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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttgtttcttcaatcacctttaccgtgatccttttctgtaggattaaaaataatgcttatgttgttttttctctattcttatttcagAGAATTCCTAGATGGTGGATCTGGTACTACTGGATTTGCCCATTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGCAAGACCCCA

Basic information

species Zea mays
transcript GRMZM2G366146_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G366146_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os06g36090.2 (Oryza sativa), 3'ss of exon 17
gttagttgtttcttcaatca--cctttaccgtgatccttttctgtaggattaaaaataatgcttatgttgttttttctctattcttatttcagAGAATTCCTAGATGGTGGATCTGGTACTACTGGATTTGCCCATTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGCAAGACCCCA
|| ||||  |||||  ||||  || || |  ||| | |||| |      |  || || |   | ||| |||| ||  | |    ||||||||||| ||||| | |||||||||||||||||||||| |||||||||||||||||||||||||||||||||| |||||||| || ||||||||  || |   ||
gtgagtt--ttcttggatcaaaccgtttctttgaactttttattcttcttggaagatcaaagtaatggtgttattcatgt---tttatttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGGACAGTGTATGGGCTCATAGTGACACAGTATGGAGACCTAGAACAAATCA

upper sequence: GRMZM2G366146_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA15G02220.1 (Glycine max), 3'ss of exon 22
-----------gttagttgtttcttcaatcacctttaccgtgatccttttctgtaggattaaaaataat-gcttatgttgttttttctctattcttatttcagAGAATTCCTAGATGGTGGATCTGGTACTACTGGATTTGCCCATTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGCAAGACCCCA
             |||||   |  | |  || |  ||     ||   |     |    |  ||  |||| |||| | |    |||    |        |||||| |||||||| ||||||| | ||||| || |||||||||||| | |||||||| || |||||| | || ||  ||||||| |||||  |  |       |
gtaagtaccattctagtttggttattatgcatcaatataagaattactcgtcatgttctctaacgtaattgcttgtatcaactttggctt--------ttcagAAAATTCCTAAATGGTGGGTTTGGTATTATTGGATTTGCCCAGTAGCATGGACTGTATATGGGTTAATTGTCTCACAATATGGAGATGTAGAGATAGAGA

upper sequence: GRMZM2G366146_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA13G43140.1 (Glycine max), 3'ss of exon 21
gttagttgtttcttcaatcacctttaccgtgatccttttctgtaggattaaaaataatgcttatgttg---ttttttctctatt--ctt----atttcagAGAATTCCTAGATGGTGGATCTGGTACTACTGGATTTGCCCATTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGCAAGACCCCA
  |   |   |    ||  |    || | |  |          || ||||    |     ||    |    |  || ||||||   |||    |||||||| |||||||| ||||||| | ||||| || |||||||||||| | || ||||| ||||||||| | || ||  ||||||| |||||  |  |       |
aatgactaaattgataaaaagaaatagcttatttagcaataaaagaattattcttgtcattttctctaacataattcctctatcaactttgacatttcagAAAATTCCTAAATGGTGGGTTTGGTATTATTGGATTTGCCCAGTAGCGTGGACTGTGTATGGGTTAATTGTCTCACAATATGGAGATGTAGAGATAGAGA

upper sequence: GRMZM2G366146_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA07G01860.1 (Glycine max), 3'ss of exon 22
gttagttgtttcttcaat-cacctttaccgtgatccttttctgtaggattaaaaataatgcttatgttgttttttctctattctta---tttcagAGAATTCCTAGATGGTGGATCTGGTACTACTGGATTTGCCCATTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGCAAGACCCCA
|| |||    |  | | | |    |||   |||  |     | |   |  | ||    | || |  |   | ||   | |   ||    ||||||| |||||||| ||||||| | ||||| ||||||||||| ||| |||||||||||||||||||  | || ||  | |||||  ||||  |  | ||||   
gtgagtaccattctaatttcgttattatattgaaacaaacatatcttac-ataatctttactaacataactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCATC

upper sequence: GRMZM2G366146_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA08G21540.1 (Glycine max), 3'ss of exon 21
gttagttgtttcttcaatcacctttaccgtgatcctttt----ctgtaggattaaaaataatgcttat--gttgttttttctctattctta---tttcagAGAATTCCTAGATGGTGGATCTGGTACTACTGGATTTGCCCATTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGCAAGACCCCA
       ||   | | ||  ||  |  ||| ||  | ||    |      ||   | ||||| ||||        | ||   | |   ||    ||||||| |||||||| ||||||| | ||||| ||||||||||| ||| |||||||||||||||||||  | || ||  | |||||  ||||  |  | |||||  
-------gtgagtaccatt-ccagtttcgtaattttattgaaacaagcatatcttacataatccttactaaaaactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCCAC

upper sequence: GRMZM2G366146_T01 (Zea mays), 3'ss of exon 17
lower sequence: AT3G16340.1 (Arabidopsis thaliana), 3'ss of exon 18
------gttagttgtttcttcaatcacctttaccgtgatccttttctgtaggattaaaaataatgcttatgttgttttttctctattcttatttcagAGAATTCCTAGATGGTGGATCTGGTACTACTGGATTTGCCCATTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGCAAGACCCCA
      ||| |||  || |     ||      | |  | |||      |    |    | |    | || | || |||| ||   ||| | || ||||||||||| | ||||||||| ||||| |||||||| || ||| |||| ||||| ||||||||  | || ||  | || ||||| ||| || | ||  | |
gttagtgttggttacttttctgg-caagaaagctgaaaccctaaatgattctctattgattctatcataagctggttttact---ttcctcttgcagAGAATTCCGAAATGGTGGATATGGTATTACTGGATCTGTCCAGTGGCTTGGACTGTGTATGGATTGATTGTTTCGCAGTACGGTGACGTGGAGGATACGA

upper sequence: GRMZM2G366146_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv09s0002g03570.t01 (Vitis vinifera), 3'ss of exon 4
gttagttg--tttcttcaatcacct--ttaccgtgatccttttctgtaggattaaa--aataatgcttatgttgttttttctctattctt----atttcagAGAATTCCTAGATGGTGGATCTGGTACTACTGGATTTGCCCATTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGCAAGACCCCA
|| ||||   |||| ||| |  | |    ||  | || | || |        | |   | ||     ||  |      | |  || | ||    |||||||| |||||| |  ||||||||||||||||| |||||||||||| | ||||||||||| || ||||| |||||  | ||||| |||||| || | ||| | |
gtaagttcattttcctcagtggcatagccactttcatgccttccaaccaacctcatccactacaaactaactcaaacctccattaatgtttaaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCACTAGCATGGACAGTTTACGGGCTGATCGTATCGCAATATGGAGACTTGGAGGACACAA

upper sequence: GRMZM2G366146_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv09s0002g03630.t01 (Vitis vinifera), 3'ss of exon 22
---------------------------------------------------------------------gttagttgtttcttcaatcacctttaccgtgatccttt-tctgtaggattaaaaataat----gcttatgttgtt---ttttctctattctta---tttcagAGAATTCCTAGATGGTGGATCTGGTACTACTGGATTTGCCCATTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGCAAGACCCCA
                                                                        | || |||||  ||  ||| || || | |     | | | |  |||||||||| |     |  |||  ||     ||   |  ||| | |    ||||||||||||| |  |||||| | |||||||| ||||| |||||| |||| |||||||| || ||  | || ||| |||| || || ||| || | ||  |||
gtaagtatccatttggatatgattttaggaagcattctaacctttctaacacttcaaaatttttatcaaaaaaattatttct--aagtaccatttccattacaagatgtttttgagattaaaaatcactgaagaatatactgacaaattcaattgattttcaaaacttcagAGAATTCCCAAGTGGTGGGTATGGTACTATTGGATATGCCCAGTGGCGTGGACAGTATACGGATTGATTGTGTCACAGTATGGGGACATGGAGGAGACCA

upper sequence: GRMZM2G366146_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv09s0002g03640.t01 (Vitis vinifera), 3'ss of exon 20
gttagttg--tttcttcaatcacct--ttaccgtgatccttttctgtaggattaaa--aataatgcttatgttgttttttctctattctt----atttcagAGAATTCCTAGATGGTGGATCTGGTACTACTGGATTTGCCCATTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGCAAGACCCCA
|| ||||   |||| ||| |  | |    ||  | || | || |        | |   | ||     ||  |      | |  || | ||    |||||||| |||||| |  ||||||||||||||||| |||||||||||| | ||||||||||| || ||||| |||||  | ||||| |||||| || | ||| | |
gtaagttcattttcctcagtggcatagccactttcatgccttccaaccaacctcatccactacaaactaactcaaacctccattaatgtttaaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCAGTAGCATGGACAGTTTACGGGCTGATCGTATCGCAATATGGAGACTTGGAGGACACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgtaggattaaaaataatgcttatgttgttttttctctattcttatttcagAGAATTCCTAGATGGTGGATCTGGTACTACTGGATTTGCCCATTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGCAAGACCCCA
                             ttgttttttctctatt  CT-rich tract
          attaaaaataatgctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttgtttcttcaatcacctttaccgtgatccttttctgtaggattaaaaataatgcttatgttgttttttctctattcttatttcagAGAATTCCTAGATGGTGGATCTGGTACTACTGGATTTGCCCATTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGCAAGACCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA