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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caacacagcaggaaagagtcttgcctgcttgactagagaatgaaatggcacaatttggtacctaaaatggtcctgatttttaagataacattcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA

Basic information

species Zea mays
transcript GRMZM2G061681_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G061681_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g42950.2 (Oryza sativa), 3'ss of exon 6
-----caacacagcaggaaagagtcttgcctgcttgactagagaatgaaatggcacaatttggtaccta-aaatggtcctgatttttaagataacattcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA
      | |       |   || | |||  ||  | |  ||| ||   | |     |||||| |||||| |||||||  | || ||  |   || ||    ||||||||||||| |||||||||||||| |||||| ||||||||||||| |||||||||||||| || ||||||||||||||||| ||||||
actaggagctttatctgcttgactgttgtttgtctaaacagacaacatact-----aatttgttacctagaaatggttataatctt-gatccaatatcgtcttcagGAGAGAGACAATATGCAGAAGACGGAGTTTCTGAAGGCATTATCGGATATGTGGAAGGACTTCGATTCCCGAGTTCTTCGGTATAAA

upper sequence: GRMZM2G061681_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G00470.1 (Glycine max), 3'ss of exon 6
-caacacagcaggaaagagtcttgcctgcttgactaga-gaatgaaatggcacaatttggtacctaaaatggtcctgatttttaagataacattcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA
  || |       |      | |    || | || | | | || | ||| || |||||   |  | || |  || ||||  |   |    | || | ||||||| |||||||| ||||||||| ||||||| || || ||||| |||||||||||||| ||||||||||| || ||  | ||||| || 
gtaagatttttttagtttagccttttagcattacaaaatgtataacatg-ca-aattttagagttgaagt--tcttgatgat-gtgtcctcctttccttcagGAAAGAGATAACATGCAGAAGTCAGAGTTCTTAAAAGCATTGTCAGATATGTGGAAAGATTTTGATTCACGTGTATTGCGATACAAG

upper sequence: GRMZM2G061681_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA12G37070.1 (Glycine max), 3'ss of exon 6
-caacacagcaggaaagagtcttgcctgcttgactagagaatgaaatggcacaatttggtacctaaaatggtcctgatttttaagataacattcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA
  || |       |      | |    || | || | |   | | ||| || |||||   |  | || |  || ||||  |   |    | || | ||||||| |||||||| ||||||||| ||||||| || || ||||| |||||||||||||| ||||||||||| || ||  | |||||||| 
gtaagatttttctagtttagccttttagcattacgaaatgttaacatg-ca-aattttagagttgaagt--tcttgatgat-gtgtcttcctttccttcagGAAAGAGATAACATGCAGAAGTCAGAGTTCTTAAAAGCATTGTCAGATATGTGGAAAGATTTTGATTCGCGCGTATTGCGATATAAG

upper sequence: GRMZM2G061681_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G71410.1 (Arabidopsis thaliana), 3'ss of exon 6
--------caacacagcaggaaagagtctt-gcctgcttgactagagaa---tgaaatggcacaatttg-gtacctaaaatggtcctgatttttaagataacattccttt----cagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA
          |  |  |    ||  || |  | | |  ||     ||||   | | |||    ||  ||  |  | | | | |      ||||    | ||  |||  ||    ||||| |||||||| ||||| ||| | ||||| || || |||||||||||||||||||| |||||||||||||| ||  | || ||||| 
gtacgtgtatatgcttccaataattgtttcagacagactgttcttagaagtcttagatgatggaaaatgtatctccacatttgataaccttttcggaacaattttctctttatccagGAAAGAGATAACATGCAAAAGTCCGAGTTCTTAAAAGCATTATCAGATATGTGGAAAGATTTTGATTCCCGTGTATTACGGTATAAG

upper sequence: GRMZM2G061681_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G22870.1 (Arabidopsis thaliana), 3'ss of exon 6
caacacagcaggaaagagtcttgcctgcttgactagagaatgaaatggc-acaatttggtacctaaaatggtcctgatttttaagataacattcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA
    |  | |    | | | |   |  | |  |      | |  ||    | | || |  || || ||      ||     |    |   |||  || ||||||||||| || ||||||||| | ||||| || || |||||||||||||||||||| || |||||||| || ||  | || ||||| 
--gtat-gtatattaaattttaatcatcgtttcagacagacgtgattttgatagttggaaacatataaaacctttggggcatt--tttttatttattgcagGAGAGAGACAACATGCAGAAGTCTGAGTTCTTAAAAGCATTATCAGATATGTGGAAAGACTTTGATTCTCGTGTATTACGGTATAAG

upper sequence: GRMZM2G061681_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv18s0089g00030.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------caacacagcaggaaagagtcttgcc---tgcttgactagagaatgaaatggcacaatttggtacctaaaatggtcctgatttttaagataacattcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA
                             |  |     |   |||| |  |         |   |  ||||| ||||    | || |||||  |  ||  |   |||| |   ||  |    ||  || ||||| || ||||| ||||||||| | |||||| | || |||||||| ||||||||||| |||||||| || || ||| | || ||||| 
gtatgaagttatatttctttggatgtcacctgcttttgacataagattactaaaaaacattgtgcatgagaaggaaaaataagaagttggtggc--aatggaatctgagtaacaaattttatttttttgcagGAAAGGGATAACATGCAGAAGTCTGAGTTTCTAAAAGCATTATCGGATATGTGGAAAGATTTTGACTCTCGTGTTTTGCGTTATAAG

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), 47 (downstream exon)
Score: 149

GTTCTTCTTTCTTCCGGGATGATACGAGGTTGCGCGCTCTTCGTTTCCTTGACCATTTGCTTgtatgttttt ... ttcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 157

GTTCTTCTTTCTTCCGGGATGATACGAGGTTGCGCGCTCTTCGTTTCCTTGACCATTTGCTTgtatgttttt ... ttcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 253

GTTCTTCTTTCTTCCGGGATGATACGAGGTTGCGCGCTCTTCGTTTCCTTGACCATTTGCTTgtatgttttt ... ttcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 152

GTTCTTCTTTCTTCCGGGATGATACGAGGTTGCGCGCTCTTCGTTTCCTTGACCATTTGCTTgtatgttttt ... ttcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcacaatttggtacctaaaatggtcctgatttttaagataacattcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA
                                     agataac  putative branch site (score: 152)
                                           cattcctttc  CT-rich tract
                              atttttaagataacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caacacagcaggaaagagtcttgcctgcttgactagagaatgaaatggcacaatttggtacctaaaatggtcctgatttttaagataacattcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - acagcag
- - - - - - - - - - -tgcctgc
- - - - - - - - - - - - - - - - - - - - tgaaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagataac