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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggtgatatttctttcttggaaatggtcatgctatacctttccaacctgttagattttaaaaacctcttacaaacctatatgaatcagGTCAGTGAATTGCTTGGGTCCTTTGGTGACAATGAACTATCTCCTGAGTGTCTTGATGGTGCTCAGAGATTCTTGAAGCCTGATGGGATTTCCATTCCTT

Basic information

species Zea mays
transcript GRMZM2G169927_T02
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169927_T03 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g04660.2 (Oryza sativa), 3'ss of exon 10
gtacggtgatatttctttcttggaaatggtcatgctatacctttccaacctgttagattttaaaaacctcttacaaacctatatgaatcagGTCAGTGAATTGCTTGGGTCCTTTGGTGACAATGAACTATCTCCTGAGTGTCTTGATGGTGCTCAGAGATTCTTGAAGCCTGATGGGATTTCCATTCCTT
||| | ||||    |  |  |  |||||| |||   ||| |||| |||  || |  | |     ||   |||| |  |  |||||   ||||||||||| |||||||| ||||||||||| |||||||| ||||| |||||||| |||||||||||||||||||||||||| ||||||||||| |||||||
gtatgttgat----ccctgctataaatggacatttcatatcttttcaaagtggttaaatc----aatggcttatatgcaaatatggtacagGTCAGTGAGTTGCTTGGTTCCTTTGGTGATAATGAACTTTCTCCCGAGTGTCTAGATGGTGCTCAGAGATTCTTGAAGCCAGATGGGATTTCTATTCCTT

upper sequence: GRMZM2G169927_T03 (Zea mays), 3'ss of exon 15
lower sequence: AT4G31120.2 (Arabidopsis thaliana), 3'ss of exon 16
----gtacggtgatatttctttcttggaaatggtcatgctatacctttccaacctgttagattttaaaaacctcttacaaacctatatgaatcagGTCAGTGAATTGCTTGGGTCCTTTGGTGACAATGAACTATCTCCTGAGTGTCTTGATGGTGCTCAGAGATTCTTGAAGCCTGATGGGATTTCCATTCCTT
    ||| |   | |  | ||| | |  |||  |||||||    | ||  |      || | || |   |  |||      ||| |   |  ||||| || ||| |||| || || ||||| ||||||||||| |||||||||||||||||||| || || || ||  ||||||| || || ||||| || || |
gtcagtatgt--acagatttttgtagctaatactcatgctga--cattata------tacagttcatctaattctcgtttgcctcttctatgcagGTTAGCGAACTGCTGGGTTCTTTTGGAGACAATGAACTTTCTCCTGAGTGTCTTGATGGAGCCCAAAGGTTTCTGAAGCCAGACGGAATTTCAATACCAT

upper sequence: GRMZM2G169927_T03 (Zea mays), 3'ss of exon 15
lower sequence: Vv04s0008g03120.t01 (Vitis vinifera), 3'ss of exon 16
gtacggtgatatttctttcttggaaatggtcatgctatacctttccaacctgttagattttaaaaacctcttacaaacctatatgaatcagGTCAGTGAATTGCTTGGGTCCTTTGGTGACAATGAACTATCTCCTGAGTGTCTTGATGGTGCTCAGAGATTCTTGAAGCCTGATGGGATTTCCATTCCTT
     || || |   |||  | |   ||   |   | |  ||| |     ||||   | |||    |||||  | ||  |  ||   | |||| ||||| ||||| || || |||||||||||||| || |||||||||||||||||||| ||||| ||||| |||||||  ||||| ||||| || || |
-----gt-atgtgggttttcttgtggtgaatacattctttcttacttctttgttgtttcttatgctcctct--ctaaattgaat--tttagGTTAGTGAGTTGCTGGGTTCTTTTGGTGACAATGAGCTGTCTCCTGAGTGTCTTGATGGAGCTCAAAGATTTTTGAAGCAAGATGGAATTTCAATACCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacctttccaacctgttagattttaaaaacctcttacaaacctatatgaatcagGTCAGTGAATTGCTTGGGTCCTTTGGTGACAATGAACTATCTCCTGAGTGTCTTGATGGTGCTCAGAGATTCTTGAAGCCTGATGGGATTTCCATTCCTT
                               ctcttac  putative branch site (score: 3)
              tgttagattttaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggtgatatttctttcttggaaatggtcatgctatacctttccaacctgttagattttaaaaacctcttacaaacctatatgaatcagGTCAGTGAATTGCTTGGGTCCTTTGGTGACAATGAACTATCTCCTGAGTGTCTTGATGGTGCTCAGAGATTCTTGAAGCCTGATGGGATTTCCATTCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC