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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacaccgatagtccaatacactggagatccaaagcaggtttacagtttgaaaaaaaaaagttaaatggtgatgtactacttccagGTAGAGACCATCCGTCAAGGTTATCTTTCGAAAAGATCTTCAAACTTGAGAGCCGACTGGAAAAGAAGGTTCTTCGTACTTGATAGTCGAGGAATGCTGT

Basic information

species Zea mays
transcript GRMZM5G872204_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G872204_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G38550.1 (Glycine max), 3'ss of exon 11
-----------------------------gtaagacaccgatagtccaatacactggagatc--caaagcaggtttacagtttgaaaaaaaaaagttaaatggtgatgtactac-ttccagGTAGAGACCATCCGTCAAGGTTATCTTTCGAAAAGATCTTCAAACTTGAGAGCCGACTGGAAAAGAAGGTTCTTCGTACTTGATAGTCGAGGAATGCTGT
                              | |||      || | |   |   |  |  |   |||  | |  ||  |||       |     |||   |  |    | | |  ||  ||||  | | ||| || ||||| |||||||| ||| |||| || || |||||||  ||||||||||||||||  || ||  |||| |||||||||||| |||
gtattttagaatttgacgtttccttctttctgagatttatgtattacttcattttaaaacttttcaattctgagttg-agtcctgtccattgccgtttcttcatcgcttgcaaaattttagGTTCAAATCATTCGACAAGGATATCTTTCTAAACGATCCTCCAATTTGAGAGGTGACTGGAAAAGAAGGTATTTTGTTGTTGACAGTCGAGGAATGTTGT

upper sequence: GRMZM5G872204_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaagacaccgatagtccaatacactggagatccaaagcaggtttacagtttgaaaaaaaaaagttaaatggtgatgtactacttccagGTAGAGACCATCCGTCAAGGTTATCTTTCGAAAAGATCTTCAAACTTGAGAGCCGACTGGAAAAGAAGGTTCTTCGTACTTGATAGTCGAGGAATGCTGT
            | |  |||     |  | ||   |   |    ||||  ||  | | |  |   | ||   |  | |  | ||| |||||  | || ||  | ||||||||||| || ||| ||||||||||| ||||||  ||||||||||||||||| || || ||||| || || |||||||| |
-----------gttgatcaacgtctttaacatatgattga----tacatcttccagagagtactattaacatttct-tggtgctttcagGTGCAAACAATAAGGCAAGGTTATCTCTCTAAACGATCTTCAAACCTGAGAGGAGACTGGAAAAGAAGGTTTTTTGTTCTTGACAGCCGGGGAATGCTCT

upper sequence: GRMZM5G872204_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv17s0000g00310.t01 (Vitis vinifera), 3'ss of exon 11
--------------------------------------gtaagacaccgatagtccaatacactggagatccaaagcaggttt---acagtttgaaaaaaaaaagttaaatggtgatgtactact--tccagGTAGAGACCATCCGTCAAGGTTATCTTTCGAAAAGATCTTCAAACTTGAGAGCCGACTGGAAAAGAAGGTTCTTCGTACTTGATAGTCGAGGAATGCTGT
                                       || ||  |  |   ||       || |    ||  |     |||    |||| | ||   ||| |  |  | | | |   |  |||  | |||||  | ||||| || ||||| |||||||| ||| | || ||||| ||||| |  |||||||| ||||||||||| || |||||||| ||||| ||| |||
gtaatggttgagatgaccacctttcctttctagtgactctaggaatctaaatttcttcctttctagcatccctcattcttttttaagcagtattaatttaaatatatgta-gctaagacagcactagtgcagGTTCAAACCATTCGACAAGGATATCTTTCAAAACGTTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTTCTTTGTTCTTGATAGCCGAGGCATGTTGT

upper sequence: GRMZM5G872204_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------------------------------------gtaagacaccgatagtcca-atacactggagatccaaagcaggtttacagtttgaaaaaaaaaagttaaatggtga-tgtactac----ttccagGTAGAGACCATCCGTCAAGGTTATCTTTCGAAAAGATCTTCAAACTTGAGAGCCGACTGGAAAAGAAGGTTCTTCGTACTTGATAGTCGAGGAATGCTGT
                                                               |||  ||   |  |  | || | ||  |  | |          |    |||  |         |      |||  || |  ||    || |||||  | |||||||| |||||||| || || ||| | || |||||| ||||||  ||||||||||||||||| || || |||||||| ||||||||||| |
gtctgaagaagcttataagttattaaggaacttcttttatagatacttatcaaaaaaaaaaaaaaggaacttcttttatagatcctctttattttcttgatgttccttgtatttctagttgttttttgtttccgtgtctgaataacaatatttcagGTTCAAACCATCCGACAAGGTTACCTCTCAAAACGCTCCTCAAACCTGAGAGGTGACTGGAAAAGAAGGTTTTTTGTTCTTGATAGCCGAGGAATGCTAT

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: 87

TGGTTTGAATGATTCTTATAATGGTGATCGAATGCAGACAATTGGCAGAAGTTCACATAAACAGATCGAGGCAGTTATGCAGTCAACTTCAAAAGGCAAGgtaagacacc ... ctacttccagGTAGAGACCATCCGTCAAGGTTATCTTTCGAAAAGATCTTCAAACTTGAGAGCCGACTGGAAAAGAAGGTTCTTCGTACTTGATAGTCGAGGAATGCTGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 36

TGGTTTGAATGATTCTTATAATGGTGATCGAATGCAGACAATTGGCAGAAGTTCACATAAACAGATCGAGGCAGTTATGCAGTCAACTTCAAAAGGCAAGgtaagacacc ... ctacttccagGTAGAGACCATCCGTCAAGGTTATCTTTCGAAAAGATCTTCAAACTTGAGAGCCGACTGGAAAAGAAGGTTCTTCGTACTTGATAGTCGAGGAATGCTGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 24

TGGTTTGAATGATTCTTATAATGGTGATCGAATGCAGACAATTGGCAGAAGTTCACATAAACAGATCGAGGCAGTTATGCAGTCAACTTCAAAAGGCAAGgtaagacacc ... ctacttccagGTAGAGACCATCCGTCAAGGTTATCTTTCGAAAAGATCTTCAAACTTGAGAGCCGACTGGAAAAGAAGGTTCTTCGTACTTGATAGTCGAGGAATGCTGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 77

TGGTTTGAATGATTCTTATAATGGTGATCGAATGCAGACAATTGGCAGAAGTTCACATAAACAGATCGAGGCAGTTATGCAGTCAACTTCAAAAGGCAAGgtaagacacc ... ctacttccagGTAGAGACCATCCGTCAAGGTTATCTTTCGAAAAGATCTTCAAACTTGAGAGCCGACTGGAAAAGAAGGTTCTTCGTACTTGATAGTCGAGGAATGCTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagcaggtttacagtttgaaaaaaaaaagttaaatggtgatgtactacttccagGTAGAGACCATCCGTCAAGGTTATCTTTCGAAAAGATCTTCAAACTTGAGAGCCGACTGGAAAAGAAGGTTCTTCGTACTTGATAGTCGAGGAATGCTGT
                                             ctacttcc  CT-rich tract
        tttacagtttgaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagacaccgatagtccaatacactggagatccaaagcaggtttacagtttgaaaaaaaaaagttaaatggtgatgtactacttccagGTAGAGACCATCCGTCAAGGTTATCTTTCGAAAAGATCTTCAAACTTGAGAGCCGACTGGAAAAGAAGGTTCTTCGTACTTGATAGTCGAGGAATGCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG