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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatctttcatgatatacatgtgtttcagaactgatgtattttcagtgctgtatctaatccgactacttatgcagtgtttgactcttgctcttctctagATTGGCGTTGGCATGTGCATGGAGGGAATAGAGCACAATCCAGTTGTTTATGAACTTATGTCTGAAATGGCATTTCATAATAAGAAGGTTGAGGTTGAG

Basic information

species Zea mays
transcript GRMZM2G033592_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033592_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA10G11720.2 (Glycine max), 3'ss of exon 13
ttcatctttcatgatatacatgtgtttcagaactgatgtatttt--cagtgctgtatctaatccgactacttatgcagtgtttgactcttgctc----ttctctagATTGGCGTTGGCATGTGCATGGAGGGAATAGAGCACAATCCAGTTGTTTATGAACTTATGTCTGAAATGGCATTTCATAATAAGAAGGTTGAGGTTGAG
       ||||     ||  ||      ||||  ||     ||   |  |  ||| |||      |  || | |  | | ||  | | ||| |     || |  || | || ||||| ||||||||||| |||||||| || || ||  ||||||||||  | ||||||||||||||||||| | ||||||| ||| | |||  |
------cttcagatgttagctggaaaaaagaaaagaaaacattgagcgattatgtttcttgattaatgacattttgatttttaaaattttgttaattattttgcagGTAGGTGTTGGTATGTGCATGGAAGGAATAGAACAGAACCCTATTGTTTATGAGTTGATGTCTGAAATGGCATTTCGTGATAAGAAAGTTAAAGTTTCG

upper sequence: GRMZM2G033592_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT5G13690.1 (Arabidopsis thaliana), 3'ss of exon 13
------------ttcatctttcatgatatacat-gtgtttcagaactgatgtattttcagtgctgtatctaatccgactacttatgcagtgtttgactcttgctcttctc-tagATTGGCGTTGGCATGTGCATGGAGGGAATAGAGCACAATCCAGTTGTTTATGAACTTATGTCTGAAATGGCATTTCATAATAAGAAGGTTGAGGTTGAG
            | |  | ||||  ||||   |    |||   | || |||| | |         ||| |  ||||  ||   ||| | |  |||    ||    | | | ||| | || || || ||||||||||| ||||||||||| || || || ||||| ||||| |  ||||||||||||||||   || |||| ||||| ||  ||
gtaactcataactacgacattcacaatatgtttcacattttttatcttatgtctataggtgagactattttctccgcttagaaatggaat-cttgttatttatgttgcacatagGTCGGTGTAGGAATGTGCATGGAAGGAATAGAGCAGAACCCGGTGGTTTACGAACTAACTTCTGAAATGGCATTTCGAGATGAGAAAGTTGATGTACAG

upper sequence: GRMZM2G033592_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv13s0064g00370.t01 (Vitis vinifera), 3'ss of exon 13
-ttcatctttcatgatatacatgtgtttcagaactgatgtattttcagtgctgtatctaatccgactacttatgcagtgt-ttgactcttgctcttctc--tagATTGGCGTTGGCATGTGCATGGAGGGAATAGAGCACAATCCAGTTGTTTATGAACTTATGTCTGAAATGGCATTTCATAATAAGAAGGTTGAGGTTGAG
  | | ||||      ||   | | || ||| | |    | |   |     |||   | |   |  || | |    |     | | | ||| | ||  |  ||| |||| ||||||||||||||||| ||||| ||||| || ||||||| |||||| || |||||||||||||||||||  | | | || ||| |  ||| |
actaaacttttgg---atgtttatattccagta-tatcatttgacctcctatgttcttgaggaggttattgacatggctcactaattattgatgtttcccatagGTTGGTGTTGGCATGTGCATGGAAGGAATTGAGCAAAACCCAGTTGCTTATGAGCTGATGTCTGAAATGGCATTTCGCAGTGAAAAAGTTCAACTTGTG

upper sequence: GRMZM2G033592_T01 (Zea mays), 3'ss of exon 13
lower sequence: PP1S329_23V6.1 (Physcomitrella patens), 3'ss of exon 13
--ttcatctttcatgatatacatgtgtttcagaactg----atgtattttcagtgctgtatctaatccgactacttatgcagtgtttgactcttgctcttctctagATTGGCGTTGGCATGTGCATGGAGGGAATAGAGCACAATCCAGTTGTTTATGAACTTATGTCTGAAATGGCATTTCATAATAAGAAGGTTGAGGTTGAG
     ||   | |   | |   |  |||  |  || |       | || || | || || | | |  || ||  || | || ||| ||    |||    |  | || | || ||||||||||| ||||| || || ||||| || |||||||| |||||  | ||| |||||||||||||||| |||   |  || |  || |||
gtaggattggtgaaagttttggttggttgtaatacagcaaagaatgttatcggggc-gtgtattaatcgtctctttcttcactgtgtg----ttgagtctggc-agGTAGGTGTTGGCATGTGTATGGAAGGCATTGAGCAGAACCCAGTTGTGTATGACTTGATGGCTGAAATGGCATTTCACAATGCAACCGTCGTTGTCGAG

upper sequence: GRMZM2G033592_T01 (Zea mays), 3'ss of exon 13
lower sequence: EFJ21415 (Selaginella moellendorffii), 3'ss of exon 13
ttcatctttcatgatatacatgtgtttcagaactgatgtattttcagtgctgtatctaatccgactacttatgcagtgtttgactcttgctcttctctagATTGGCGTTGGCATGTGCATGGAGGGAATAGAGCACAATCCAGTTGTTTATGAACTTATGTCTGAAATGGCATTTCATAATAAGAAGGTTGAGGTTGAG
                             | |  |||   ||||     || | ||  |    |  | |||   || |          | |  | |||||||||||||||| ||||||||||| || || || || || ||||| || || ||||||||| ||||||||||||| |     |  |     |   |  ||
-----------------------------gtatcgatacgttttt----ctatttccga---aagcaattagcaaggg----------ggttgtttctagATTGGCGTTGGAATGTGCATGGAAGGCATCGAACAAAACCCAGTCGTCTACGAACTTATGGCTGAAATGGCATTCCGCTCAACTAGAAACGCTCTGAAG

upper sequence: GRMZM2G033592_T01 (Zea mays), 3'ss of exon 13
lower sequence: EFJ23779 (Selaginella moellendorffii), 3'ss of exon 13
ttcatctttcatgatatacatgtgtttcagaactgatgtattttcagtgctgtatctaatccgactacttatgcagtgtttgactcttgctcttctctagATTGGCGTTGGCATGTGCATGGAGGGAATAGAGCACAATCCAGTTGTTTATGAACTTATGTCTGAAATGGCATTTCATAATAAGAAGGTTGAGGTTGAG
                             | |  |||   ||||     || | ||  |    |  | |||   || |          | |  | |||||||||||||||| ||||||||||| || || || || || ||||| || || ||||||||| ||||||||||||| |     |  |     |   |  ||
-----------------------------gtatcgatacgttttt----ctatttccga---aagcaattagcaaggg----------ggttgtttctagATTGGCGTTGGGATGTGCATGGAAGGCATCGAACAAAACCCAGTCGTCTACGAACTTATGGCTGAAATGGCATTCCGCTCAACTAGAAACGCTCTGAAG

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|91873217|gb|EB403174.1|EB403174
EST:     CAATTTCATCTGGCCCCATTGATGCCCGTACAAGTTACAATTCAACAATG                         ATTGGCGTTGGCATGTGCATGGAGGGAATAGAGCACAATCCAGTTGTTTAT
genomic: CAATTTCATCTGGCCCCATTGATGCCCGTACAAGTTACAATTCAACAATGgtaagtgcaa ... tcttctctagATTGGCGTTGGCATGTGCATGGAGGGAATAGAGCACAATCCAGTTGTTTAT
EST: gi|166446942|gb|EG090152.1|EG090152
EST:     ATTCAACAATG                         ATTGGCGTTGGCATGTGCATGGAGGGAAAAGAGCACAATCCAGTTGTTTAT
genomic: ATTCAACAATGgtaagtgcaa ... tcttctctagATTGGCGTTGGCATGTGCATGGAGGGAATAGAGCACAATCCAGTTGTTTAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 120

CATGTTACACAACTTTGGTGGGAACATTGAAATGTATGGCATACTTGATTCAATTTCATCTGGCCCCATTGATGCCCGTACAAGTTACAATTCAACAATGgtaagtgcaa ... tcttctctagATTGGCGTTGGCATGTGCATGGAGGGAATAGAGCACAATCCAGTTGTTTATGAACTTATGTCTGAAATGGCATTTCATAATAAGAAGGTTGAGGTTGAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 101

CATGTTACACAACTTTGGTGGGAACATTGAAATGTATGGCATACTTGATTCAATTTCATCTGGCCCCATTGATGCCCGTACAAGTTACAATTCAACAATGgtaagtgcaa ... tcttctctagATTGGCGTTGGCATGTGCATGGAGGGAATAGAGCACAATCCAGTTGTTTATGAACTTATGTCTGAAATGGCATTTCATAATAAGAAGGTTGAGGTTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 153

CATGTTACACAACTTTGGTGGGAACATTGAAATGTATGGCATACTTGATTCAATTTCATCTGGCCCCATTGATGCCCGTACAAGTTACAATTCAACAATGgtaagtgcaa ... tcttctctagATTGGCGTTGGCATGTGCATGGAGGGAATAGAGCACAATCCAGTTGTTTATGAACTTATGTCTGAAATGGCATTTCATAATAAGAAGGTTGAGGTTGAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 120

CATGTTACACAACTTTGGTGGGAACATTGAAATGTATGGCATACTTGATTCAATTTCATCTGGCCCCATTGATGCCCGTACAAGTTACAATTCAACAATGgtaagtgcaa ... tcttctctagATTGGCGTTGGCATGTGCATGGAGGGAATAGAGCACAATCCAGTTGTTTATGAACTTATGTCTGAAATGGCATTTCATAATAAGAAGGTTGAGGTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgctgtatctaatccgactacttatgcagtgtttgactcttgctcttctctagATTGGCGTTGGCATGTGCATGGAGGGAATAGAGCACAATCCAGTTGTTTATGAACTTATGTCTGAAATGGCATTTCATAATAAGAAGGTTGAGGTTGAG
                                      ctcttgctcttctct  CT-rich tract
       tatctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcatctttcatgatatacatgtgtttcagaactgatgtattttcagtgctgtatctaatccgactacttatgcagtgtttgactcttgctcttctctagATTGGCGTTGGCATGTGCATGGAGGGAATAGAGCACAATCCAGTTGTTTATGAACTTATGTCTGAAATGGCATTTCATAATAAGAAGGTTGAGGTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - tttcatg
- - - - - - - -atacatg
- - - - - - - - - - - tgtttca
- - - - - - - - - - - - - - - - ctgatgt
- - - - - - - - - - - - - - - - - - - - - - - gtgctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtttg