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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtgccttcttcgctcaaactcaaaccatacgtaacggcgcatgcatactcatccgtcaccgtcaccgccaccgcagGCATCATCAAGGGCACCATGACCACCACCCACTTCTACACCTGCGATCAGAGGCTGCTGGACGCGAGCCACCGCGACCTGCGCCGCGCCCGCGCCGCCGC

Basic information

species Zea mays
transcript GRMZM5G821433_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G821433_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g38600.2 (Oryza sativa), 3'ss of exon 3
gtgcgtgc-cttcttcgctcaaactcaaaccatacgtaacggcgcatgcatactcatccgtcaccgtc------accgccaccgcagGCATCATCAAGGGCACCATGACCACCACCCACTTCTACACCTGCGATCAGAGGCTGCTGGACGCGAGCCACCGCGACCTGCGCCGCGCCCGCGCCGCCGC
|| ||||| |     ||| ||    | | ||      ||     |   |   |||   |      |        | |     |||||||||||||||||| || |||||||||||||||| ||||||| |||| ||||||||||| |||||||||||||| ||||| || ||||| || || || ||
gtacgtgcgcacacgcgcgcatcagcgatcctcgaccaattttactctctctctctctctctgatgcttaaccaatcaatggcgcagGCATCATCAAGGGGACGATGACCACCACCCACTCCTACACCGGCGACCAGAGGCTGCTCGACGCGAGCCACCGTGACCTCCGGCGCGCGCGTGCGGCGGC

upper sequence: GRMZM5G821433_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA19G28240.1 (Glycine max), 3'ss of exon 4
--------gtgcgtgccttcttcgctcaaactcaaaccatacgtaacggcgcatgcatactcatccgtcaccgtcaccg------------ccaccgcagGCATCATCAAGGGCACCATGACCACCACCCACTTCTACACCTGCGATCAGAGGCTGCTGGACGCGAGCCACCGCGACCTGCGCCGCGCCCGCGCCGCCGC
             ||| | |     |  |    ||   ||  | |     |     || |||  |  |    | ||  |            |||   |||| ||||||||||| |||||||||||||| |||| ||||||| | || || ||||| || || ||||||||||| |||||| | || ||  | || || ||
ctaaaatgacttatgcatgcaatatttgagactaatttatgtgaagaaaagatcatattctctactatgcatgccaatggaaaatgacaatccatgacagGTATCATCAAGGGTACCATGACCACCACTCACTCCTACACCGGTGACCAAAGGCTTCTTGATGCGAGCCACCGTGACCTGAGGCGTGCAAGGGCAGCAGC

upper sequence: GRMZM5G821433_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G04940.1 (Glycine max), 3'ss of exon 4
-----------------------gtgcgtgccttcttcgctcaaac-tcaaaccatacgtaacggcgcatgcatactcatccgtcaccgtcaccg-ccaccgcagGCATCATCAAGGGCACCATGACCACCACCCACTTCTACACCTGCGATCAGAGGCTGCTGGACGCGAGCCACCGCGACCTGCGCCGCGCCCGCGCCGCCGC
                       |||   |  | | |   | |||  ||| |  || |   ||   ||||||     ||   |  ||   |||   |||   |||| |||||||||||||||||||||||||| |||| ||||||| |||| || ||||| || |||||||||||||| |||||| | |||||| | || || ||
ggaatacaatattagagactaaagtgaaggtttacatgttttaaagatcatattattctctactatgcatgc-----caatagaaactcacacaatccatgacagGTATCATCAAGGGCACCATGACCACCACTCACTCCTACACCGGCGACCAAAGGCTTCTCGACGCGAGCCACCGTGACCTGAGGCGCGCCAGGGCGGCAGC

upper sequence: GRMZM5G821433_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv14s0068g00680.t01 (Vitis vinifera), 3'ss of exon 4
------gtgcgtgccttcttcgctcaaactcaaaccatacgtaacggcgcatgcatactcat--ccgtcaccgtcaccgccaccgcagGCATCATCAAGGGCACCATGACCACCACCCACTTCTACACCTGCGATCAGAGGCTGCTGGACGCGAGCCACCGCGACCTGCGCCGCGCCCGCGCCGCCGC
       | | | ||   |||| ||    |   |||||      |    |||   |    ||    |   |    |    ||  ||||| |||||||||||||||||||| || || || | ||||||  | || |||||||| || ||||| |||||||| |||||  | || ||  | || || ||
gtaattttacatacccctttcg-tctgtttgtcaccatggtcttccctccatcgctttgaatgatgggagcttaaaaattcatggcagGAATCATCAAGGGCACCATGACAACAACTCATTCCTACACTGGGGACCAGAGGCTCCTTGACGCCAGCCACCGTGACCTTAGACGTGCGAGAGCTGCAGC

upper sequence: GRMZM5G821433_T01 (Zea mays), 3'ss of exon 2
lower sequence: EDP09609 (Chlamydomonas reinhardtii), 3'ss of exon 4
------------------------------------------------------------------------------------------------------gtg-cgtgccttcttcgctca---aactcaaaccatacgtaacggcgcatgcatactcatccgtcaccgtcaccgccaccgcag-
                                                                                                       |  | || ||| |  |||||     |||  |||   |    |  |     | |   | |     |||      ||    ||||       ||||  |||||||||| |||||||||||||||| ||||||| | || ||| | ||||||||||||  ||||||||||||||                   
gtaaggaagcttacgcatgttgcttgctgtggctttttcgtcaggaataaatgcggggggcggcaagagcgtccacggtgttgcgggtccgagtgccctgggatatcttgtcttgtcagctcacctgtctctgacccggcccttcccctttcccctctcccttgcctaccccagGTGCTGGAGCAGAAGTTCGGCATTGTCAAGGGCACGATGACCACCACCCACTCCTACACCGGTGACCAGCGCCTGCTGGACGCGTCCCACCGCGACCTGC-------------------

upper sequence: GRMZM5G821433_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S11_397V6.2 (Physcomitrella patens), 3'ss of exon 3
----------gtgcgtgccttcttcgctcaaactcaaaccatacgtaacggcgcatgcatactcatccgtcaccgtcaccgccaccgcagGCATCATCAAGGGCACCATGACCACCACCCACTTCTACACCTGCGATCAGAGGCTGCTGGACGCGAGCCACCGCGACCTGCGCCGCGCCCGCGCCGCCGC-----------
            |   ||  || |     |  |      || |   ||| || | |||   ||    |       |   ||  |     || ||||||||||| ||||||||||| ||||||| ||||||  | || ||||||||||| || ||   |||||| ||| || |  | || || ||||| ||           
ctataagcactcggacgctatcattagcaacgcctcgtgcacaaccaactgc-cttgctcccttcgtcaaggtgttggacgagaagttcggaatcatcaagGGAACCATGACCACTACCCACTCCTACACTGGTGACCAGAGGCTGCTCGATGCCTCCCACCGTGACTTGAGGAGAGCGCGTGCCGCAGCCCTGAACATTG

upper sequence: GRMZM5G821433_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S11_397V6.3 (Physcomitrella patens), 3'ss of exon 3
----------------------gtgcgtgcct-tcttcgctcaaactcaaaccatacgtaacggcgcatgcatactcatccgtc--accgtcaccgccaccgca---------------gGCATCATCAAGGGCACCATGACCACCACCCACTTCTACACCTGCGATCAGAGGCTGCTGGACGCGAGCCACCGCGACCTGCGCCGCGCCCGCGCCGCCGC
                      | ||  | || |   | |||  || | |  |||  | |||| | | |||| |  || | | |   |   |  || ||  |                 || ||||||||||| ||||||||||| ||||||| ||||||  | || ||||||||||| || ||   |||||| ||| ||                    
caccttcgttgtgggtgtgaacgagcaggactataagcactcggacgcta-tcattagcaacgcctcgtgcacaaccaactgccttgctcccttcgtcaagGTGTTGGACGAGAAGTTCGGAATCATCAAGGGAACCATGACCACTACCCACTCCTACACTGGTGACCAGAGGCTGCTCGATGCCTCCCACCGTGACTTGA-------------------

upper sequence: GRMZM5G821433_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ13677 (Selaginella moellendorffii), 3'ss of exon 4
gtgcgtgccttcttcgctcaaactcaaaccatacgtaacggcgcatgcatactcatccgtcaccgtcaccgccaccgcagGCATCATCAAGGGCACCATGACCACCACCCACTTCTACACCTGCGATCAGAGGCTGCTGGACGCGAGCCACCGCGACCTGCGCCGCGCCCGCGCCGCCGC
                   ||  ||   | | |  |  |     ||  || ||     |  ||  |  |  |  ||  ||| ||||||||||| |||||||| || || ||||  |||||| | || ||| | ||||| ||||| |||||||| ||||| ||||| || |||||||| ||
-----------------gtaagttcctccaaaagctctctctcgatcgatgcta----gaaactcttgcaacttcc--agGGATCATCAAGGGAACCATGACAACAACACACTCGTACACCGGAGACCAGCGCCTGCTCGACGCCAGCCACCGGGACCTCCGCCGAGCTCGCGCCGCGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaccatacgtaacggcgcatgcatactcatccgtcaccgtcaccgccaccgcagGCATCATCAAGGGCACCATGACCACCACCCACTTCTACACCTGCGATCAGAGGCTGCTGGACGCGAGCCACCGCGACCTGCGCCGCGCCCGCGCCGCCGC
       acgtaac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtgccttcttcgctcaaactcaaaccatacgtaacggcgcatgcatactcatccgtcaccgtcaccgccaccgcagGCATCATCAAGGGCACCATGACCACCACCCACTTCTACACCTGCGATCAGAGGCTGCTGGACGCGAGCCACCGCGACCTGCGCCGCGCCCGCGCCGCCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA