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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcccaactttctataccttggttttgtcatactacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG

Basic information

species Zea mays
transcript GRMZM2G140328_T03
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 16
gtatgttcccaactttctataccttggttttgt-catactacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG
             |         ||||| |||| | | ||  ||  |||  ||   ||||| || | |          ||  |  | |||||||||||||| |||||||||||||| |||||||| ||||||||||| ||||| |||||||| || ||  | ||||| ||||||
----------gtatgctcgcttgttggtattgtgcttgcttgttattcctgca--aaatgcatt-ctcttgagtgggttaatgcttatagGTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAG

upper sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 15
gtatgttcccaactttctataccttggttttgtcatactacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG
|||||        | | | ||| ||   |  ||  |   || | |    ||||   |  |||||         |  |  || | ||||||| |||||||||||||| || || || ||||| ||||||||||| || |||||||| |||||||| || || ||| | ||||||
gtatgccaattgatgtttgtacttttagtcggttttg--acataaat--acatgtgaaactttgtttatattgtaacattgaattgtagGTAAGGAGGCTTTCTGCCTGCGAGACCATGGGCTCTGCCACAACCATATGCAGTGATAAGACTGGTACATTGACTATGAATCAG

upper sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 15
gtatgttcccaactttctataccttggttttgtcatactacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG----
|||||        | | | | | || |  || |   |   ||  ||  || |   |||||| |  |   | ||   |  || | |  |||| |||||||||||||| ||||| || ||||| || |||||||| || |||||||| |||||||| || || ||| | ||||||    
gtatgccaatttttgtttgtgctttaggatttttgcatatct--atttgaga---aatgctgtttaatataac--acattgaattacagGTGAGGAGGCTTTCTGCCTGTGAGACAATGGGGTCAGCCACAACCATTTGCAGTGATAAGACTGGAACATTGACTATGAATCAGGTTA

upper sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 15
gtatgttcccaactttctataccttggttttgtcatactacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG
|||||        | | | ||| |    |  ||  |   || | |    ||||   |  |||||     |   |  |  || | ||||||| |||||||||||||| ||||| || ||||| ||||||||||| || || ||||| ||||||||||| || ||  | ||||||
gtatgccaattgatgtttgtacttataatcagttttg--acataaat--acatgtgaaactttgtttaatatgtcacattgaattgtagGTAAGGAGGCTTTCTGCCTGTGAGACCATGGGCTCTGCCACAACCATATGTAGTGATAAGACTGGCACATTGACCATGAATCAG

upper sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 18
gtatgttcccaactttctataccttgg--ttttgtcata-ctacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG
|||||    |   | | | | |  | |  ||||| |||| ||| ||||   || ||    || ||   |    ||| |    || | || |||| |||||||||||||| ||||| || ||||| || |||||||| || |||||||| |||||||| || || ||| | ||||||
gtatgccaacttttgtttgtgctataggattttggcatatctatttga---gaaat--gctgtttgatataa-cacat----tgaattgcagGTGAGGAGGCTTTCTGCCTGTGAGACAATGGGGTCAGCCACAACCATTTGCAGTGATAAGACTGGAACATTGACTATGAATCAG

upper sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 18
gtatgttcccaactttctataccttggttttgtcatactacttgatccgacattgaatgctttgcacgctcacttcctatggaat-gtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG
    ||    | | || ||| | |   | || |  |  |  ||  |     |  | || ||||     || ||  || | | | | | ||||  || |||| || || |||||||| ||||| |||||||||||||| |||||||| ||||| || || || || |||||||||
----gtaagtatcattttatgcatcaatctttttgttatttttagttt--taaggcatccttt-----ctaacagccaaggaatttgcagGTACGGCGGCTATCAGCCTGTGAAACTATGGGCTCTGCCACAACAATTTGCAGTGATAAGACAGGAACATTGACCTTAAATCAG

upper sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA07G00630.1 (Glycine max), 3'ss of exon 18
gtatgttcccaactttctataccttggttttgtcatactacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG
    ||    | | || ||| | |   | || |  |  |  ||  |     |  | || ||||     || ||     |     || ||||  || |||| || || |||||||| ||||| |||||||||||||| |||||||| ||||| || || || || |||||||||
----gtaagtatcattttatgcatctatctttttgttatttttagttt--taaggcatccttt-----ctaacagtaaaaaatttgcagGTACGGCGGCTATCGGCCTGTGAAACTATGGGCTCTGCCACAACAATTTGCAGTGATAAGACAGGAACATTGACCTTAAATCAG

upper sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 16
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 15
gtatgttcccaactttctataccttggttttgtcatactacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG
          |   |   |     || | | |   || | |||  | |    ||  ||  | ||  |  |    ||  |||  |   |||| || |||||||| || |||||||| ||||| || || |||||||||||||||||||| ||||| || |||||||| ||||||
-------gtaagaatcagaaggagtgttctcgctttagttctttcttcttggtt--attgtctgaccatttttctcaaatgccaaacagGTTAGAAGGCTTTCAGCTTGTGAAACCATGGGATCAGCAACAACAATCTGCAGTGACAAAACTGGAACTTTAACTTTGAATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG
                                cgctcac  putative branch site (score: 3)
                                      cttcctat  CT-rich tract
                 attgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttcccaactttctataccttggttttgtcatactacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG