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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtttatctttcgtagtttcgtactataatttatgttgctcaagtggattgaccaacaagtaatacatttctgtgctgaagtatggcagtctatgctctatgctcatctatctctgcagATGTGTGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAA

Basic information

species Zea mays
transcript GRMZM2G170412_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170412_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g46700.1 (Oryza sativa), 3'ss of exon 13
--------gttgtttatctttcgtagtttcgtactataatttatgttgctcaagtggattgaccaacaagtaatacatttctgtgctgaagtatggcagtc----tatgctctatgctcatctatctctgcagATGTGTGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAA
         |||  |    |    ||| || ||  |  ||| || |||  |||        |  || | ||  |  || |    | |||| ||    | ||    |||||| ||| |||||| ||  || ||||||||||| ||||||| ||||||||||||||| ||||| || |||||||||||||| ||||| ||||||||||| ||||||||||||||||||||| | |
gtagtataattggatgatatattaagtgtcttaagaagattaatcttgaacaat-------attaaaatgtcttgtatattgaagttgaactacaaaactctaattatgct-tattctcatccattgctccagATGTGTGTCATTTGTAGGCAAATACATGGTTCGTGTACACAGTGCTACAGGTGCTCAACTTATTACCATGCCATCTGTGCATCAAGGGCAGGCTATAGGA

upper sequence: GRMZM2G170412_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 14
gttgtttatctttcgtagtttcgtactataatttatgttgctcaagtggattgaccaacaagtaatacatttctgtgctgaagtatggcagtctatgctctatgctcatctatctctgcagATGTGTGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAA
                   | | |    |     |  ||  |  | ||| ||  |     |    |     ||    || | | ||  || ||||          | |  |   | | ||||| ||||| |||||||||||||| |||||||| ||||| ||||| | || ||| |||||||| | ||||||||| ||||| |||||||| || |||||||
------------------ctccatttggtggg--agcttcttgcattgggtttccttttgatgtctcttggtccactctaatgaata-caatctaaaagtctgcattacttgaattttcagATTTGTGTTATTTGTAAGCAAATTCATGGTTCGTGTACACAATGTTGCAAGTGTTCTACTTATTTCCATGCCATGTGTGCTTCAAGGGCCGGTTATCGAA

upper sequence: GRMZM2G170412_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA19G17460.1 (Glycine max), 3'ss of exon 5
---gttgtttatctttcgtagtttcgtactataatttatgttgctcaagtggattgaccaacaagtaatacatttctgtgctgaagtatggcagtctatgctctatgctcatctatctctgcagATGTGTGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAA
   | || | |   ||  |  |||      ||||||| | | |     ||| ||   |   |  ||  |||||  |  ||            | | ||   |||    | ||  |  |   ||||| ||||| ||||||||| |||| |||||||| || || ||||| | || ||| || ||||| | |||||| || |||||||||||||| || ||||| |
aaagctgataagtatttctgatttg-----ataatttctctcg-----gtgaatct-cagtccggttgtacatgccaatgt-----------aatttaaagtctgctataattgaattt--cagATTTGTGTTATTTGTAAGGAAATTCATGGTTCGTGCACACAATGTTGCAAGTGTTCCACTTATTTCCATGCTATGTGTGCATCAAGGGCTGGTTATCGGA

upper sequence: GRMZM2G170412_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 13
--------------gttgtttatctt--tcgtagtttcgtacta-taatttatgttgctcaagtggattga--ccaac-----aagtaatacatttctgtgctgaagtatggcagtctatgctctatgctcatct--atct-ctgcagATGTGTGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAA
                ||  |||| |  |||   | ||||  || |||  |  | | ||  |||   |||   | |||       | | |     | |||||  || ||         |  |  ||| ||  | |  || |  | ||||| ||||| || || |||||||||||||| ||||| ||||| || | || ||||||||| || || |||||||| ||||| ||  | || || ||| |||
gtacatacctgattcctggatatcatattcggcctatcgtgataataagattagctcctgcagttacttgtttctaaccttttgggaagtttcactatgtgcaaaactaaaaagccagaaaccttatcctgtttttgatatattccagATTTGTGTAATATGCAAGCAAATACATGGCTCATGCACTCAGTGTTGCAAGTGCTCTACGTATTATCATGCCATGTGTGCTTCCCGAGCTGGGTATAGAA

upper sequence: GRMZM2G170412_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv16s0098g00350.t01 (Vitis vinifera), 3'ss of exon 14
gttgtttatctttcgtagt-ttcgtactataatttatgttgctcaagtggattgaccaacaagtaatacatttctgtgctgaagtatggcagtctatgctctatgctcatctatctctgcagATGTGTGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAA
          |||   | | || | |  ||  || || |||    ||| | ||  |   ||  | |   || |    ||||| ||    | |  | |||  | |  ||||  |  ||   |||| || || || ||||||||||||||||||||||| || || || | || ||| ||||||||||||||||| || |||||||||||||| || ||||| |
----------tttgaaaatgttagcatgatgtttaatattg----agttggttttcttgcacatga---atcttca-gctgatgtg-atctgagtttgccttgttttcatgaaattc---agATTTGCGTAATCTGTAAGCAAATACATGGTTCATGCACACAGTGTTGCAAGTGTTCTACTTACTACCATGCAATGTGTGCATCAAGGGCGGGGTATCGTA

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: 48 (upstream exon), 48 (downstream exon)
Score: 46

GACATGTGCATGGTTTCAGTCACAGGTTGCTTTTGCTAGTGATGAGCTCATGGAACCTGCTATTGGGATATTGAACATTCAACCTTTGTTATTTATGAAGgttgtttatc ... atctctgcagATGTGTGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 12

GACATGTGCATGGTTTCAGTCACAGGTTGCTTTTGCTAGTGATGAGCTCATGGAACCTGCTATTGGGATATTGAACATTCAACCTTTGTTATTTATGAAGgttgtttatc ... atctctgcagATGTGTGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 27

GACATGTGCATGGTTTCAGTCACAGGTTGCTTTTGCTAGTGATGAGCTCATGGAACCTGCTATTGGGATATTGAACATTCAACCTTTGTTATTTATGAAGgttgtttatc ... atctctgcagATGTGTGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 34

GACATGTGCATGGTTTCAGTCACAGGTTGCTTTTGCTAGTGATGAGCTCATGGAACCTGCTATTGGGATATTGAACATTCAACCTTTGTTATTTATGAAGgttgtttatc ... atctctgcagATGTGTGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatttctgtgctgaagtatggcagtctatgctctatgctcatctatctctgcagATGTGTGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAA
                                          tctatctct  CT-rich tract