Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAGgtgcaatcaaatggcatttctcgttacatggccacatagctcatttttgtcgccttttccaatgaaaacctaattgtttgcttatacag

Basic information

species Zea mays
transcript GRMZM2G019267_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019267_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g72790.1 (Oryza sativa), 5'ss of exon 11
AGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAGgtgcaatcaaatggcatttctcgttacatggccacatagctcatttttgtcgccttttccaatgaaaacctaattgtttgcttatacag
|||||||| ||||||||||||||||| ||||| ||||||||||||||||||||||| || |||||||| |||| || |   ||||      | || ||   || |  ||||| | || |     |||| |   ||| |                      
AGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCCTTACCGTGTGATCCAAAGAGgtaca-tatgatggttaaatttgtcacgctgctaactagcttaattctaataactttgcatctgatacag-------------------

upper sequence: GRMZM2G019267_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA02G44400.1 (Glycine max), 5'ss of exon 12
AGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAGgtgcaatcaaatg-gcatttctcgttacatggccacatagctcatttttgtcgccttttccaatgaaaacctaattgtttgcttatacag------------
|| ||  | || ||||||||||||||||| || ||||||||||| ||||| |||||||||||||| || ||||   | |      | |  |   ||||  |      | |       ||||      | |  |||   |   ||| || |       || |            
AGAATTACTGCGAAAGATGCACTTGATGCTGAGTATTTCTGGACAGATCCATTACCATGCGATCCCAAGAGgtaagaccttccatgtacattaagttatttattttgagaatgttactttgaaattatgtgaaatagga--ttaaatgctatgaagcacggacattgctcatc

upper sequence: GRMZM2G019267_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA14G04410.1 (Glycine max), 5'ss of exon 11
AGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAGgtgcaatcaaatggcatttctcgttacatggccacatagctcatttttgtcgcctt----ttccaat-gaaaacctaattgtttg-cttatacag---------------------------------------------------------------------------------------
|| ||  | || ||||||||||||||||| || ||||||||||| ||||| ||||| |||||||| || ||||   | |            | ||||  |      | |       ||||      |    |   ||| | |    ||| ||| || || ||  |                                                                                        
AGAATTACTGCGAAAGATGCACTTGATGCTGAGTATTTCTGGACAGATCCATTACCGTGCGATCCCAAGAGgttagaccttccatgtacattagttatttattttgagaatgttactttgaaattatgtgatcttaataggaggattaaatgtctgtctcattgattcctttcctttttactttattgtttctactcaactaatccttttctggtcaatacctttcaacttcatactcttctgtatggcttag

upper sequence: GRMZM2G019267_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA20G10960.1 (Glycine max), 5'ss of exon 10
AGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAGgtg--------caatcaaatggcatttctcgttacatggccacatagctcatttttgtcgccttttccaatgaaaacctaattgtttgcttatacag----------------------------------------------------------------------------------------------------
|| ||  | || || |||||||||||||| || ||||||||||| ||||| |||||||| ||||| || ||||         |||||  |||  |||     ||   |    |  |   |    || |  |   | |   ||    |    |||  ||||||||                                                                                                        
AGAATTACTGCCAAGGATGCACTTGATGCTGAGTATTTCTGGACGGATCCATTACCATGTGATCCTAAGAGgtatgacctcccaatcccatgatattgaatatttactaaatat-tgattttccttcgaggaaatatgtgatcttcataggattaattgcttatctcatttgttctttccccatatgtttgttgtttcaatcaactatcatttactattttttatttttgaactcaccaagtcactattactcctatgtttggcttag

upper sequence: GRMZM2G019267_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv00s0805g00020.t01 (Vitis vinifera), 5'ss of exon 9
AGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAGgtgcaatcaaatggcatttctcgttacatggccacatagctcatttttgtcgccttttccaatgaa----aacctaattgtttgcttatacag------------
|| ||||| || || ||||| || ||||| ||||||||||||| ||| |||||||| |||||||| || ||||||  |         ||||   || |      | ||||    || |||  |  |||||  || ||    |||  |||  | ||  |  | |             
AGAATATCTGCCAAGGATGCTCTGGATGCTGAATATTTCTGGAATGACCCCTTACCTTGCGATCCCAAGAGgtgc--ttgcccaatgtttcaaatttcca---tatatagaattttattgatgaattttcagattaacataaacagaatactatgtctccataacatgaaaacaat

upper sequence: GRMZM2G019267_T01 (Zea mays), 5'ss of exon 11
lower sequence: PP1S121_162V6.1 (Physcomitrella patens), 5'ss of exon 10
AGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAGgtgca-atcaaatggcatttctcg-------ttacatggccacatagctcatttttgtcgccttttccaatgaaaacctaattgt----ttgcttatacag-------------------------------------
 | || |  || ||||||||||| || || ||||||||||||||||| ||||| || ||| | ||||  |||||   |  |  ||||| |    |       | ||    ||    |||| | | |  ||     || |  ||  ||   | ||||    | | || ||                                        
CGAATCTGTGCTAAAGATGCACTCGACGCCGAATATTTCTGGACTGAACCCTTTCCCTGCCAACCAAGCAGgtgggcaggatctggcactcgatgaagtagttcactgatccggtcagctaagtctgatcaggactttctttgtgaagaaagttgtgacatggtttttaatattaatgttgctgatcgacaatttgtgtgttttcgtag

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|93282558|gb|EB674822.1|EB674822
EST:     CTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAG                         CTTGCCCAAGTATGAGGCATCGCATGAATTCCAGACTAAGAAAAAGCGTCA
genomic: CTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAGgtgcaatcaa ... gcttatacagCTTGCCCAAGTATGAGGCATCGCATGAATTCCAGACTAAGAAAAAGCGTCA
EST: gi|32804528|gb|CD956764.1|CD956764
EST:     CTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAG                         CTTGCCCAAGTATGAGGCATCGCATGAATTCCAGACTAAGAAAAAGCGTCA
genomic: CTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAGgtgcaatcaa ... gcttatacagCTTGCCCAAGTATGAGGCATCGCATGAATTCCAGACTAAGAAAAAGCGTCA
EST: gi|32804625|gb|CD956861.1|CD956861
EST:     CTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCAATCCAAAAAG                         CTTGCCCAAGTATGAGGCATCGCATGAATTCCAGACTAAGAAAAAGCGTCA
genomic: CTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAGgtgcaatcaa ... gcttatacagCTTGCCCAAGTATGAGGCATCGCATGAATTCCAGACTAAGAAAAAGCGTCA
EST: gi|149099518|gb|EE185556.2|EE185556
EST:     CTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAG                         CTTGCCCAAGTATGAGGCATCGCATGAATTCCAGACTAAGAAAAAGCGTCA
genomic: CTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAGgtgcaatcaa ... gcttatacagCTTGCCCAAGTATGAGGCATCGCATGAATTCCAGACTAAGAAAAAGCGTCA

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: 368

AGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAGgtgcaatcaa ... gcttatacagCTTGCCCAAGTATGAGGCATCGCATGAATTCCAGACTAAGAAAAAGCGTCAGCAACAGAGGCAAGCAGAGGAAGCTGCAAAGCGTCAAAAACTTAACCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 202

AGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAGgtgcaatcaa ... gcttatacagCTTGCCCAAGTATGAGGCATCGCATGAATTCCAGACTAAGAAAAAGCGTCAGCAACAGAGGCAAGCAGAGGAAGCTGCAAAGCGTCAAAAACTTAACCAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 278

AGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAGgtgcaatcaa ... gcttatacagCTTGCCCAAGTATGAGGCATCGCATGAATTCCAGACTAAGAAAAAGCGTCAGCAACAGAGGCAAGCAGAGGAAGCTGCAAAGCGTCAAAAACTTAACCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 205

AGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAGgtgcaatcaa ... gcttatacagCTTGCCCAAGTATGAGGCATCGCATGAATTCCAGACTAAGAAAAAGCGTCAGCAACAGAGGCAAGCAGAGGAAGCTGCAAAGCGTCAAAAACTTAACCAT