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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagcccccccctcttgacatagcctcaaaattttcaacaacatgctttgtgatgcaacaggaggcctaatttcattttttgtttatcttttctccaatagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCAAGCTGGCTGAGAGGTGCTAAATTTATTGTTGATTGGCATAAGTTTGGATATACATTGC

Basic information

species Zea mays
transcript GRMZM2G045979_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045979_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g08300.1 (Oryza sativa), 3'ss of exon 5
aagcccccccctcttgaca-tagcctcaaaattttcaacaacatgctttgtgatgcaacaggaggcctaatttcattttttgtttatcttttctccaatagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCAAGCTGGCTGAGAGGTGCTAAATTTATTGTTGATTGGCATAAGTTTGGATATACATTGC
 |   ||  |   |||| | |  |     | || | ||    |   | |   |  | |     |  || |||   || || | | ||||| | ||||| ||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||||||||| |||||||| || |||||||| |||||||||||| |||
-aaatccttctatttgatacttacaatttatttgttaattcgaaaatctcacacactagcatggaactgattcttttattcgatcatcttctgtccaacagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCTAGCTGGCTAAGAGGTGCTAAGTTTATTGTGGACTGGCATAACTTTGGATATACACTGC

upper sequence: GRMZM2G045979_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g36890.1 (Oryza sativa), 3'ss of exon 4
aagcccccccctcttgacatagcctcaaaattttcaacaacatgctttgtgatgcaacaggaggcctaatttcattt-tttg-----tttatcttttctccaatagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCAAGCTGGCTGAGAGGTGCTAAATTTATTGTTGATTGGCATAAGTTTGGATATACATTGC
           |  | | | | ||||| |  |  |   | | ||   |   ||   |  |||   || ||||| ||| ||||      | ||||| | ||  | ||||||||||||||||||||||||||||||||||||||||||| ||| |||| ||||||||||| | |||||| ||||||||||| |||||||||||| |||
---ttatttgttaattagaaaacctcatacgtgactg-atcgtgtcgtacaattggaatggaa--ctgatttcttttatttgatcatctcatcttctgtctgacagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCTAGCGGGCTAAGAGGTGCTAAGTCTATTGTGGATTGGCATAACTTTGGATATACACTGC

upper sequence: GRMZM2G045979_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0001g08980.t01 (Vitis vinifera), 3'ss of exon 5
-aagcccccccctcttgacatagcctcaaaattttcaa----caacatgctttgtgatgcaacaggaggcctaatttcattttttgtttatcttttc----------------tccaatagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCAAGCTGGCTGAGAGGTGCTAAATTTATTGTTGATTGGCATAAGTTTGGATATACATTGC
        |  || ||  ||| | ||    || | |      ||   || |   || |  |  ||  | |    ||| || |||  |||||  ||||                | |   |||||||||| ||||||||||| ||||  ||||| |||  ||||||||||||||||  | |   ||||||||||||||||||||| ||||||||||| ||  
gtgagattcatcttttaccattgactatggatgtgctgacttcagtttgttgcatgcttgattagatgtctctgtttaatatttcatttattatttcatgattaactgtttgcttcttcagAATCCACCTTCTGTTCCAACCTTGGTGGCTGTTAAATGGGCAAGCTGGCTGAGAAATTCAGCATTTATTGTTGATTGGCATAACTTTGGATATACTTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgatgcaacaggaggcctaatttcattttttgtttatcttttctccaatagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCAAGCTGGCTGAGAGGTGCTAAATTTATTGTTGATTGGCATAAGTTTGGATATACATTGC
                  gcctaat  putative branch site (score: 3)
                        tttcattttttgttta  CT-rich tract
                     taatttcattttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagcccccccctcttgacatagcctcaaaattttcaacaacatgctttgtgatgcaacaggaggcctaatttcattttttgtttatcttttctccaatagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCAAGCTGGCTGAGAGGTGCTAAATTTATTGTTGATTGGCATAAGTTTGGATATACATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - caacaac
- - - - - - - - - - - - - - - - - - - - -atgcttt
- - - - - - - - - - - - - - - - - - - - - - - - gtgatgc