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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaagtaattcctcctttgcatggtgccagagatggcacattcatttttgcaagtttcaaattcacatgcaaaactcttgctattttaatttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC

Basic information

species Zea mays
transcript GRMZM2G374881_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G374881_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g53060.1 (Oryza sativa), 3'ss of exon 2
---agaaagtaat--tcctcctttgcatggtgccagagatggcacattcatttttgcaagtttcaaattcacatgcaaaactcttgctattttaatttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC
   ||    || |  ||  | | |   |  |  |||  | ||||  | ||    | ||    |   ||||||||| |||  | |   | | |   | |  |||||||||||||||||||||| ||||| || ||| |||| ||||| ||||||||||||||
tgtagttgttagtagtcggcttctaattattatcagctaaggcatttccaagagtccag---tagtattcacatgtaaatatttgtttctctctgtct--cacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC

upper sequence: GRMZM2G374881_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g04800.1 (Oryza sativa), 3'ss of exon 2
agaaagtaattcctcctt-tgcatggtgccagagatggcacattcatttttgcaagtttcaaattcaca----tgcaaaactcttgctattttaatt-tatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC
      |  ||| |  || |  || || |   |    | |  |   | ||  ||  |     |||  ||    | ||  | | ||    || | ||| | ||||||||||| || ||||||||||||||||| ||| |||| ||||| ||||||||||||||
------tttttcatagttgttaatagtccagtactaagtaagtaagtattatcagatacagcatttccaatagttcactagtattatatttctcattgtctcacagGCTGCCGACACACAAGTCATTTCGGAATATGTACGCTATTTTCTCCACCAACACAC
















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|211274177|gb|FK988507.1|FK988507
EST:     ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
genomic: ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
EST: gi|211272373|gb|FK988497.1|FK988497
EST:     ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
genomic: ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
EST: gi|211274173|gb|FK988503.1|FK988503
EST:     ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
genomic: ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
EST: gi|78543575|gb|DV621073.1|DV621073
EST:     ACAGACAATGTGTACGTTTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATGTACGTTATTTCCTCCACCAA
genomic: ACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
EST: gi|50338298|gb|CO533424.1|CO533424
EST:     ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
genomic: ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
EST: gi|211274171|gb|FK988501.1|FK988501
EST:     ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
genomic: ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
EST: gi|211274176|gb|FK988506.1|FK988506
EST:     ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
genomic: ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
EST: gi|78109399|gb|DV527815.1|DV527815
EST:     ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
genomic: ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
EST: gi|91049302|gb|EB159720.1|EB159720
EST:     ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
genomic: ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
EST: gi|211272372|gb|FK988496.1|FK988496
EST:     ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
genomic: ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
EST: gi|211274179|gb|FK988509.1|FK988509
EST:     ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATATACGTTAT
genomic: ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTAT
EST: gi|76915113|gb|DV165828.1|DV165828
EST:     ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
genomic: ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
EST: gi|211272370|gb|FK988494.1|FK988494
EST:     ACAAGATTACCCAATTGACAGACAATGTGTACGTYTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
genomic: ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
EST: gi|211274172|gb|FK988502.1|FK988502
EST:     ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATATACCTTATTTCCTCCACCAA
genomic: ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
EST: gi|91872633|gb|EB402590.1|EB402590
EST:     ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
genomic: ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
EST: gi|78109398|gb|DV527814.1|DV527814
EST:     ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
genomic: ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
EST: gi|211272369|gb|FK988493.1|FK988493
EST:     ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
genomic: ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
EST: gi|37378375|gb|CF625874.1|CF625874
EST:     TTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATGTACGTTATTTCCTCCACCAA
genomic: TTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
EST: gi|211274170|gb|FK988500.1|FK988500
EST:     ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
genomic: ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
EST: gi|211274174|gb|FK988504.1|FK988504
EST:     ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
genomic: ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
EST: gi|148967409|gb|EE018635.2|EE018635
EST:     ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA
genomic: ACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAA

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), 48 (downstream exon)
Score: 247

GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 222

GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 175

GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 288

GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTgtaagtgttg ... tttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgcaagtttcaaattcacatgcaaaactcttgctattttaatttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC
                                       ttttaat  putative branch site (score: 288)
                                 ttgctattttaattta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaagtaattcctcctttgcatggtgccagagatggcacattcatttttgcaagtttcaaattcacatgcaaaactcttgctattttaatttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC

-gaaagtaa
- - - - - - - - - tgcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcttgc