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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgatattcttgttcagttgtaatacggcttggcctcattgacaggaactgactagctatttgtcatcttcag

Basic information

species Zea mays
transcript GRMZM2G164185_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 11
TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagt-ctgatattcttgttcagttgtaatacggcttggcctcattgacaggaactgactagctatttgt-----catcttcag
 |||||||||||||||||||||| || |||||||| || |||||||| |||||||| || ||||||||  |||||||||||||||| |||||||  | ||  |  || |  |||||| |  ||| ||| || ||| || |   ||||| | |     ||  |     |   |||||
CTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAGgtgttgcttttgctcat-ctcagttatggtactgctcggtctccttcatgtgaactaattgttagttgatgtatgctctttcag

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 11
TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgatattcttgttcagttgtaatacggcttggcctcattgacaggaactgactagctatttgtcatcttcag------
 | |||||||||||||||||||| ||||||||||| || ||||||||||||| |||||||||||||||  | ||  |||||||||| ||||||||     | |  |||  ||  |     |  || |  | |    |        ||   ||    |||||    ||         
CTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAGgtatggatacaaacttaatctatc----tgtggttctgtcattcttgagtctgcttcttactattttgtttcatttgataccag

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 11
TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgata-----ttcttgttcagttgtaatacggcttggcctcattgacaggaactgactagctatttgtcatcttcag----
 | |||||||||||||||||||| ||||| || || || || || ||||||| |||||||||||||||  | |||||||||||||| |||||||  |||||||     ||  | | | |||  |   | | | |   |  ||  |  | |         | | | |||  |   |    
CTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAGgtc-tctgatacaaacttaatctgcggttcaatcgccgttggaattgtttatcctgcatcttacgattttgtttcacttgttgacag

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA08G20830.4 (Glycine max), 5'ss of exon 11
TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgatattcttgttcagttgtaatacggcttggcc-tcattga--caggaactgactagctatttg---tcatcttcag
 | |||||||||||||||||||| ||||||||||| || ||||||||||||| |||||||||||||||  | ||  ||||||| || ||||||||   ||  |||     | | |    ||  || |  |   |  ||||  | | | || ||||  |  ||    |    | |||
CTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAGgta---tgggattaaaacttaatctatatgtggttctgttattcttgagcctgcatcttactattttgtttcatttgattccag

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA13G42800.1 (Glycine max), 5'ss of exon 11
TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgatatt--cttgttcagttgt---aatacggcttggcctcattgacaggaactgactagctatttgtcatcttcag----
 | || ||||||||||||||||||||||| ||||| || || || ||||||| |||||||||||||||  |  ||||||||||||| |||||||  |||||||    |||  || || ||     |   | | |   |  ||  |  | |         | | | |||  ||  |    
CTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAGgtc-tctgatacaaacttaatccgtggttcagttgtcgttggaattgtttatcctgcatcttacgattttgtttcactttttgacag

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 11
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 13
TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgta----------------gtctgatattcttgttca-gttgtaatacggcttggcctcattg---acaggaactgactagctatttgtcatcttcag
 | |||||||||||||||||||| || || |||||||| || |||||||||  ||||||  |||| ||  ||| ||| || ||||| ||||||||                 ||| || || || |||   || |   | | ||  |  || |||   | |  |  ||    | |   |    | | |||
CTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAGgtatgccaagaagcagagcatcttattttgttattcgcattttcgaatgactatgattccttgtataaatcatttgttcggtttcatacactttccag

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 11
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 11
TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgatat---tcttgttcagttgtaatacggcttggcctcattgacagga---actgactagctatttgtcatcttcag---------------
 |||| ||| |||||||||||||||| || ||||| ||||||||||||||||  ||||| |||||||| || |||||||| ||||| ||||||| | ||    |   |  || ||| |||   |||   |  | ||  |  |  | |   ||| |  | | |||| | ||  | |                
CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgcttgtcttctggtca-ttgctgtacttttctgtcttgtataaggaataaactaatgaccaatttattatacttaatctccggtgaaccag

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 11
TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtag---tctgatattcttgttcagttgtaatacggcttggcctcattgacagga--actgactagctatt--tgtcatcttcag
|| |||||||||||||||||||| ||||| ||||| |||||||| |||||||  |||||||||||| |  | ||||| || ||||| |||||||     | | | ||| |  ||       | |    ||||  | |  |  || ||  ||| ||     |||  ||| |||  |||
TTGTGTGATTTATATGAAAATGATTCAATCTTTGATAAATTTGAATGTTGTCTGAGTGGTGATGGAATGCGTGTAGCTACAGGTTCTTACAGgtccgttttttaaattttctttatccaccattgtttcttgaaccctctaccatgagtactaacataaaattgatgtgatcc-cag

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 5'ss of exon 11
TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgatattcttgttcagttgtaatacggcttggcctcatt----gacaggaa----ctgactagctatttgtcatcttcag---------------------
 | |||||||||||||||||||| || || || |||||||||||||||||||  ||||| |||||| || |||| || |||||||||||||||| ||    ||| |||| ||  |  | |||  | |       ||     | || ||       | ||   ||||||   |  |  |                     
CTGTGTGATTTATATGAAAATGATTCTATCTTCGACAAATTTGAGTGTTGTCTGAGTGGAGATGGACTACGAGTGGCGACTGGTTCCTACAGgt-gtgatttatgcttgatccataattatagtgatcaataaaatcctgggccaagatgccttcgcctgaatatttgatgtaatgtggtttttttcatgtgattgcag

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 5'ss of exon 11
TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgatattcttgttcagttgtaatacggcttggcctcattgacaggaactgactagctattt--gtcatcttcag---------------------------------------------------------------------
|| || ||||| ||||||||||| ||||| |||||||| |||||||||||||  ||||| ||||||    |||| ||||||||||| ||||||||      |    || || | || |   |   | |  | |  ||  |         ||  |  |||  ||  || | |                                                                      
TTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAGgta------tgccttttttaaatttttgcagaaccttccttttttttcccccttcttctttccttttaggttgtcattaaggttggaagggatctggttgttgaaaccctttggaatgtgcaatactaatactgtttccatggtcccag

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 11
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 11
TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgata--ttcttgttcagttgtaatacgg--cttggcctcattgacaggaac-----tgactagctatttgtcatcttcag----------------------------------------------------------------
 | |  |||||||| ||||||||||| ||||| ||||| |||||||||||||  ||||| |||||  |  | ||||| ||||||||||||||||| | || ||  | |    |  | || | |   |  ||||     | |||  | |||     ||||  |   ||| |    ||                                                                   
CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgtattgtgttagctacacagtttgatggattcaagtccttgaatgaagtgaatgaaacatacatgacaggactttttttgcgttgtatcacagtattcttgtatgctatgttttatggaggagtatgactgaagtattctctgtgtcgcag

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|91057148|gb|EB167566.1|EB167566
EST:     GAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG                         CAACATTTTCCGTGTGTTTGGTTGTGGTACTGGTAACAGTGAGGCGACAAC
genomic: GAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgat ... tcatcttcagCAACATTTTCCGTGTGTTTGGTTGTGGTACTGGTAACAGTGAGGCGACAAC
EST: gi|67032341|gb|CO461090.1|CO461090
EST:     GAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG                         CAACATTTTCCCGTGTGTTTGGTTGCGGTACTGGTAACAGTGAGGCGACAA
genomic: GAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgat ... tcatcttcagCAACATTTTCC-GTGTGTTTGGTTGTGGTACTGGTAACAGTGAGGCGACAA
EST: gi|71425474|gb|DR806698.1|DR806698
EST:     GAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG                         CAACATTTTCCGTGTGTTTGGTTGTGGTACTGGTAACAGTGAGGCGACAAC
genomic: GAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgat ... tcatcttcagCAACATTTTCCGTGTGTTTGGTTGTGGTACTGGTAACAGTGAGGCGACAAC
EST: gi|113686848|gb|DW842058.1|DW842058
EST:     ATTAAGAGTAGCAACTGGTTCCTACAG                         CAACATTTTCCGTGTGTTTGGTTGTGGTACTGGTAACAGTGAGGCGACAAC
genomic: ATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgat ... tcatcttcagCAACATTTTCCGTGTGTTTGGTTGTGGTACTGGTAACAGTGAGGCGACAAC

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: 47 (upstream exon), 49 (downstream exon)
Score: 124

TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgat ... tcatcttcagCAACATTTTCCGTGTGTTTGGTTGTGGTACTGGTAACAGTGAGGCGACAACACTTGAAGCAACCCGAAACCCTACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 78

TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgat ... tcatcttcagCAACATTTTCCGTGTGTTTGGTTGTGGTACTGGTAACAGTGAGGCGACAACACTTGAAGCAACCCGAAACCCTACAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 88

TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgat ... tcatcttcagCAACATTTTCCGTGTGTTTGGTTGTGGTACTGGTAACAGTGAGGCGACAACACTTGAAGCAACCCGAAACCCTACAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 116

TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgat ... tcatcttcagCAACATTTTCCGTGTGTTTGGTTGTGGTACTGGTAACAGTGAGGCGACAACACTTGAAGCAACCCGAAACCCTACAAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgatattcttgttcagttgtaatacggcttggcctcattgacaggaactgactagctatttgtcatcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA