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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttacttaactaataacctatctatgtatctgtagtttcttgttcttgttaattgtaccatatatctctcaaacggtgcatatgtttccagCCAATAAAATACGCCTTTGGAACAAGGGTGTTGACTCAGAAAGCTTCCATCCTCGTTTCCGCAACATGGAAATGCGTTCAAGGCTAAC

Basic information

species Zea mays
transcript GRMZM2G100652_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100652_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g01030.1 (Oryza sativa), 3'ss of exon 6
gtttacttaacta---ataaccta---tctatgtatctgtagtttcttgttcttgt-taattgtaccatatatctct-----caa------acggtgcat-atgtttccagCCAATAAAATACGCCTTTGGAACAAGGGTGTTGACTCAGAAAGCTTCCATCCTCGTTTCCGCAACATGGAAATGCGTTCAAGGCTAAC
|||  | |  |||   |||   |    | | | || || ||   |||| ||||    || ||  ||| | | |  ||     |||      | | ||  | || |||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||| |||||||| ||    ||||||||| ||||||||||
gttgtcatggctatacatagttttgtttttttttacctttaccatcttattctgacatagtttcaccttcttttgctattaccaatttattatgatgggtcatatttccagCCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAAC

upper sequence: GRMZM2G100652_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA01G27840.1 (Glycine max), 3'ss of exon 7
--------------------------------------gtttacttaactaataacc-tatctatgtatctgtagtttcttgttct----tgttaattgtaccatatatc-tctcaaacggtgcatatgtt----tccagCCAATAAAATACGCCTTTGGAACAAGGGTGTTGACTCAGAAAGCTTCCATCCTCGTTTCCGCAACATGGAAATGCGTTCAAGGCTAAC
                                       ||  || |  | ||||    ||||    ||  ||| ||| || | ||    ||| |||    | || | |  ||| |  |  | |   ||||    |||||| || || ||  | |||||||||||||||||||| || ||||| |||||||| || |||     |   |||||||| | ||| || | 
gtgaactcaaacaccccttatgaagtgatttcatagctcttcgctgagttgataatagcatctgaacataagtatttttttatactacattgtcaatgcagcaattttttgtctaactcaattctactgttgatgtccagCGAACAAGATTTGTCTTTGGAACAAGGGTGTTGATTCTGAAAGTTTCCATCCGCGATTCAAGTCCCATGAAATGCGATTAAGACTGAG

upper sequence: GRMZM2G100652_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT5G01220.1 (Arabidopsis thaliana), 3'ss of exon 7
gtttacttaactaataacctatctatgtatctgtagtttcttgttcttgttaattgtaccatatatctctcaaacggtgcatatgtttccagCCAATAAAATACGCCTTTGGAACAAGGGTGTTGACTCAGAAAGCTTCCATCCTCGTTTCCGCAACATGGAAATGCGTTCAAGGCTAAC
||  |   |  | |||   ||  | | | |    || |   || |  |   ||   ||| || |   |||       | ||||| ||   ||| ||| || | || |||||||| |||||||| || |||||||||||| |||| ||||||||       |||||||||  ||| || | 
gtgaagaaagatcatacattacatttttgtaca-agctctatgattgttcaaaacttac-attttcttcttctttttttcatatattga-agCTAATCAACTTCGACTTTGGAATAAGGGTGTCGATTCAGAAAGCTTCAATCCCCGTTTCCGTTCTCAAGAAATGCGTATAAGACTGAG

upper sequence: GRMZM2G100652_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv08s0007g01940.t01 (Vitis vinifera), 3'ss of exon 7
--gtttacttaactaataacctatctatgtatctgtagtttcttgttcttgttaattgtaccatat--atctctcaaacggtgcatatgtttcc-----agCCAATAAAATACGCCTTTGGAACAAGGGTGTTGACTCAGAAAGCTTCCATCCTCGTTTCCGCAACATGGAAATGCGTTCAAGGCTAAC
  |  |   |  | | |   | |    || |     |  || |  |  | || ||| |  | ||||  |   || ||  | |  || | ||| |     ||| || | ||| || |||||||| ||||| |||||||| ||||| ||||||||||||| |         |||||||||| ||| |||| 
gtgcatggatgtccattgtgcaactgttgcaaaaacaaattgtaatgat-gtcaatggatcaatattgaaaactaaattgctttatctctttgctttgcagCTAACAGAATTCGTCTTTGGAATAAGGGGGTTGACTCTGAAAGTTTCCATCCTCGTTACTATTCTCACGAAATGCGTTTAAGACTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgttcttgttaattgtaccatatatctctcaaacggtgcatatgtttccagCCAATAAAATACGCCTTTGGAACAAGGGTGTTGACTCAGAAAGCTTCCATCCTCGTTTCCGCAACATGGAAATGCGTTCAAGGCTAAC
          tgttaat  putative branch site (score: 3)
                                              tgtttcc  putative PPT
         ttgttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttacttaactaataacctatctatgtatctgtagtttcttgttcttgttaattgtaccatatatctctcaaacggtgcatatgtttccagCCAATAAAATACGCCTTTGGAACAAGGGTGTTGACTCAGAAAGCTTCCATCCTCGTTTCCGCAACATGGAAATGCGTTCAAGGCTAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA