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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtcagctagcactctactatttgtcttgtggatctaaacaacagtttttaagggaaacaaatcttaagttaaaaattggggaaaaattacact...

Basic information

species Zea mays
transcript GRMZM2G129954_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129954_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os11g04720.1 (Oryza sativa), 5'ss of exon 4
GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtcagctag---cactctactatttgtcttgtggatctaaacaacagt-ttttaagggaaacaaatct-taagttaaaaattggggaaaaattacact
|| ||||| | | | || || ||||| || ||||||||||| || || |||||||||||||||||||||||||||||| ||   | |    ||  || |||||      |  ||   || |  ||  | ||| |  |     ||    | |  |||    |  |   |  |     
GAATCGTCTTATTTAAGGGACATCCCAGTTGTGATCATGTCATCGGATAACATTCCTTCAAGGATCAATAGgtgagcactcttatggatctaccatattatttcgaccatctattacaatacaagcatcttatgatatttggatgaacatgccaaagtcagatgtgcagat-----

upper sequence: GRMZM2G129954_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os12g04500.1 (Oryza sativa), 5'ss of exon 4
GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtcagctag---cactctactatttgtcttgtggatctaaacaacagt-ttttaagggaaacaaatct-taagttaaaaattggggaaaaattacact
|| ||||| | | | || || ||||| || ||||||||||| || || ||||||||||||||||||||||||||| || ||   | |    ||  || |||||      |  ||   || |  ||  | ||| |  |     ||    | |  |||    |  |   |  |     
GAATCGTCTTATTTAAGGGACATCCCAGTTGTGATCATGTCATCGGATAACATTCCTTCAAGGATCAATAGgtgaacactcttatggatctaccatattatttcgaccatctattacaatacaagcatcttatgatatttggatgaacatgccaaagtcagatgtgcagat-----

upper sequence: GRMZM2G129954_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv13s0067g03430.t01 (Vitis vinifera), 5'ss of exon 4
GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtcagctagcactctactatttg--tcttgtggatctaaac--aacagtttttaagggaaacaaatcttaagttaaaaat---tggggaaaaattacact
|||||  | ||||| | ||| || || || ||||||||||||||||||||||| ||||||||||| || ||||||| |  |   |     |||   | |||  |  |    ||| |||   ||     |||    ||  ||| |  |||  | | |||   ||  |   | |||    
GAGTCTACATCTCTGAAAGACATACCAGTTGTGATCATGTCCTCTGAGAACATCCCTTCAAGGATTAACAGgtgagaaaactattgaatatcttggaattgaattcttctcatccaaaagaaatgaaattttgttgattcaatttctaatatgagaatgtttgatgggtatttatcag

upper sequence: GRMZM2G129954_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv13s0067g03490.t01 (Vitis vinifera), 5'ss of exon 5
GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtcagct--agcactctactatttgtcttgtggatctaaacaacagtt---tttaagggaaacaaatcttaagttaaaaattggggaaaaatta-cact------
||||| || ||||| | ||| || || || ||||||||||||||||||||||| ||||||||||| || ||||||| |  |  ||  || | |||   |||    ||    ||| |||  | | |    ||||   ||| ||| |  | |  | | |||    |   |||    | |      
GAGTCTTCATCTCTGAAAGACATACCAGTTGTGATCATGTCCTCTGAGAACATCCCTTCAAGGATTAACAGgtgagaaaactacttaaggattctggaattgaattttctcatccaaaagaaaatgaaatttagttgaatcaatttctgatgtgagaatgtatgtttaatgggtattgatcag

upper sequence: GRMZM2G129954_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv13s0067g03510.t01 (Vitis vinifera), 5'ss of exon 4
GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtcagctagcactctactatttg---tcttgtggatctaaacaacagtttttaagggaaacaaatcttaagttaaaaattggggaa---aaattacact-
|| || || ||||| | ||| || || || |||||||||||||||||||| || || |||||||| || ||||||| |      |     | |   | |||   |||| |    | ||| ||  |    |  |   |   | | |  |       |||||  ||    ||||   |  
GAATCTTCATCTCTGAAAGACATACCAGTTGTGATCATGTCCTCTGAGAATATCCCCTCAAGGATTAACAGgtgaggaaaatattgaagattttggaattgaattcttctcatccaaaagaaatgaaaatttgttgattcagtttctaacctgggattggttaatgggaattgatcag

upper sequence: GRMZM2G129954_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv13s0067g03460.t01 (Vitis vinifera), 5'ss of exon 4
GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagca-gtcagctagcact--ctactatttgtcttgtggatctaaacaacagtttttaagggaaacaaatc-------------ttaagttaaaaattggggaaaaattacact-----------
|||||  | ||||| | ||  ||||| || |||||||||||||||||||| || ||||| ||||| || ||||||| |  | |   |  | |  | ||| |||   || ||   | |   ||   ||   |    |||||||||             || | ||   |||  | |||   | |               
GAGTCTACATCTCTTAAAGGCATCCCAGTTGTGATCATGTCCTCTGAGAATATCCCTTCTAGGATTAACAGgtgagaacattattgaagattgtccactttttcctttttgatacaattgaattcttcacatttaaaacaaatcaatggtttgttgattcactttctaatctgagaatggtcaatgggtattgatcag

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|74237751|gb|DT645665.1|DT645665
EST:     GATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAG                         GTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
genomic: GATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
EST: gi|211399019|gb|FL440142.1|FL440142
EST:     ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAG                         GTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
genomic: ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
EST: gi|91878635|gb|EB408592.1|EB408592
EST:     ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAG                         GTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
genomic: ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
EST: gi|40303893|gb|CK348280.1|CK348280
EST:     ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAG                         GTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
genomic: ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
EST: gi|211213579|gb|FL456137.1|FL456137
EST:     ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAG                         GTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
genomic: ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
EST: gi|5895964|gb|AW037210.1|AW037210
EST:     ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAG                         GTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
genomic: ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
EST: gi|19822364|gb|BQ048388.1|BQ048388
EST:     ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAG                         GTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
genomic: ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
EST: gi|211009672|gb|FL207156.1|FL207156
EST:     ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAG                         GTGCTTG-AGGAA
genomic: ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAA
EST: gi|76933672|gb|DV173539.1|DV173539
EST:     TCCCGGTGGTGATCATGTCCTCTGAGACCATTCC-TCAAAGGATCAATAG                         GTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
genomic: TCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTC-AAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
EST: gi|37382649|gb|CF628283.1|CF628283
EST:     ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAG                         GTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
genomic: ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
EST: gi|76933673|gb|DV173540.1|DV173540
EST:     ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAG                         GTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
genomic: ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
EST: gi|5597298|gb|AI891396.1|AI891396
EST:     ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAG                         GTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
genomic: ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
EST: gi|40335323|gb|CK369393.1|CK369393
EST:     ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAG                         GTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
genomic: ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
EST: gi|91869452|gb|EB400392.1|EB400392
EST:     ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAG                         GTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
genomic: ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
EST: gi|113704219|gb|EE681723.1|EE681723
EST:     ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAG                         GTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
genomic: ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
EST: gi|74237752|gb|DT645666.1|DT645666
EST:     ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAG                         GTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
genomic: ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
EST: gi|211012453|gb|FL207171.1|FL207171
EST:     ATCCCGGTGGTGATCATGTCCTCCGAGAACATTCCTTCAAGGATCAATAG                         GTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC
genomic: ATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATC

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: 42 (upstream exon), 46 (downstream exon)
Score: 42

GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATCAGACATGAACAAGCTCAAGCCCCACATACTGAAAAGCAGATGCAACCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 199

GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATCAGACATGAACAAGCTCAAGCCCCACATACTGAAAAGCAGATGCAACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATCAGACATGAACAAGCTCAAGCCCCACATACTGAAAAGCAGATGCAACCAG


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 29

GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtc ... tctgaaccagGTGCCTGGAGGAAGGAGCTGACGAGTTCTTCCTAAAACCTGTGCGGCTATCAGACATGAACAAGCTCAAGCCCCACATACTGAAAAGCAGATGCAACCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAGgtgagcagtcagctagcactctactatttgtcttgtggatctaaacaacagtttttaagggaaacaaatcttaagttaaaaattggggaaaaattacact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaaat