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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataatccttaataaactttagatttgctgccaagtattaagttaaataattggctaatgtttaattgtag

Basic information

species Zea mays
transcript GRMZM2G148323_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 5'ss of exon 11
CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataa-tcctta--ataaa-ctttagatttgctgccaagtattaagttaaataattggctaatgttta-attgtag
|||||||||||||||||||||||| || |||||||| || || |||||||||||||| || |||||||||||||||||||||||||||||||||||||||||||| | || | |||   ||||| |  |  |||  |||  ||  ||  |  |||  | |||| | || |||  |||  ||
CTTAAAACGGTGTAAACTCTCAGGGAATATATTCAACATCCTATTCAATCTCAACAAATTTATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgatcacaacttcttgccataaagcagtgaattcactgttaatcatctaaataacaagttggatcatctttttatttcag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA03G41180.1 (Glycine max), 5'ss of exon 11
CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataatccttaataaactttagatt-tgctgccaagt-attaagttaaataattg--gctaatgtttaattgtag-----------------------
| | ||| |  |||||||||||||||   | |||||||| || |||||||| || ||||||||||| |||||||||||||| |||||  | ||||| ||||||  |  |||  || |||||  |   ||| |||||   ||| | || | |  |  ||||  | |||  ||| | ||                          
CCTGAAAGGTGGTAAACTCTCAGGAAGTGTTTTCAATATCCTGTTCAATCTGAATAAGTTCATGGCCTTTGAAACTCGTGACCCATTTTTGATTCGTCAGgtgcatg-aatatttgataaaagtgttattgtgctgttgagtcagtatgattgactattgttggtaagttttgactgccttggtatatgtcttgtgtgaacag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA20G35090.1 (Glycine max), 5'ss of exon 11
CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataatccttaataaactttagatttgctgccaagtattaagttaaataat-tggctaatgtttaattgtag------------------
  | ||| |  ||||||| || |||||  | ||||||||||||||||||||||||||||| ||  | || || |||||||||||||| ||||| || ||||| |  ||||   |||| |  || ||   |  ||  ||| ||  | | | | |||| |   |||  | | |||  |                   
TGTTAAAGGCAGTAAACTTTCTGGAAATGTTTTCAATATTCTTTTCAATCTCAACAAGTTTATTACTTTCGAGACTCGTGATCCATTTCTCATACGTCAGgtaaaaataaga-ttaagatcctata---tcactaacaatta--aggcttagtaatgttagtaaattctgattacaacaagggtattttgtttag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA10G30930.1 (Glycine max), 5'ss of exon 11
CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataatccttaataaactttagatttgctgccaagtattaagttaaataattggctaatgtt--taattgtag--------------------------------
| | ||| |  ||||||| |||||||   | ||||| || || |||||||| || ||||||||||| |||||||||||||| |||||  | || || ||||||  |  |||  || ||||| ||||   ||||   |  |  |||   |  ||  ||||||| ||||  | | |                                    
CCTGAAAGGTGGTAAACTTTCAGGAAGTGTTTTCAACATCCTGTTCAATCTAAATAAGTTCATGGCCTTTGAAACTCGTGACCCATTTTTGATCCGTCAGgtgcatgaaatatttgataaaattta---ttgcattcttgagttagtatgtatgcttggctactgttagtgacttccttggtaattggtatgcatatcttgtgtgaatag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA10G32500.1 (Glycine max), 5'ss of exon 11
CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataatccttaataaactttagatttgctgccaagtattaagttaaataat-tggctaatgtttaattgtag------------------
  | ||| |  | ||||| || |||||  | ||||||||||||||||||||||||||||| || || || || |||||||||||||| ||||| || ||||| |  ||||   |    | |   || ||   ||  ||| ||  | | | | |||| |    ||  | | |||  |                   
TGTTAAAGGCAGCAAACTTTCTGGAAATGTTTTCAATATTCTTTTCAATCTCAACAAGTTTATTGCTTTCGAGACTCGTGATCCATTTCTCATACGTCAGgtaaaaataagattg---agatcctatatc-actaacaatta--aggcttagtaatcttagcaagttctgattacaacaagggtattttgtttag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT1G03960.2 (Arabidopsis thaliana), 5'ss of exon 11
CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataatcc-ttaataaactttagatttgctgccaagtattaagttaaataattggcta-atgtttaattgtag------------------------------------------------------------------------
  | ||| | |  ||||| |||| |||| | |||||||| || ||||| || || |||||||||||||||||||| ||||| ||||| |||||||||||||| | | |        | |  | |||  ||  ||   |||| |   |   ||||||      | |||  |  || ||                                                                         
TCTGAAAGGATCGAAACTTTCAGCAAACGTTTTCAATATACTCTTCAACCTTAATAAGTTCATGGCATTTGAAACACGTGACCCATTTCTCATTCGCCAGgtaagtttggcttaccagtggagtttttata-gcactcaag-agggaaaaaaataacaaagaatatgacttcttttaactgctaaaggcagtttgtagtagttcggattgaggcaattagaacaagtataattctctttcattgctgtag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 5'ss of exon 11
CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataatccttaataaactttagatttgctgccaagtattaa----gttaaataat-tggctaatgtttaattgtag---
| | ||| | |  || ||||| |||||| | ||||| || || || ||||||||||| || |||||||||||||| || ||||||||||||||||| |||||  | || |||  ||||  || ||     | || |  |  |  |     ||   ||||  |  |||||||  ||  | |    
CCTGAAAGGCTCAAAGCTCTCTGGAAACGTCTTCAACATCCTATTTAATCTCAACAAATTTATGGCATTTGAAACCCGGGATCCATTCCTCATTCGTCAGgtactaatcatc--taatttaccttgctacttcttcacaccaccacatgcgtcttataacatttctaatgtcaaacggaaacag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 5'ss of exon 10
CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataatccttaataaa--ctttagatttgctgccaagtattaagttaaata---attggctaatgtttaattgtag--------
 || ||  | | |||||| || |||||  | ||||| || ||||| || ||||||||||| ||||| |||||||| |||||||| |||||||| |||||||| || | ||    || ||||  | ||| |  |      |  || | |   | |||   |||    |||| || ||||  |        
TTTGAAGGGTTCTAAACTTTCTGGAAATGTCTTCAACATACTTTTTAACCTCAACAAGTTTATGGCGTTTGAAACGCGTGATCCCTTCCTCATCCGCCAGgt-atcacaaaatatagtaaataccttaaagctagctatacatacttatagagatattcatttctcaatgattgattgctgatacatag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 5'ss of exon 10
CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgat----tataatccttaataaactttagatttgctgccaagtattaag--ttaaataat-tggctaatgtttaattgtag---
| | ||| | |  || ||||| |||||| | ||||| || ||||| ||||| ||||| || |||||||||||||| || ||||| ||||||||||| |||||  |     |   |   || | ||| ||    ||      |   | |  |  |   ||||  |  | |||||  ||    |    
CCTGAAAGGCTCAAAGCTCTCTGGAAACGTCTTCAACATCCTTTTTAATCTAAACAAATTTATGGCATTTGAAACCCGGGATCCGTTCCTCATTCGTCAGgtactactccacgtttgatattcaaccttgctgttttcttgacacaatgggcctcttataacatttcaaatgtcaaacgaaaacag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv07s0005g03730.t01 (Vitis vinifera), 5'ss of exon 12
CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataat-ccttaataaac-tttagatttgctgccaagtattaagttaaataattggctaatgtttaattgtag------------------------------
||| ||  | || ||||| || |||||  | |||||||||||||||||||| || ||||||||||| |||||||||||||||||||| || || |||||||| | |  ||    || |||     |   | |        | |   |||||   || ||   |  | |   ||| |||                              
CTTGAAGGGATGCAAACTTTCTGGAAATGTTTTCAATATTCTTTTCAATCTTAATAAGTTCATGGCTTTTGAAACTCGTGATCCATTTCTAATACGCCAGgtaaattcaacatttttataggtgctcctagtaatcaatcattgccaagtt--gtattttattcctttagcattatagtattcccattggcatttatttggcaagcag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 11
lower sequence: PP1S34_411V6.1 (Physcomitrella patens), 5'ss of exon 11
CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataatcctta----ataaactttagatttgctgccaagtattaagttaaataattggctaatgt-ttaattgtag--------------------
| | || ||||||||| | || || ||  | ||||||||||| ||||| || ||||||||| | |||||||| |||||||| || || |||||||| ||||| |||| | | || |      |||| |    ||   | |  |||      | ||   | || | | |   ||| |   |                     
CCTGAAGCGGTGTAAATTATCTGGGAATTTTTTCAATATTCTCTTCAACCTGAACAAGTTCGTAGCATTTGAGACTCGTGACCCTTTTCTCATTCGTCAGgt-attacattactcatatcgaaaacctggatttcaattcttagttggtcataaagcgagtgtccagttcattattcacaattatgaactaaatcttattt

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 11
lower sequence: PP1S147_62V6.2 (Physcomitrella patens), 5'ss of exon 11
CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataatccttaat--aaactttagatttgctgccaagtattaagttaaataattggctaatgtttaattgtag-----------------------
 || || || |||||| | || || ||| | |||||||| || ||||||||||| |||||| | || ||||| |||||||| || |||||||| || |||||  ||      |||| |  | |  | ||  |  | | ||  |  |||| |  ||| |||    | |   ||  |                          
TTTGAAGCGATGTAAATTGTCTGGGAACTTCTTCAATATACTCTTCAATCTCAATAAGTTCGTTGCTTTTGAGACTCGTGACCCCTTCCTCATCCGTCAGgtatttcgtcctcttattcaagatctcagcatatcagtcatcttctaagcttgata-ttgtagtacgaaaaacaggtccctttcgacgtttataaattgcc

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 11
lower sequence: PP1S7_163V6.2 (Physcomitrella patens), 5'ss of exon 11
CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataatccttaat---aaactttagatttgctgccaagtatt-----aagttaaataattggctaatgtttaattgtag-----------------
|||||| || || ||| | || |||||| | |||||||| ||||| || |||||||| ||| | || ||||| ||||||||||| ||||| ||||| ||||| || ||  ||    ||   | |||| |   |      ||  || |      | | | || |  |  | | |   |  |||                   
CTTAAAGCGATGCAAATTATCTGGAAACTTCTTCAATATCCTTTTTAACCTCAACAAATTCGTAGCTTTTGAGACTCGTGATCCTTTCCTTATTCGTCAGgtaat-atgttctcacatttaagacttcaacatcttaatcagttagttctgagaatgatatcacagcgtgaagaacagatgttcacctaggttggtcatag

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|23199690|gb|BU582255.1|BU582255
EST:     TCAACAAGTTCATGGCGTTTGAAACTCGTGATCCGTTCCTCATTCGCCAG                         GAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
genomic: TCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
EST: gi|4612853|gb|AI603692.1|AI603692
EST:     TCATGGC-TTTG-AACTCGTGATCCATTCNTCATTCGCCAG                         GAACGTGAAAATCCAACTCTAACTGAGTGGGNCCGGTTTGCACATAGAGAA
genomic: TCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
EST: gi|83279222|gb|DV943230.1|DV943230
EST:     TCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAG                         GAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
genomic: TCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
EST: gi|211505070|gb|FK974738.1|FK974738
EST:     CCTCATTCGCCAG                         GAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
genomic: CCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
EST: gi|23199745|gb|BU582310.1|BU582310
EST:     TCAACAAGTTCATGGCGTTTGAAACTCGTGATCCGTTCCTCATTCGCCAG                         GAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
genomic: TCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
EST: gi|211372413|gb|FL431585.1|FL431585
EST:     TCCTCATTCGCCAG                         GAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
genomic: TCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
EST: gi|12972292|gb|BG267909.1|BG267909
EST:     CCATTCCTCATTCGCCAG                         GAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
genomic: CCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
EST: gi|26560172|gb|CA832407.1|CA832407
EST:     TCAACAAGTTCATGGCGTTTGAAACTCGTGATCCGTTCCTCATTCGCCAG                         GAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA
genomic: TCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAA

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: 48 (upstream exon), 47 (downstream exon)
Score: 159

CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 142

CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 144

CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 113

CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataa ... ttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA