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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatcttaactcttaagtatgttattaatggtctaatctaaaatttaaaagttgtatcattggatattgctcacaaagttttcttacctaatttccagCTGAGGTATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTA

Basic information

species Zea mays
transcript GRMZM2G124883_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124883_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 13
gtatatcttaactcttaagtatgttattaatggtctaatctaaaatttaaaagttgtatcattggatattgctcacaaagttttcttacctaatttccagCTGAGGTATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTA
|||||| |||       || | |   |||||     ||   |||||||   |    ||   ||| | |||||||||||  |||| ||   ||| |  ||||||| || ||||| |||||||||||| |||| ||||||||||||||||| || ||||| ||||||||||| ||||| |||||||| || ||||| || ||
gtatatattagtaa--gagcaggaatttaattaaagaaaaaaaaatttggca----tacagttgaacattgctcacaagcttttatttgataactcacagCTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATA

upper sequence: GRMZM2G124883_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G04580.1 (Glycine max), 3'ss of exon 5
gtatatcttaactcttaagtatgttattaatggtctaatctaaaatttaaaagttgtatca----ttggatattgctcacaaagttttcttacctaatt-tccagCTGAGGTATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTA
  |  | |||    | |  | | |||| |  | |     || |  || |   ||| | | |    |   || |||  |  || | | |   |   |||  | |||| ||||||| |||||| || ||| |  | || ||||||||||| ||||| | ||||||||| || ||||| ||||| |||||||| || || || |||||
--aggttttaggattaattttttttatcacagtttctccctga--ttaagttgttatgttaacattctaatgttgtac-taatgatattaaattgaataatgcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA

upper sequence: GRMZM2G124883_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 13
-------------------------------gtatatcttaactcttaagtatgttattaatggt--ctaatctaaaatttaaaagttgtatcattggatattgctcacaaagttttcttacctaatttccagCTGAGGTATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTA
                               |  |||  | | | |||    | |||||| ||||   |  | |  | | |  || ||| ||  |    | |  || | |      | ||   |  |||  ||  ||  |||||   || |  |||||  ||||  |||| |||||||||||||  ||||| || || ||||| |||||||||||||| || |||||||| ||
gtactgcgtttttttttcttttctctttcatgattattattattattattattattattattggtacttgttttctattgttgaaattg-atagtaatgtttaacttatatgtcaatatt--tttctttgtagAGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATA

upper sequence: GRMZM2G124883_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G35130.1 (Glycine max), 3'ss of exon 11
---gtatatcttaactcttaagtat-gttattaatggtctaatctaaaatttaaaagttgtatcattggatattgctcacaaagttttcttacctaatttccagCTGAGGTATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTA
    ||    | |  | || |  |  |||  |     | | |  |   || | ||  || ||   |||     | || |  |  ||   ||   ||||   |||| ||||||| |||||| || ||| |  | || ||||||||||| ||||||| ||||||||| || ||||| ||||| |||||||| || || || |||||
gttttaagattaatttttttaacacagtttctcccttttttagttgttatgttaaccttctaatgttg-----tactaatgatattaaattgaataat--gcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGGTATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA

upper sequence: GRMZM2G124883_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G63640.1 (Arabidopsis thaliana), 3'ss of exon 13
gtatatcttaactcttaagtatgttattaatggtctaatctaaaatttaaaagttgtatcattggatattgctcacaaagttttcttacctaatttccagCTGAGGTATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTA
            | | ||     ||     |  | || | | |   ||      | ||  ||  ||||||  |  |     | | ||| || || |  ||  ||||| ||||  ||||  | |||  | ||  ||||  |||||||||| | |||||| || || |||||||||||||| ||||| || ||||| |||||
-----------gtttaaacctctttccctcttatgtattgttagcgttttcctctataatatatgatattcatatcctgaatctgttatcttatgtagAG--GAGGTTTTCTTAGATACTCGACCATTAATTCGATCCATTCTTGATGGCTATAATGTTTGTATATTTGCCTATGGTCAGACTGGTTCTGGAAAAACTTA

upper sequence: GRMZM2G124883_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G18410.1 (Arabidopsis thaliana), 3'ss of exon 12
----------gtatatcttaa------ctcttaagtatg-ttattaatggtctaatctaaaatttaaa--agttgtatcattggatattgctcacaaagttttcttacctaatttc--cagCTGAGGTATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTA
          || |  || |        |||| | |||  || ||  |||  |  | |    ||   |  | |   |  | |  ||||  || |     || | |    |||||    ||||||||||||| || |||||  ||||||| ||  ||||||||||||| ||||  ||||| || || ||||| |||||||| || ||||| || || |||||
gtgttcttttgtttgcctgaggaatttttcttcaatatactttttgttggattggtgtgttcttgggactaatcaaaaaaattaatat-acttatgtcattgtatcttttaattcttgcagCTGAGGTATTTTCAGATATAAAACCTCTTATTCGATCAGTTCTTGACGGGTACAATGTATGTATCTTTGCATATGGTCAGACAGGATCAGGGAAAACTTA

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: 223

GAAAATGGTGAGATTCTCATCACAAATCCCTTCAAGCAAGGGAAGGATGTGTGTCGAATGTTCAAGTTTAATAAAGTGTTTAATACACATGCTTCTCAAGgtatatctta ... taatttccagCTGAGGTATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 37

GAAAATGGTGAGATTCTCATCACAAATCCCTTCAAGCAAGGGAAGGATGTGTGTCGAATGTTCAAGTTTAATAAAGTGTTTAATACACATGCTTCTCAAGgtatatctta ... taatttccagCTGAGGTATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 29

GAAAATGGTGAGATTCTCATCACAAATCCCTTCAAGCAAGGGAAGGATGTGTGTCGAATGTTCAAGTTTAATAAAGTGTTTAATACACATGCTTCTCAAGgtatatctta ... taatttccagCTGAGGTATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 119

GAAAATGGTGAGATTCTCATCACAAATCCCTTCAAGCAAGGGAAGGATGTGTGTCGAATGTTCAAGTTTAATAAAGTGTTTAATACACATGCTTCTCAAGgtatatctta ... taatttccagCTGAGGTATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaaagttgtatcattggatattgctcacaaagttttcttacctaatttccagCTGAGGTATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTA
                                   ttttcttacct  CT-rich tract
                               aaagtttt  TA-rich tract