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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcatgtgtgcctggcaactatcctcctttcatcagattagttattcttcactacagttgatgtgataacctcttaaccaatgcccaatctccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG

Basic information

species Zea mays
transcript GRMZM2G014069_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014069_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os08g44530.1 (Oryza sativa), 3'ss of exon 11
tgcatgtgtgcctggcaactatcctcctttcatcagattagttatt--cttcactacagttgatgtgataacctcttaaccaatgcccaatctccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG
              | |  |||| | || || || || |   |  |  |||  ||   |      |||| |    |||||   |   ||| |  || |||||||||| ||||||||||| ||||| |||||||||||||| ||||||||||||||||| || ||||| || ||||||||||||
--------------gtagttatcttgctgtcttctgaatgtctgataactttccttgtgacagc-tgatcaatatttaacttgtattcaaacatcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG

upper sequence: GRMZM2G014069_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 11
tgcatgtgtgcctggcaactatcctcctttcatcagattagttattcttcactacagttgatgtgataacctcttaacca-atgcccaatctccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG
|   |||       | || | || |  |        || | | ||  |     ||   || || |||  | | | || || ||   |  |    | | |||||    ||  |  |||| ||||| |||||||| ||||| |||||||||||||| || || || ||||| ||||||||||||
tatttgtagaaactgaaaatgtctttttcaagctttatgaatcataataatgaacctatgctg-gatggcatttcaagcatattgtcttttgatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTTGTGGTTGGCCATATATGTCCTGAAGCACAG

upper sequence: GRMZM2G014069_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 11
-tgcatgtgtgcctggcaactatcctcctttcatcagattagttattcttcactacagttgatgtgataacctcttaaccaatgcccaatctccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG
 |     | ||  | |  ||     || ||| |||   || ||   | | |   |       |   ||||  |   ||    |  | | |      | ||||| || ||  | ||||| |||||||| || ||||| |||||||| || |||||||| || ||||| ||||||||||| |||
ttatgcttatgg-tagtgacctaaatctttttatctactttgtccatatccgagaacacaccttatataaagtgccaatatgttgctattgggtgatgcagGAATGTGCATTACTGACTGATGGTAGGTTCTCTGGTGGGTCACACGGTTTTGTTGTTGGCCACATTTGCCCTGAAGCTCAG

upper sequence: GRMZM2G014069_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv05s0051g00830.t01 (Vitis vinifera), 3'ss of exon 11
tgcatgtgtgcctggcaactatcctc---ctttcatcagattagttattcttcactacagttgatgtgataacctcttaaccaatgcccaatctc-cattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG
   ||||   | | |  |   |       | | | | | | |   ||  |||   | || ||||||| ||     ||||   |||       ||    |  |||||    ||  || |||| |||||||| ||||| ||||| |||||||||| |||||| || |||||||| ||||||||||| 
--tatgttctcttagacatattttatgaacctgcttaacactgagtac-ctttgtttcatttgatgtaatg-ttacttatggaattttattccttatgtggcagGATGTTGCTTTGTTGACTGATGGTAGGTTTTCAGGAGGTTCACATGGATATGTTGTTGGCCACATATGTCCTGAAGCACAT

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|211042827|gb|FL411666.1|FL411666
EST:     CCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT
genomic: CCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT
EST: gi|149101994|gb|EE188015.2|EE188015
EST:     AAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT
genomic: AAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT
EST: gi|71311152|gb|DR791882.1|DR791882
EST:     CCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT
genomic: CCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT
EST: gi|9953481|gb|BE640064.1|BE640064
EST:     CCGAAATGTTGACTCCAGCAAGCGCAATAATGGGTGCTGGTCTTGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT
genomic: CCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT
EST: gi|33095072|gb|CF055066.1|CF055066
EST:     CCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT
genomic: CCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT
EST: gi|211152609|gb|FL453070.1|FL453070
EST:     CCGAAATGTTGACTCCAACAAGCSCAATAATGGGTGCTGGTCTTGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT
genomic: CCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT
EST: gi|45568073|gb|CK985888.1|CK985888
EST:     CCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT
genomic: CCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT
EST: gi|74234928|gb|DT642842.1|DT642842
EST:     CCGAAATGTTGACTCCGACAAGCGCAATAATGGGTGCTGGTCTTGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT
genomic: CCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT
EST: gi|5895787|gb|AW037033.1|AW037033
EST:     CCGAAATGNTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT
genomic: CCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT
EST: gi|211085449|gb|FL413518.1|FL413518
EST:     CCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT
genomic: CCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTT

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: 162

AAAGGTAGTAGTGATCCGAGGAGAAGGACCAAAAGGCGGGCCAGGGATGCCCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 113

AAAGGTAGTAGTGATCCGAGGAGAAGGACCAAAAGGCGGGCCAGGGATGCCCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 74

AAAGGTAGTAGTGATCCGAGGAGAAGGACCAAAAGGCGGGCCAGGGATGCCCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 85

AAAGGTAGTAGTGATCCGAGGAGAAGGACCAAAAGGCGGGCCAGGGATGCCCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcactacagttgatgtgataacctcttaaccaatgcccaatctccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG
                          tcttaac  putative branch site (score: 85)
                                           tctccatt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcatgtgtgcctggcaactatcctcctttcatcagattagttattcttcactacagttgatgtgataacctcttaaccaatgcccaatctccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC