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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatcttagatatgtcagagttttaaaacttcatctgtagattttcttgacctactatggtcaagatcttataactgcctcctcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATAT

Basic information

species Zea mays
transcript GRMZM2G170037_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170037_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 21
-ta-atcttagatatgtcagagttttaaaacttcatctgtagattttcttgacctactatggtcaagatcttataactgcctcc--tcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATAT
 || || || |    |   |||| ||| |  ||         |||||||  |  ||     |||      | | || ||||||   | |||   ||  ||||||||||||||||| |||||||| || ||| ||||||| ||||| ||||| |||||||| || |||||||||||| ||| ||| ||||| ||||| || ||||
ctatattttgggacggatggagtattatatgttggctacctaattttctctattta----agtcctatcttaaaaattgcctctggtaaatctgttacttgcagCCTTGCAAGGGAATATTGCTGTTTGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATAT

upper sequence: GRMZM2G170037_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 17
--taatcttagatatgtcagagttttaaaacttcatctgtagattttcttgacctactatggtcaagatcttataactgcctcctcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATAT
   ||   |    || | ||   ||||||           |||  || ||||     |   | || |    ||  ||    |  | | | | ||   |  |||||||||| || ||||||||||| ||  |||||||||| |||||||| |||||||| || || ||||||||| |||  || || ||||| || || || |
gtgaaagattttcattttagttgtttaaatgacttgtgaaagaaattgttgagtagatcatgccatgtgtgtagcacctaattgtaattactttgggtatagCCTTGCAAAGGAATATTGCTTTTTGGCCCTCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTTATTAACATTT

upper sequence: GRMZM2G170037_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
-----taatcttagatatgtcagagttttaaaacttcatctgtagattttcttgacctactatggtcaagatcttataactgcctcctcaattcatt--ctttg----cagCCTTGCAAGGGGATATTGCTTTTCGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATAT
     ||   ||   | | |    | ||||||     |   | | |  || || |     |    |  | ||| | |   |  | ||||| |  | |  |||||     ||||||||||||| ||||||||||| ||  | |||||||| |||||||| |||||||| || || ||||||||| |||  || || |||||||| || || |
gttggtagattttc-tttttagttgctttaaatgacaagtggaacacattttttagtagatgatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT

upper sequence: GRMZM2G170037_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 17
----taatcttagatatgtcagagttttaaaacttcatctgtagattttcttgacctactatggtcaagatcttataactgcctcctcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATAT
     ||   |    || | ||   ||||||           |||  || || |     |   | || |    ||  ||    |  | | | | ||   |  ||||||||||||| ||||||||||| ||  | |||||||| |||||||| |||||||| || || || |||||| |||  || || ||||| || || || |
gtgaaaaatattttcattttagttgtttaaatgacttgtgaaagacattgttaagtagatcatgccatgcgtgtagcacctaattgtaattactttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT

upper sequence: GRMZM2G170037_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 16
------taatcttagatatgtcagagttttaaaacttcatctgtagattttcttgacctactatggtcaagatcttataactgcctcctcaattcatt--ctttg----cagCCTTGCAAGGGGATATTGCTTTTCGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATAT
        || ||   | |    |  ||  |  ||||       | ||||| ||     |  ||  || | ||| | |   |  | ||||| |  | |  |||||     ||||||||||||| ||||||||||| ||  | |||||||| |||||||| |||||||| || || ||||||||| |||  || || |||||||| || || |
gttgatagattttctttttagttgctttaaatgacttgtggaacacatttt-ttagtagatcatattcga-atcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT

upper sequence: GRMZM2G170037_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
taatcttagatatgtcagagttttaaaacttcatctgtagattttcttgacctactatggtcaagatcttataactgcctcctcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATAT
         |  | | |  | | ||    || || |||   || | |   ||||| ||     | | |    ||     |  |  ||   ||   ||||||||   || || ||| || | || ||| ||||||| |||||||| || ||||| || ||||||||||||||| | |  ||||| |||||||||||||| |
-------gtaccttttattgctatacggatttatttgttagttgt-tactcctac-ataactgaaacc----aaacatatatttgat--gtttaatgcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 9 (downstream exon)
Score: 29

TGATATTGGAGCCTTGGAGAATGTAAAGGACACGTTAAAGGAGCTGGTGATGCTCCCTTTGCAAAGACCTGAGTTGTTCTGCAAAGGGCAGTTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGGATATTGCTTTTCGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATAT


Block sizes: 49 (upstream exon), 9 (downstream exon)
Score: 49

TGATATTGGAGCCTTGGAGAATGTAAAGGACACGTTAAAGGAGCTGGTGATGCTCCCTTTGCAAAGACCTGAGTTGTTCTGCAAAGGGCAGTTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGGATATTGCTTTTCGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATAT


Block sizes: 49 (upstream exon), 9 (downstream exon)
Score: 51

TGATATTGGAGCCTTGGAGAATGTAAAGGACACGTTAAAGGAGCTGGTGATGCTCCCTTTGCAAAGACCTGAGTTGTTCTGCAAAGGGCAGTTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGGATATTGCTTTTCGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATAT


Block sizes: 49 (upstream exon), 9 (downstream exon)
Score: 31

TGATATTGGAGCCTTGGAGAATGTAAAGGACACGTTAAAGGAGCTGGTGATGCTCCCTTTGCAAAGACCTGAGTTGTTCTGCAAAGGGCAGTTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGGATATTGCTTTTCGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgacctactatggtcaagatcttataactgcctcctcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATAT
                       ttataac  putative branch site (score: 31)
                                         ttcattcttt  putative PPT
                    atcttataa  TA-rich tract