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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgtacttgcgagccctccaggtcagtaccttcgcattggtgcagctgatatctccgcttcgtattcctgtttaactaaccttacattttgtaatgcagCATTACTCAGAGTTGCCTGATATCAAGCGTGCCATTGTAAATACCCATGTCATTGAACCACAG

Basic information

species Zea mays
transcript GRMZM2G352837_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G352837_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 17
gttgtacttgcgagccctccaggtcagtaccttcgcattggtgcagctgat-atctccgcttcgtattcctgtttaactaaccttacattttgtaatgcagCATTACTCAGAGTTGCCTGATATCAAGCGTGCCATTGTAAATACCCATGTCATTGAACCACAG
             |  ||     ||  ||  |||  ||    | |  | || |||||   || | ||   | || |||      |  || ||||   |||||||||  | ||||||||||| ||||| |||| |||||| ||||| |||| |||||| ||||||
-------------gttctttgcttct-taagttctgatgacagta--taatgatctcttgttagaatatttcttgaaccgtgtctgtatattgt---gcagCATTATACTGAGTTGCCTGACATCAAACGTGTCATTGTGAATACACATGCCATTGAGCCACAG

upper sequence: GRMZM2G352837_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 16
gttgtacttgcgagccctccaggtcagtaccttcgcattggtgcagctgatatctccgcttcgtat-tcctgtttaactaaccttacattttgtaatgcagCATTACTCAGAGTTGCCTGATATCAAGCGTGCCATTGTAAATACCCATGTCATTGAACCACAG
        |     | | |||  |  ||   ||   |||  ||    |  ||| |   |        | || ||| ||| |    ||  ||| |  ||||||||||| |||||||||| ||||| || ||||  ||||||||||| ||||  ||||| ||||||
-------gtaatgactcaccaaat--gtgttttattattactggttttcttatttaacccaaaagccttctcttttactgattacactatttttggtgcagCATTACACAGAGTTGCCAGATATAAAACGTGTGATTGTAAATACACATGCAATTGAGCCACAG

upper sequence: GRMZM2G352837_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 17
gttgtacttgcgagccctccaggtcagtaccttcgcattggtgcagctgatatctccgcttcgtattcctgtttaactaaccttacattt-tgtaatgcagCATTACTCAGAGTTGCCTGATATCAAGCGTGCCATTGTAAATACCCATGTCATTGAACCACAG
             |  ||     ||  ||  |||  ||   || |  | || |   |  ||   | |  |  ||    ||||||   | | | |  ||||||||||  | ||||||||||| ||||| |||| |||||| ||||| |||| |||||| ||||||
-------------gttctttgcttct-taagttctgatgactgta--taatgttctctttttagaatatttcttg---aaccttgtctgtgtattgtgcagCATTATACTGAGTTGCCTGACATCAAACGTGTCATTGTGAATACACATGCCATTGAGCCACAG

upper sequence: GRMZM2G352837_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 15
gttgtacttgcgagccctccaggtcagtaccttcgcattggtg--cagctgatatctccgcttcgtattcctgtttaactaaccttacattttg-taatgcagCATTACTCAGAGTTGCCTGATATCAAGCGTGCCATTGTAAATACCCATGTCATTGAACCACAG
                     | ||  | | |      |  ||     ||| ||| ||   |  | ||   |  || |     |||   | ||| |  |||||||||| || ||||||||||| ||||| |||| |||||| ||||| |||| ||| ||||| |||
---------------------gttctttgcttctattcttatgactgactgttatttcttgtcagaataatttcttgaaccttcttgtgtgttgcttgtgcagCATTATTCCGAGTTGCCTGACATCAAACGTGTCATTGTGAATACACATGCCATCGAACCGCAG

upper sequence: GRMZM2G352837_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 16
gttgtacttgcgagccctccaggtcagtacc-ttcgcattggtgcagctgatatctccgcttcgtattcctgtttaactaaccttacattttgtaatgcagCATTACTCAGAGTTGCCTGATATCAAGCGTGCCATTGTAAATACCCATGTCATTGAACCACAG
        |     | | |||  |  ||    |||  | ||||    || || |  || |   |   | || ||| | | |    |   ||| |  ||||||||||| |||||||||| ||||| || ||||  ||||||||||| ||||  ||||| ||||||
-------gtaatgactcaccaaatgtgttttattcttactggtttt-cttatttaacc-caaaggccttctcttttattgattacattatttttggtgcagCATTACACAGAGTTGCCAGATATAAAACGTGTAATTGTAAATACACATGCAATTGAGCCACAG

upper sequence: GRMZM2G352837_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 17
gttgtacttgcgagccctccaggtcagtaccttcgcattggtg--cagctgatatctccgcttcgtattcctgtttaactaaccttacattttg-taatgcagCATTACTCAGAGTTGCCTGATATCAAGCGTGCCATTGTAAATACCCATGTCATTGAACCACAG
                     | ||  | | ||     |  ||     |||  || ||   |  | ||   |  || |     |||   | ||| | ||||||||||| || || |||||||| ||||| |||| |||||| ||||| |||| ||| |||||||||
---------------------gttctttgcttttattcttatgactgactgtaatttcttgtcagaataatttcttgaaccttcttgtgtgttgcttatgcagCATTATTCCGAATTGCCTGACATCAAACGTGTCATTGTGAATACACATGCCATCGAACCACAG

upper sequence: GRMZM2G352837_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 17
gttgtacttgcgagccctccaggtcagtaccttcgcattggtgcagctgatatctccgcttcgtattcctgtttaactaaccttacattt-tgtaatgcagCATTACTCAGAGTTGCCTGATATCAAGCGTGCCATTGTAAATACCCATGTCATTGAACCACAG
         |      ||| | |||  | | ||   |||  ||   || |||  |    ||  | ||||  | |||||    || | |||   |  ||||||||||||||||||| ||||||||||| ||||  ||||| || || ||||  ||||| ||||||
---------gtttttgctcaatgtc--ttctttaatattcttg-gcctaatagatgtatttttttttcccctctaacttcgtttccttttgctttgtgcagCATTACTCAGAGTTACCTGATATCAAACGTGTAATTGTGAACACACATGCTATTGAGCCACAG

upper sequence: GRMZM2G352837_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 17
gttgtacttgcgagccctccaggtcagtaccttcgcattggtgcagctgatatctccgcttcgtattcctgtttaactaaccttacattttgtaatgcagCATTACTCAGAGTTGCCTGATATCAAGCGTGCCATTGTAAATACCCATGTCATTGAACCACAG
   ||   | |  |   |  |   || |     ||      |  |  |   |||| |   ||   ||||   ||   |  | ||  ||||     ||||||||||||||||||| |||||||| || ||||  |||||||| || ||||  || || ||||||
---gttggtacatgtttttta--ccatttttaccggccaaatagatttatcatcttc---tcaccttccaacttcttttccttttgattt----gtgcagCATTACTCAGAGTTACCTGATATAAAACGTGTAATTGTAAACACACATGCTATCGAGCCACAG

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), 49 (downstream exon)
Score: 225

GGAGCAGTTCACAAAATGCCTCAAAAGAAGCATATATAGTCAGGTCGCTTTAGAAGTCAACAAATCAACCGTTGATGACATGAAATGCAGCATCTGTCAGgtaagcggta ... tgtaatgcagCATTACTCAGAGTTGCCTGATATCAAGCGTGCCATTGTAAATACCCATGTCATTGAACCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

GGAGCAGTTCACAAAATGCCTCAAAAGAAGCATATATAGTCAGGTCGCTTTAGAAGTCAACAAATCAACCGTTGATGACATGAAATGCAGCATCTGTCAGgtaagcggta ... tgtaatgcagCATTACTCAGAGTTGCCTGATATCAAGCGTGCCATTGTAAATACCCATGTCATTGAACCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

GGAGCAGTTCACAAAATGCCTCAAAAGAAGCATATATAGTCAGGTCGCTTTAGAAGTCAACAAATCAACCGTTGATGACATGAAATGCAGCATCTGTCAGgtaagcggta ... tgtaatgcagCATTACTCAGAGTTGCCTGATATCAAGCGTGCCATTGTAAATACCCATGTCATTGAACCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 142

GGAGCAGTTCACAAAATGCCTCAAAAGAAGCATATATAGTCAGGTCGCTTTAGAAGTCAACAAATCAACCGTTGATGACATGAAATGCAGCATCTGTCAGgtaagcggta ... tgtaatgcagCATTACTCAGAGTTGCCTGATATCAAGCGTGCCATTGTAAATACCCATGTCATTGAACCACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgatatctccgcttcgtattcctgtttaactaaccttacattttgtaatgcagCATTACTCAGAGTTGCCTGATATCAAGCGTGCCATTGTAAATACCCATGTCATTGAACCACAG
                                     ttacattttgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtacttgcgagccctccaggtcagtaccttcgcattggtgcagctgatatctccgcttcgtattcctgtttaactaaccttacattttgtaatgcagCATTACTCAGAGTTGCCTGATATCAAGCGTGCCATTGTAAATACCCATGTCATTGAACCACAG

- - tacttgc
- - - - - - - ccctcca
- - - - - - - - - - - - cagtacc
- - - - - - - - - - - - - - - - - - - - - gcagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacattt