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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaagcttcgaggcaatagtttataatacagccgatcctgttatatcatccatagctgttagaataacgatgactttttag

Basic information

species Zea mays
transcript GRMZM2G070273_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070273_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g57140.1 (Oryza sativa), 5'ss of exon 10
ACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgt--attctaaagcttcg--aggcaatagtttataatacagccgatcctgttatatcatccatagctgttagaataacgatgactttttag
||| ||||| |||||||||||||| ||||||||||| ||||| |||||||||||| | || ||||||||||||||||||||||| |||||||| ||||||||   || |||| ||     ||| |||| || ||| ||  |   |  |||| | || | |    | | ||                     
ACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAATGAGAGTCGCTGGTGTTCTTCATATCTTTCAGTTTGAAACTAAGCAGgttagttttaaatctctaccaggaaataattcatactat-gtgtaggctgtgaaataaccatctgatatttag------------------

upper sequence: GRMZM2G070273_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA01G35950.1 (Glycine max), 5'ss of exon 12
ACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaagcttcgaggcaatagtttataatacagccgatcctgttatatcatccatagctgttagaataacgatgactttttag-------------------------------------
  | || ||||| ||||||||||| |||||||||||||| || || ||||||||||| ||||| ||||||||||| || ||||| ||||||||||||||||||||   | |||  | | ||    | ||   |||           ||    | |    |  | ||   ||    || |||||  ||                                     
GTTGAGGGACATAATGCAATTTGGAAGCAGCAATACTGCAGTATTTTTTAAAATGCGAGTTGCAGGTGTTCTTCACATATTTCAGTTTGAAACAAAGCAGgtattagcatgctcagggacat---tctactctaccaatttcttaatttcggcctttggacttattcatatcttcattactttggagttattttatattattagtattttatcattctttgaag

upper sequence: GRMZM2G070273_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA16G21340.1 (Glycine max), 5'ss of exon 15
ACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaagcttcgaggcaatagtttataatacagccgatcctgttatatcatccatagctgttagaataacgatgactttttag
  | |||||||| ||||||||||| |||||||||||||| ||||| ||||||||||| ||||| |||||||| || || || || |||||||| ||||||||||  ||   ||| |  |   | |   | | |      |    | || | |||       ||| ||   || |  |   || |   
GTTGAGAGACATAATGCAATTTGGAAGCAGCAATACTGCAGTCTTTTTTAAAATGCGAGTTGCAGGTGTTCTCCACATATTCCAGTTTGAAACCAAGCAGgtataata--cctttgttgatgttgcacaaactttctttggaattattttgtcac-----actggtattttatctcttggttgtag-

upper sequence: GRMZM2G070273_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA09G32740.1 (Glycine max), 5'ss of exon 12
ACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaagcttcgaggcaatagtttataatacagccgatcctgttatatcatccatagctgttagaataacgatgactttttag--
  | |||||||| ||||||||||| ||||| |||||||| ||||||||||||||||| ||||| |||||||| || || || || |||||||| ||||||||||  ||    ||   |   ||     | || ||    | | || |   || ||          |   ||       | || ||    
GTTGAGAGACATAATGCAATTTGGAAGCAGTAATACTGCAGTCTTCTTTAAAATGCGAGTTGCAGGTGTTCTCCACATATTCCAGTTTGAAACCAAGCAGgtataatacc-tttgttgatgatgtcacacaa-acccttgtttctttggaattattttgcctcactgatattttatctatttgttgtag

upper sequence: GRMZM2G070273_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA11G09480.1 (Glycine max), 5'ss of exon 12
ACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaagcttcgaggcaat-----------agtttataat----acagccgatcctg--ttatatcatccatagctgttagaataacgatgactttttag--------------------
| | |||||||| ||||||||||| |||||||||||||| || || ||||||||||||||||| ||||||||||| || || || ||||||||||||||||||||   | | |  | | || |           ||||  ||||    ||    |  | ||  | ||||| | |||  || ||  | | |   |   || || |                    
ATTGAGAGACATAATGCAATTTGGAAGCAGCAATACTGCAGTATTTTTTAAAATGCGGGTTGCAGGTGTTCTTCACATATTCCAGTTTGAAACAAAGCAGgtattggcatgttcagggacactgtactcttcctagttcttaatttcgacctttggacttgactcatatc-ttcattact-ttgaagttattttattttattggtattttatcattctttgaag

upper sequence: GRMZM2G070273_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT5G65930.1 (Arabidopsis thaliana), 5'ss of exon 9
ACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgtat---tctaaagcttcgaggcaatagtttataatacagccgatcctgttatatcatccatagctgttagaataacg-atgactttttag
|||| | ||||||||||||||||| ||||| || ||||||||||| || |||||| | || |||||||||||||| || ||||| || || ||||| ||||| |     | |   || | || |  | | ||| ||  |||   ||||  |     || ||      || |  ||||   |   ||| |||
ACTACGTGACATCATGCAATTTGGCAGCAGTAACACTGCTGTCTTTTTCAAAATGAGAGTCGCTGGTGTTCTTCACATATTTCAGTTCGAGACAAAACAGgtttaaacatcactatttgtgg-atcattatattatgaagcaattccttatgagatattca-----atttgggtaacttgtatgtttgtag

upper sequence: GRMZM2G070273_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 11
ACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaagcttcgaggcaata-gtttata-atacagc------------cgatcctgttatatcatccatag-----ctgttagaataacgatgactttttag-----------------------------
||||||||| || ||||||||||||||||||||||||||||| || ||||| ||| | ||||| ||||| || || || || || |||||||| || ||||| |  |||   || |||    ||  | |||| ||| | |              |  || || | || |  ||        |||| |  || | |  | || |||                              
ACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGATGAGAGTTGCAGGTGTCCTCCACATATTCCAGTTTGAAACTAAACAGgt-tcttaatcttttgagtttctatatgtatatatataacatttttagagttttagtctcttttttcttttatgtattccttgtttgcctatcaaaaaattattatttgatagagttctattccattttatgcag

upper sequence: GRMZM2G070273_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S199_47V6.1 (Physcomitrella patens), 5'ss of exon 13
ACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaagcttcgaggcaatagt----ttataatacagccgatcctgttatatcatccatagctgttagaataacgat----gactttttag---------------
 ||  | || ||||||||||| || || || |||||||| || || ||||| ||||| |||||||| ||||||||||| || || || |||||||||||||||||   ||     | |  | | ||    | |||    ||| | | | ||  | | ||   |   |  ||   |    ||    ||  | |  |               
GCTGCGTGATATCATGCAATTCGGCAGTAGTAATACTGCCGTTTTTTTTAAGATGCGTGTTGCTGGAGTTCTTCATATTTTCCAGTTCGAAACAAAGCAGgtatttataaatcaagtgtaagtcgtacggtcatatccaagctgctgcggtggttttatgagtcatttataacttggtaatttatgatgtgtgggattggcttcaaacag

upper sequence: GRMZM2G070273_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S83_25V6.1 (Physcomitrella patens), 5'ss of exon 12
ACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgtat----tctaaagcttcgaggcaatagttta--taatacagcc--gatcctgttata-tcatccat-agctgttagaataacgatgactttttag---
  |  |||| |||||||| ||||| || || || |||||||| || ||||||||||| || ||||| || || ||||| ||||| || ||||||||||||||||    ||| ||  |    ||  ||| |  |  |  | | |    |||    || || | ||   | | |  ||  |   |  ||  ||||  |    
GTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAATGCGAGTCGCTGGAGTCCTACATATTTTTCAGTTCGAAACAAAGCAGgtatctattcttaatgtctatggtcatactcaagcttctgcggtgtggatttaattttagttatgagtcaacaatttaatgtaaaatccctttgaaacag

upper sequence: GRMZM2G070273_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S364_50V6.1 (Physcomitrella patens), 5'ss of exon 13
ACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgt-attctaaagcttcgaggcaatagtttataatacagccgatcctgttatatcatccatagctgttagaataacgatgactttttag---
|||  | ||||| |||||||||||||||||||| || || ||||| || |||||||| || || ||||| || ||||| ||||| ||||| || |||||||| ||| |    | |  ||    |  ||| || |   ||  ||||   ||||| ||         |||   |     || ||| | ||   
ACTGCGCGACATTATGCAATTTGGTAGCAGCAACACAGCCGTCTTTTTCAAAATGCGTGTAGCGGGTGTACTGCATATTTTTCAGTTTGAGACTAAGCAGgttattttcgtacct--agatcttgctttgtactt--gcaaatccc--tatattattttggagatttatttttggtttgtcttgtgagcag

upper sequence: GRMZM2G070273_T01 (Zea mays), 5'ss of exon 10
lower sequence: EFJ30174 (Selaginella moellendorffii), 5'ss of exon 11
ACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaagcttcgaggcaatagtttataatacagccgatcctgttatatcatccatagctgttagaataacgatgactttttag
 || |||||||||||||||||||| || |||||||| || || || ||||||||||| || || || ||| | || || ||||| |||||||| || ||||| |  |   |  |    |   |||||  |     |     | ||||   |                                    
GCTGAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAATGCGTGTGGCGGGAGTTTTGCACATTTTTCAGTTTGAAACTAAACAGgtgtctttgtggctttccgtg-tagttcttctctaaat---ttctgtcgcag-----------------------------------

upper sequence: GRMZM2G070273_T01 (Zea mays), 5'ss of exon 10
lower sequence: EFJ06058 (Selaginella moellendorffii), 5'ss of exon 11
ACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaagcttcgaggcaatagtttataatacagccgatcctgttatatcatccatagctgttagaataacgatgactttttag
 || |||||||||||||||||||| || |||||||| || || || ||||||||||| || || || ||| | || || ||||| |||||||| || ||||| || |   |  |    |   |||||  |     |     | ||||   |                                    
GCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAATGCGTGTGGCGGGAGTTTTGCACATTTTTCAGTTTGAAACTAAACAGgtgtttttgtggctttccgtg-tagttcttctctaaat---ttctgtcgcag-----------------------------------

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|60345856|gb|DN212829.1|DN212829
EST:     AAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAG                         GGCGAGGAAATATGTGTAGCACTTCAAACACATATAAATGATGTCATGCTC
genomic: AAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaa ... gactttttagGGCGAGGAAATATGTGTAGCACTTCAAACACATATAAATGATGTCATGCTC




















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), 49 (downstream exon)
Score: 217

ACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaa ... gactttttagGGCGAGGAAATATGTGTAGCACTTCAAACACATATAAATGATGTCATGCTCCGCAGATATTCAAAAGCACGCTCTGGTAATAGTGTTACATCACAAAATG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 33

ACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaa ... gactttttagGGCGAGGAAATATGTGTAGCACTTCAAACACATATAAATGATGTCATGCTCCGCAGATATTCAAAAGCACGCTCTGGTAATAGTGTTACATCACAAAATG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 19

ACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaa ... gactttttagGGCGAGGAAATATGTGTAGCACTTCAAACACATATAAATGATGTCATGCTCCGCAGATATTCAAAAGCACGCTCTGGTAATAGTGTTACATCACAAAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

ACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaa ... gactttttagGGCGAGGAAATATGTGTAGCACTTCAAACACATATAAATGATGTCATGCTCCGCAGATATTCAAAAGCACGCTCTGGTAATAGTGTTACATCACAAAATG