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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgctacatttagtttaaccttcccttttttgtcacttctcacattggttctgattattatcgaaacatgtgtcatatctgcagGCTGCCAAAGAATACTCTGAGCAGCTAGGGGTTGATGCTTGCATAAAACTGTTTGAGCAATTCAAATCTTACGAGGGCCTTTACTTTTTCTTGGGAGCTT

Basic information

species Oryza sativa
transcript LOC_Os11g01380.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 17
--------------gtatttgc---tacatttagtttaaccttcccttttttgtcacttctcacattggttctgattattatcgaaacatgtgtcatatctgcagGCTGCCAAAGAATACTCTGAGCAGCTAGGGGTTGATGCTTGCATAAAACTGTTTGAGCAATTCAAATCTTACGAGGGCCTTTACTTTTTCTTGGGAGCTT
              ||   ||     |  |||  |  | ||| |   |||   || | | |   | |   | | | | || || |||| |||| || ||||| ||||||| |||||||| ||||| || ||||| |||||||||||||||||| | ||||| |||||||||||||| |||||||| ||||||||||||||| | |
gtaaatattgctccgttcctgtaaacatttttgttccaccctactgctttccctcccctgttcaagta--tataacttttgtc-aaacctgtggcacatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCT

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G102756_T01 (Zea mays), 3'ss of exon 3
gtatttgctacatttagtttaaccttcccttttttgtcacttctcacattggttctgattattatcgaaacatgtgtcatatctgcagGCTGCCAAAGAATACTCTGAGCAGCTAGGGGTTGATGCTTGCATAAAACTGTTTGAGCAATTCAAATCTTACGAGGGCCTTTACTTTTTCTTGGGAGCTT-------------
                                           | | |||   ||| |||||| |  ||   || |  | |||||||||| || |||||||| ||||||||||||||||||||||||| ||| ||| | |||||||||||||||||||| ||||| |||||||||||||||||| | |             
-------------------------------------------tgaaatta--tctaattattgtaaaattttgggggacatctgcaggccgcgaaagaataatctgagcagctaggggttgatgcttccatcaaattatttgagCAATTCAAATCTTATGAGGGTCTTTACTTTTTCTTGGGATCCTATCTGAGCTCCAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 19
gtatttgctacatttagtttaaccttcccttttttgtcacttctcacattggttctgattattatcgaaacatgtgtcatatctgcagGCTGCCAAAGAATACTCTGAGCAGCTAGGGGTTGATGCTTGCATAAAACTGTTTGAGCAATTCAAATCTTACGAGGGCCTTTACTTTTTCTTGGGAGCTT
            | | ||     | |   |||| | | ||||   || |      | ||| ||  | || | |  || || | | |||| ||| |||||||| | ||||||  | || |||||||| ||||||||||| ||||||||||| |  || || || || || ||||||||| | ||| | |
-----------gtatggtggtgtcattg-ttttctataacttggaacttcttaaataattgttgacaaagctttcgt-atgtgttcagGTTGCTAAAGAATATTGTGAGCAATTGGGTGTTGATGCCTGCATAAAACTTTTTGAGCAATTTAGGTCATATGAAGGACTGTACTTTTTCCTTGGATCAT

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 19
---------------gtatttgctacatttagtttaaccttcccttttttgtcacttctcacattggttctgattattatcgaaacatgtgtcatatctgcagGCTGCCAAAGAATACTCTGAGCAGCTAGGGGTTGATGCTTGCATAAAACTGTTTGAGCAATTCAAATCTTACGAGGGCCTTTACTTTTTCTTGGGAGCTT
                  ||||| | |       |   ||    | |||| | | |||    |||  |    |  |  |||  |  | ||      | ||||| |||| || ||||| ||||||||| | || |||||||| ||||| ||||| ||||||||||||||||| || || || || |||||||||||||| || |
gtactgtttctggataattttgccataagagtcatgttctattttattttttgaattccgcaattcatctataagaaaatcttacta-gtacatggtttgcagACTGCTAAGGAATATTCTGAGCAGTTGGGTGTTGATGCATGCATTAAACTCTTTGAGCAATTCAAATCCTATGAAGGACTATACTTTTTCTTGGGTGCAT

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 17
--------------------------------gtatttgctacatttagtttaaccttcccttttttgtcacttctcacattggttctgattattatcgaaacatgtgtcatatctgcagGCTGCCAAAGAATACTCTGAGCAGCTAGGGGTTGATGCTTGCATAAAACTGTTTGAGCAATTCAAATCTTACGAGGGCCTTTACTTTTTCTTGGGAGCTT
                                || |     | ||||     ||   ||  ||||| ||   ||   |  ||   |   |  ||  |   |  |  ||    || ||||| |||| || ||||| | ||| ||||| || |||||||| ||||| ||||| |||||||||||||| || || || || || |||||||||||||| || |
gtactgtattagggcttggtagtcggtataatgtttccatgatatttttaacaattatctttttttggtttttttataatttcaataaaagaatcttactagtacatg----atttgcagACTGCTAAGGAATATTGTGAACAGCTGGGTGTTGATGCATGCATTAAACTCTTTGAGCAATTCAAGTCCTATGAAGGACTATACTTTTTCTTGGGTGCAT

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 19
------------------------------gtatttgctacatttagtttaaccttcccttttttgtcacttctcacattggttctgattattatcgaaacatgtgtcatatctgcagGCTGCCAAAGAATACTCTGAGCAGCTAGGGGTTGATGCTTGCATAAAACTGTTTGAGCAATTCAAATCTTACGAGGGCCTTTACTTTTTCTTGGGAGCTT
                               | ||| | |   |   ||| ||  |    ||||| |   || |   ||   ||||    |  |     ||  ||    ||| ||||| ||||||| ||||| | ||| ||||| || || ||||| ||||| ||||| |||||||||||||| || || || || || |||||||||||||| || |
gtactgtattagggcttggtagtcggtataatgttt-ccatgatattttttacaattatatttttttgggtttttttataatttctataaaagaatcttactagtacattatttgcagACTGCCAAGGAATATTGTGAACAGCTCGGTGTAGATGCATGCATTAAACTCTTTGAGCAATTCAAGTCCTATGAAGGACTATACTTTTTCTTGGGTGCAT

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 19
-----------gtatt-tgctacatttagtttaaccttccctttt--ttgtcacttctcacattggttctgattattatcgaaacatgtgtcatatctgcagGCTGCCAAAGAATACTCTGAGCAGCTAGGGGTTGATGCTTGCATAAAACTGTTTGAGCAATTCAAATCTTACGAGGGCCTTTACTTTTTCTTGGGAGCTT
           ||||  || | |  | || || |  |||  ||||  || |    |  |||| |   |||       |     ||  ||     || | ||| |||| || ||||| ||||||||| | || |||||||| ||||| ||||| ||||| ||||||||||| || || ||  | |||||||||||||| || |
gtactgtttctgtataatgttgccataagattcatgttctattttattttttgaattccacaattcatctataagagaatcttactagtacatgatttacagACTGCTAAGGAATATTCTGAGCAGTTGGGTGTTGATGCATGCATTAAACTCTTTGAACAATTCAAATCCTATGAAGGATTATACTTTTTCTTGGGTGCAT

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 19
gtatttgctacatttagtttaaccttcccttttttgtcacttctcacattggttctgattattatcgaaacatgtgt-catatctgcagGCTGCCAAAGAATACTCTGAGCAGCTAGGGGTTGATGCTTGCATAAAACTGTTTGAGCAATTCAAATCTTACGAGGGCCTTTACTTTTTCTTGGGAGCTT
   | || |    | ||| |    |||  |   |||  |||| | | |         ||| ||  | || | |   |   | | | |||| ||| |||||||| | ||||||  | || |||||||| ||||||||||| ||||||||||| |  || || ||||| || ||||||||| | ||| | |
--gtatggtggtgtcagtgt---tttctataacttggaacttattaaac-------aattgttgacaaagctttcttatgtgtgttcagGTTGCTAAAGAATATTGTGAGCAATTGGGCGTTGATGCCTGCATAAAACTTTTTGAGCAATTTAGGTCATATGAGGGACTGTACTTTTTCCTTGGATCAT

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 19
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 19
gtatttgctacatt-tagtttaaccttcccttttttgtcacttctcacattggttctgattattatcgaaacatgtgtcatatctgcagGCTGCCAAAGAATACTCTGAGCAGCTAGGGGTTGATGCTTGCATAAAACTGTTTGAGCAATTCAAATCTTACGAGGGCCTTTACTTTTTCTTGGGAGCTT
|||| ||||  ||| | ||   |  |    ||| ||||    | | ||| ||           | ||    ||||| |      ||||||||  ||| || |||| |||||| || || |||||||| ||||| ||||| |||||||||||||| || ||||| || || ||||||||| | ||  | |
gtatgtgctgtattgttgtaagatgtgaattttattgtttaatgtgacactgacg--------tgtc----catgtct-----ttgcagGCTTGCAAGGAGTACTGTGAGCAACTTGGTGTTGATGCATGCATTAAACTCTTTGAGCAATTCAAGTCGTACGAAGGGCTGTACTTTTTCCTAGGTTCAT

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 19
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 19
gtatttgctacatttagtttaaccttcccttttttgtcacttctcacattggttctgattattatcgaaacatgtgtcatatctgcagGCTGCCAAAGAATACTCTGAGCAGCTAGGGGTTGATGCTTGCATAAAACTGTTTGAGCAATTCAAATCTTACGAGGGCCTTTACTTTTTCTTGGGAGCTT
|||      |  | |  | | |       |        |||| | |  ||  ||||   | |      || ||  |||   | ||||| ||||||||||||| ||||||||  | || ||||||   ||| ||||||| ||||||||||| ||||| ||||| ||  | ||||||||  ||||  |||
gtacccatcat-tgtcttctgatggatgatccagatcgacttgtaaacttatttcttgctttcgct--aatattggtc---tgtgcagACTGCCAAAGAATATTCTGAGCAATTGGGTGTTGATCAATGCGTAAAACTCTTTGAGCAATTTAAATCATACGAAGGATTGTACTTTTTTCTGGGTTCTT

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 19
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 19
gtatttgctacatttagtttaaccttcccttttttgtcacttctcacattggttctgattattatcgaaacatgtgtcatatctgcagGCTGCCAAAGAATACTCTGAGCAGCTAGGGGTTGATGCTTGCATAAAACTGTTTGAGCAATTCAAATCTTACGAGGGCCTTTACTTTTTCTTGGGAGCTT
      |  | ||   ||||    |      || |      |  ||||||  |    |  ||| | |     |  ||||| | ||||| ||||||| || || ||||| ||| | || ||||| || || ||||||||||||||||| ||||| ||||| || ||  | ||||||||||||||  | |
------gtaaaatagtgttttgtatatgtgattattgattattccacattcataaaaa--attgtggctcactaagtcatttgtgcagACTGCCAAGGAGTATTCTGAACAGTTGGGTGTTGAGGCATGTATAAAACTGTTTGAGCAGTTCAAGTCTTATGAAGGATTATACTTTTTCTTGGGGTCAT

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 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 74 (downstream exon)
Score: 53

TGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTGTACAGgtatttgcta ... atatctgcagGCTGCCAAAGAATACTCTGAGCAGCTAGGGGTTGATGCTTGCATAAAACTGTTTGAGCAATTCAAATCTTACGAGGGCCTTTACTTTTTCTTGGGAGCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcacttctcacattggttctgattattatcgaaacatgtgtcatatctgcagGCTGCCAAAGAATACTCTGAGCAGCTAGGGGTTGATGCTTGCATAAAACTGTTTGAGCAATTCAAATCTTACGAGGGCCTTTACTTTTTCTTGGGAGCTT
                      tgattattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgctacatttagtttaaccttcccttttttgtcacttctcacattggttctgattattatcgaaacatgtgtcatatctgcagGCTGCCAAAGAATACTCTGAGCAGCTAGGGGTTGATGCTTGCATAAAACTGTTTGAGCAATTCAAATCTTACGAGGGCCTTTACTTTTTCTTGGGAGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT