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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taataacacgtgccctgacagactgaccttccaatctaaaattagttctgtttgattgcatccttgctgagctgtatccgatccacatttttttttccagGTCCCCATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG

Basic information

species Zea mays
transcript GRMZM2G575696_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G575696_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 3
taataacacgtgccctgacagactga--ccttccaatctaaaattagttctgtttgattgc---atccttgctgagctgtatccgatccaca---tttttttttccagGTCCCCATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
          ||  | | |  |   |  |||| |||   |||  |  |   ||   | ||    |||||| ||   |   ||  ||  || |    ||   ||| ||||| ||||||||||||||||||||||||||| | || ||||||||||| ||||| ||||||||||||||| | ||||||||||||||||| |||||| |||
--------tctgttccgtccaatctatgcctttcaaaaaaaatgttttcaagtgctaatgtcctatccttactacacctcattggactcataaaaattgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG

upper sequence: GRMZM2G575696_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 3
taataacacgtgccctgacagactgaccttccaatctaaaattagttctgtttgat-tgcatccttgctgagctgtatccgatccacatttttttttccagGTCCCCATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
   | | |  |   || | ||  |       |  |  || |     |||| |  || || ||  ||   |  |   ||  | |     | |  | || |||||||| || || |||||| ||||  | ||||  |||||||||||||| || ||||| |||||||||||| | ||||| || |||||||| ||||||||||
--gtga-aaatttgctaagagtatatgtgatc--ttcaacacaccctctgatacatatgtattattttagtccaacatttgttgtttctataatgttgcagGTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAATCTGACCAGAATTGGATGGTTG

upper sequence: GRMZM2G575696_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 3
-taataacacgtgccctgacagactgaccttccaatctaaaattagttctgtttgat-----tgcatccttgctgagctgtatccgat---ccacattttttt----ttccagGTCCCCATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
 |||  | |  ||||  |||    ||   |   || |   ||    | ||  || ||     || ||| | | | | | || ||  ||        ||| | |    || |||||||| || || |||||| | ||  | ||||  || ||||||||||| ||||||||||| ||||||||| | |||||||| ||||||||||||||| |||
gtaaaga-atatgccgagactagatgcgatcttaaacatcaacatatcctcgttaatacatttgtatcat-gttcatcagtgtctaataatttctgtttctatggtgttgcagGTCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGCAAATATTCCACACACACACCTTGCACATGAGAAGTCTGACCAGAACTGGATGATTG

upper sequence: GRMZM2G575696_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G35120.4 (Glycine max), 3'ss of exon 3
taataacacgtgccctgacagactgaccttccaatctaaaattagttctgtttgattgcatccttgctga----gctgtatccgatccacatttttttttccagGTCCCCATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
                       |||   |     |||| | ||  | || |       || ||  ||||    | ||||   | |    || |  | || ||||| || || || |||||| ||||  | ||||  || ||||||||||| || ||||| |||||||||||| | |||||||| |||||||| ||||||  ||
----------------------gtgaaaatttg--ctaagagtatatgtgatcttcaatatactctctgatactgatgtaattgttgtttatataatgttgcagGTTCCTATTAAGTGGCCACAAAGCAGAGATGAGGTGTGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAGTCTGACCAGAATTGGATGACTG

upper sequence: GRMZM2G575696_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 2
-taataacacgtgccctgac--agactgaccttccaatctaaaat-----------tagttctgtttgattgcatccttgctgagctgtatccgatccacatttttttttccagGTCCCCATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
 |||  | |  ||||  |||      ||| |||| | |  || ||           ||  | ||| | |||   ||  |||| |     |   | |     | |  | || ||| |||| || || |||||| | ||  | ||||  || ||||||| ||| ||||||||||||||||||||| | |||||||| ||||||||||||||| |||
gtaaaga-atatgccgagactcgatgtgatcttcaacttcaacatatcctcattaatacatttgtataattttgtcaatgctaaa--acaattgttgtttctatggtgtttcagATCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGTAAATATTCCACACACTCACCTTGCACACGAGAAGTCTGACCAGAACTGGATGATTG

upper sequence: GRMZM2G575696_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
taataacacgtgccctgacagactgaccttccaatctaaaattagttctgtttgattgcatccttgctgagctgtatccgatccacatttttttttccagGTCCCCATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
         ||| |   |  ||       | || | | |   | | | || ||  || |    |  |  | |||| | |  | |  || | ||||   |||| || || ||||||||||||||  | |||| ||| |||||||  ||||| || || ||||| |||||| | |||||||| ||||| |||||||||||||
---------gtgtct--atcgatatgttatacagtttta---tcgatatgattagttacg--atgacataactgttttctcttccaatatgtttt---agGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG

upper sequence: GRMZM2G575696_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G04430.1 (Arabidopsis thaliana), 3'ss of exon 3
taataacacgtgccctgacagactgaccttccaatctaaaattagttctgtttgattgcatccttgctgagctgtatccgatccacatttttttttccagGTCCCCATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
   |   |  |   ||  |    |   |||   || |   ||| ||||    | |     || |      | | | | |  |  |    |||   |  |||| || || || ||||| || ||| | |||| ||| |||||||||||||| || |||||||||||||||||||||||||| || ||||||||||||||||
--gtgctatatttgctttcttgttttgcttt-gatttgtgattggttcctggttacattgtcttgatattgttttgttctttgtattgatttgcgtttagGTTCCTATTAAGTGGCCTAAGAGTAGAGATGAAGTGTGGAAAGCAAACATACCTCACACTCACCTTGCAAAAGAGAAGTCTGATCAGAACTGGATGGTTG

upper sequence: GRMZM2G575696_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 3
taataacacgtgccctgacagactgaccttccaatctaaaattagttctgtttgattgcatccttgctgagctgtatccgatccacatttttttttccagGTCCCCATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
                |  ||| ||  | |  |   ||| | ||     | |   ||| |   || || |  | | |    |     | ||   || ||| |||| || || |||||||||||  | |||| |||||||||||||||||| || || |||||||||||| | ||||| || |||||||| ||||||||||
----------------gtgagaatgtgcgta-agcttaatagtaacaagggt--gttgaagtttt-cttatttttgt---gtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG

upper sequence: GRMZM2G575696_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv07s0005g03630.t01 (Vitis vinifera), 3'ss of exon 2
-------taataacacgtgccctgacagactg--accttccaatctaaaattagttctgtttgattgcatccttgctgagctgtatccgatccac-atttttttttccagGTCCCCATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
       |      | ||    ||| | | ||  |||    ||  | | ||| ||| |  ||     |||     || || ||  ||   ||  |  |      |  |||||||| || || ||||| |||||  | ||||  || |||||||| || || || || || ||||||||||  |||||||| |||||||||||||||||||
gtgagtctgtgcttaagttttttgaaatattgggaccaaggaagtttatatt-gttttcattatccacatgtac-ctaagatgattctcttctgctgtgggcggtaacagGTCCCAATCAAGTGGCCTAAAAGCAGAGATGAGGTGTGGAAAGCCAATATACCTCATACCCACCTTGCAACTGAGAAGTCTGACCAGAACTGGATGGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgtttgattgcatccttgctgagctgtatccgatccacatttttttttccagGTCCCCATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
    gtttgat  putative branch site (score: 5)
                                    tccacatttttttttc  putative PPT
                                       acattttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taataacacgtgccctgacagactgaccttccaatctaaaattagttctgtttgattgcatccttgctgagctgtatccgatccacatttttttttccagGTCCCCATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - cacgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatccac