTGTGGCAATAGAGAATGCTCTTCAATTGTTCTCACCGGCGCTTGCAATTGTTGATGAACATTTAACCAGACACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 246

CAAGTCAAATCCCTGTGAGCCACCAGCTGGATGTCTAAACTTTAGGAAACTTGTTGCTGGATTTATGAAGAGCTACCATCACATTCCTCTAACTCCTGATgtaagatttg ... ctatcactagAATGTCGTTGTGTTCCCTTCTCGCTCTGTGGCAATAGAGAATGCTCTTCAATTGTTCTCACCGGCGCTTGCAATTGTTGATGAACATTTAACCAGACACT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 118

CAAGTCAAATCCCTGTGAGCCACCAGCTGGATGTCTAAACTTTAGGAAACTTGTTGCTGGATTTATGAAGAGCTACCATCACATTCCTCTAACTCCTGATgtaagatttg ... ctatcactagAATGTCGTTGTGTTCCCTTCTCGCTCTGTGGCAATAGAGAATGCTCTTCAATTGTTCTCACCGGCGCTTGCAATTGTTGATGAACATTTAACCAGACACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctatgtttctttcctatgattcacatgatgctgatttttctcctatcactagAATGTCGTTGTGTTCCCTTCTCGCTCTGTGGCAATAGAGAATGCTCTTCAATTGTTCTCACCGGCGCTTGCAATTGTTGATGAACATTTAACCAGACACT
                               tgctgat  putative branch site (score: 118)
                                     tttttctcctatcact  CT-rich tract
                                  tgattttt  TA-rich tract