Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATAAAGTCAGGAGCTTGGTGGGCATATGTGATTCTGATCCTTACATCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccataaacagaagctgacattttcttatctgctgtggtaattgaatatatgggatctgataacaaattttccag

Basic information

species Zea mays
transcript GRMZM2G102021_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102021_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g17280.1 (Oryza sativa), 5'ss of exon 2
----TATAAAGTCAGGAGCTTGGTGGGCATATGTGATTCTGATCCTTACATCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccataaacagaagctga------cattttcttat-----ctgctgtggta-attga--atatatgg----gatctgataacaaattttccag-------------------------------------------
    |||||  ||||||||||||||| | ||||  ||||| |||||||||||||| ||||| |||||||||| ||||||||| ||||||| ||||||||||||||||||||||||    ||| |||      ||  || ||||        |||| ||  ||| |  || ||| |    ||| | || |   |  ||  ||                                           
TCCCTATAAGATCAGGAGCTTGGTGGCCGTATGCAATTCTTATCCTTACATCTGTTGCATTTCAAGAAGGCATTCGTCTTGTCTTTTGGAGGCTTTACAAgtaggtaaaccataattgaaagttgaacttcacacctttttatggcagtccctgtagtgtattcactatgtatagagatgatataattatggaacttgaagttgatttatgtctttatgatatgtgatggttactgtttttcag
















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|50328021|gb|CO523147.1|CO523147
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177675|gb|FL258734.1|FL258734
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177674|gb|FL258733.1|FL258733
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177670|gb|FL258729.1|FL258729
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|22546043|gb|BU098364.1|BU098364
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211287765|gb|FL258742.1|FL258742
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTAC-A--A-                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|91876597|gb|EB406554.1|EB406554
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTAC-A--A-                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211287768|gb|FL258745.1|FL258745
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177673|gb|FL258732.1|FL258732
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177668|gb|FL258727.1|FL258727
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177671|gb|FL258730.1|FL258730
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|87156122|gb|DY400911.1|DY400911
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177672|gb|FL258731.1|FL258731
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177676|gb|FL258735.1|FL258735
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211287764|gb|FL258741.1|FL258741
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|148946111|gb|EC891405.2|EC891405
EST:     TTTGGATGCTTTACAAGTAG                         A
genomic: TTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccag-
EST: gi|148946111|gb|EC891405.2|EC891405
EST:     TTTGGATGCTTTACAAGTAG                         A
genomic: TTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccag-
EST: gi|211177678|gb|FL258737.1|FL258737
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCCAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211287771|gb|FL258748.1|FL258748
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|26559868|gb|CA832103.1|CA832103
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211287767|gb|FL258744.1|FL258744
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|22818908|gb|BU498998.1|BU498998
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|149048871|gb|EE048372.2|EE048372
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTAC-A--A-                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177679|gb|FL258738.1|FL258738
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177677|gb|FL258736.1|FL258736
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|148946112|gb|EC891406.2|EC891406
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAG                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|40336955|gb|CK371025.1|CK371025
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|87155707|gb|DY400496.1|DY400496
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|37395770|gb|CF635168.1|CF635168
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTAC-A--A-                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211287770|gb|FL258747.1|FL258747
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211287769|gb|FL258746.1|FL258746
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211105119|gb|FL057785.1|FL057785
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177681|gb|FL258740.1|FL258740
EST:     TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAG-A-                         -AAA-TGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|33285553|gb|CF075348.1|CF075348
EST:     GAAGGCACTCGTCTTGTGTTTTGGATGCTTTAC-A--A-                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: GAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG

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 1 RNA-Seqlibrary.


Block sizes: 27 (upstream exon), 26 (downstream exon)
Score: 2

TATAAAGTCAGGAGCTTGGTGGGCATATGTGATTCTGATCCTTACATCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccata ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACGTCTTAGATTGACTGACAAGATGCTGATTTCTTTAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATAAAGTCAGGAGCTTGGTGGGCATATGTGATTCTGATCCTTACATCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTAGgtaaaccataaacagaagctgacattttcttatctgctgtggtaattgaatatatgggatctgataacaaattttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG