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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataatttaatctcaacgaagttaaactaagtttcttaatggaatgtgtaatgcttagctaagatgcacatatttgattttcgctttattcgcaattacagGAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT

Basic information

species Zea mays
transcript GRMZM2G129034_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129034_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g32948.1 (Oryza sativa), 3'ss of exon 3
--ataatttaatctcaacga---agttaaactaagtttcttaatggaatgtgtaatgcttagctaagatgcacatatttgattttcgctttattcgcaattacagGAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT---------------------------------
   |  |||  || || ||    | ||     ||  ||   | |  | |||| ||  || |    ||    || || | ||| ||   | | ||  ||||||||||||| | |||||||||||||| ||| |||||||  | |||||||| |||||||||||||| ||||||                                 
aacttttttgttcacatcgttccaatttcttcaaactttcaattttagtgtggaa--ctaaatacagcctaacttagtagatctt---tctgttgacaattacagGAATCTTCTTGGTGAAGATCTTGGGACACTTGGCATAAAAGAGCTAGAGCAGCTTGAGAAACAACTTGATTCATCCTTGAGGCACATTAGATCCACAAGG
















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|22490837|gb|BU050760.1|BU050760
EST:     GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
genomic: GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAGgcaagttgac ... gcaattacagGAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
EST: gi|94474168|gb|EB703126.1|EB703126
EST:     GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
genomic: GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAGgcaagttgac ... gcaattacagGAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
EST: gi|24774115|gb|CA409369.1|CA409369
EST:     GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
genomic: GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAGgcaagttgac ... gcaattacagGAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
EST: gi|24773736|gb|CA408990.1|CA408990
EST:     GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
genomic: GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAGgcaagttgac ... gcaattacagGAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
EST: gi|24773921|gb|CA409175.1|CA409175
EST:     GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
genomic: GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAGgcaagttgac ... gcaattacagGAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
EST: gi|24773896|gb|CA409150.1|CA409150
EST:     GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
genomic: GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAGgcaagttgac ... gcaattacagGAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
EST: gi|78116199|gb|DV534586.1|DV534586
EST:     GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
genomic: GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAGgcaagttgac ... gcaattacagGAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
EST: gi|24773906|gb|CA409160.1|CA409160
EST:     GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
genomic: GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAGgcaagttgac ... gcaattacagGAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
EST: gi|24773483|gb|CA408737.1|CA408737
EST:     GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
genomic: GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAGgcaagttgac ... gcaattacagGAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
EST: gi|50339220|gb|CO534346.1|CO534346
EST:     GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGAT
genomic: GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAGgcaagttgac ... gcaattacagGAATTTGCTTGGTGAAGAT
EST: gi|71305624|gb|DR788955.1|DR788955
EST:     AGTACCTCAAGCTGAAAGCGAGGGTGGATAAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCCAAGAGCTTGAGCA
genomic: AGTACCTCAAGCTGAAAGCGAGGGTGGATAA-TTTACAGAGGACTCAGAGgcaagttgac ... gcaattacagGAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
EST: gi|24773751|gb|CA409005.1|CA409005
EST:     GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA
genomic: GAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAGgcaagttgac ... gcaattacagGAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCA

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 388

TTAGTCCAGAGCAGTCGTAATGAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAGgcaagttgac ... gcaattacagGAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT


Block sizes: 26 (upstream exon), 41 (downstream exon)
Score: 10

TTAGTCCAGAGCAGTCGTAATGAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAGgcaagttgac ... gcaattacagGAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 791

TTAGTCCAGAGCAGTCGTAATGAGTACCTCAAGCTGAAAGCGAGGGTGGATAATTTACAGAGGACTCAGAGgcaagttgac ... gcaattacagGAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaatgcttagctaagatgcacatatttgattttcgctttattcgcaattacagGAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT
                         atttgat  putative branch site (score: 791)
                     acatatttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataatttaatctcaacgaagttaaactaagtttcttaatggaatgtgtaatgcttagctaagatgcacatatttgattttcgctttattcgcaattacagGAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - caacgaa
- - - - - - - - - - - aaactaa
- - - - - - - - - - - - - - - - - - - - gaatgtg
- - - - - - - - - - - - - - - - - - - - - - - - -atgctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgcac