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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGGCCAGGTTTTTTTAGATTCAAGGCTGAAATTGgtatattctttatattctggcatttcaccatatatctaaaacagttagttacatgattttcatcatttcagttcgtatgtgtgatagcatgtccagtcct...

Basic information

species Zea mays
transcript GRMZM2G065839_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065839_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g23180.1 (Oryza sativa), 5'ss of exon 10
GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGGCCAGGTTTTTTTAGATTCAAGGCTGAAATTGgtatattctttatattctggcatttcaccatatatctaaaacagttagttacatgattttcatcattt-cagttcgtatgtgtgatagcatgtccagtcct-----
||||||||||||||||||||||||||||||||||||||||| ||||| || ||||||||||| ||||||||||||| |    ||||| |||||| |||| ||| ||   |||  |||||| ||  ||  || || |||||| ||||| |||  |||||| ||||||| | |  |     
GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTGgtacagctcttataatctggc-tttctccaaat--ttaaggcagttattt-tatttttgtcgtcattttcagttagtacttgtgat-gcatgtc-atttttagttt

upper sequence: GRMZM2G065839_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA07G02280.2 (Glycine max), 5'ss of exon 9
GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGGCCAGGTTTTTTTAGATTCAAGGCTGAAATTGgtatattctttatattctggcatttcaccatatatctaaaacagttagtta-catgattttcatcatttcagttcgtatgtgtgatagcatgtccagtcct--
||||||||| | || ||||||||||||||||| || |||||||| || || || ||||| ||||| ||||| ||| ||   ||   ||  | |  |   |   | | | |||   || | |  |  || ||| | |  ||||   ||  |||     ||  |   |    |  |  
GTTGTAGATTCCCTCTATGATTGCAAAAGTGAAGTTATTGGGCCTGGATTCTTCAGATTTAAGGCAGAAATAGgt-tacctttctcatctttgt-tactattctttgtgtaatttaggttgcgaatataattctgaa-atttgtctttatataaaatatgtcccatttgtttgtgc

upper sequence: GRMZM2G065839_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA08G23740.2 (Glycine max), 5'ss of exon 10
GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGGCCAGGTTTTTTTAGATTCAAGGCTGAAATTGgtatattctttatattctggcatttcaccatatatctaaaacagttagttacatgattttcatcatttcagttcgtatgtgtgatagcatgtccagtcct
||||||||| | || ||||||||||||||||| || |||||||| || || || ||||| ||||| ||||| |||   ||  | || ||      || ||  ||  |  |||   | |  |    ||| | || | |   ||| ||| ||  ||  | ||             
GTTGTAGATTCCCTCTATGATTGCAAAAGTGAAGTTATTGGGCCTGGATTCTTCAGATTTAAGGCAGAAATAGgttcctttctcatcttt----gttacagaattcagataatgaattatgcatgatggtgttaagctgatca-ttctta-atgaaacag-------------

upper sequence: GRMZM2G065839_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv09s0054g00220.t01 (Vitis vinifera), 5'ss of exon 10
GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGGCCAGGTTTTTTTAGATTCAAGGCTGAAATTGgtatattctttatattctggcat-ttcaccatatatctaaaacagttagttacatgattttcatcatttcagttcgtatgtgtgatagcatgtccagtcct---
|| || |||||||| |||||||| ||||||||||||||||| || || || ||||| || ||||| ||||| |||| |   ||   |   |  | | ||   || || | ||      || ||||  |     |||  || ||  |  | || |    || ||| ||||  ||    
GTAGTTGATGCTCTATATGATTGTAAAAGTGAGGTGATTGGACCTGGGTTCTTTAGGTTTAAGGCAGAAATAGgta-acctttgccacagtaacttatttttcagatttttatgtggtttggttatctataggtcaatatctctatgaggatat---ctaacatctccacacccata

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|60342269|gb|DN209242.1|DN209242
EST:     CAAAAGTGAGGTGATTGGGCCAGGNNNNNNNAGATTCAAGGCTGAAATTG                         ATTTCAATGGAGTTGTTCTGGTACAAAATTATTTGGAAAGGACTGGACGTG
genomic: CAAAAGTGAGGTGATTGGGCCAGGTTTTTTTAGATTCAAGGCTGAAATTGgtatattctt ... cgtcttacagATTTCAATGGAGTTGTTCTGGTACAAAATTATTTGGAAAGGACTGGACGTG
EST: gi|67021225|gb|CO449974.1|CO449974
EST:     CAAAAGTGAGGTGATTGGGCCAGGNNNNNNNAGATTCAAGGCTGAAATTG                         ATTTCAATGGAGTTGTTCTGGTACAAAATTATTTGGAAAGGACTGGACGTG
genomic: CAAAAGTGAGGTGATTGGGCCAGGTTTTTTTAGATTCAAGGCTGAAATTGgtatattctt ... cgtcttacagATTTCAATGGAGTTGTTCTGGTACAAAATTATTTGGAAAGGACTGGACGTG
EST: gi|74233385|gb|DT641299.1|DT641299
EST:     CAAAAGTGAGGTGATTGGGCCAGGNNNNNNNAGATTCAAGGCTGAAATTG                         ATTTCAATGGAGTTGTTCTGGTACAAAATTATTTGGAAAGGACTGGACGTG
genomic: CAAAAGTGAGGTGATTGGGCCAGGTTTTTTTAGATTCAAGGCTGAAATTGgtatattctt ... cgtcttacagATTTCAATGGAGTTGTTCTGGTACAAAATTATTTGGAAAGGACTGGACGTG
EST: gi|71318478|gb|DR796004.1|DR796004
EST:     CAAAAGTGAGGTGATTGGGCCAGGNNNNNNNAGATTCAAGGCTGAAATTG                         ATTTCAATGGAGTTGTTCTGGTACAAAATTATTTGGAAAGGACTGGACGTG
genomic: CAAAAGTGAGGTGATTGGGCCAGGTTTTTTTAGATTCAAGGCTGAAATTGgtatattctt ... cgtcttacagATTTCAATGGAGTTGTTCTGGTACAAAATTATTTGGAAAGGACTGGACGTG

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), 48 (downstream exon)
Score: 120

GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGGCCAGGTTTTTTTAGATTCAAGGCTGAAATTGgtatattctt ... cgtcttacagATTTCAATGGAGTTGTTCTGGTACAAAATTATTTGGAAAGGACTGGACGTGGGAGTTGGGCAAAACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 98

GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGGCCAGGTTTTTTTAGATTCAAGGCTGAAATTGgtatattctt ... cgtcttacagATTTCAATGGAGTTGTTCTGGTACAAAATTATTTGGAAAGGACTGGACGTGGGAGTTGGGCAAAACAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 74

GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGGCCAGGTTTTTTTAGATTCAAGGCTGAAATTGgtatattctt ... cgtcttacagATTTCAATGGAGTTGTTCTGGTACAAAATTATTTGGAAAGGACTGGACGTGGGAGTTGGGCAAAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGGCCAGGTTTTTTTAGATTCAAGGCTGAAATTGgtatattctt ... cgtcttacagATTTCAATGGAGTTGTTCTGGTACAAAATTATTTGGAAAGGACTGGACGTGGGAGTTGGGCAAAACAG