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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtccaacattcattccaattcttatctcattgatgccgtaaccgcagttcagtagctaatcctttacccatttttatttgtagACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATATAACAAAGGTGTTCTGAACAATTTTCTAGAGATATTCTGCACTGCTATCC

Basic information

species Zea mays
transcript GRMZM5G821611_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G821611_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 4
gtaggtccaacattcattccaattcttatctcattgatgccgtaaccgcagttcagtagctaatcctttacccatttttatttgtagACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATATAACAAAGGTGTTCTGAACAATTTTCTAGAGATATTCTGCACTGCTATCC
||||||   |  |||  | ||    | || || |  |  |    |   || |||| ||||||||| | || || | ||  |||| ||||||| |||||||| ||||| |||||||| ||| | || | |||||| ||||||| ||| ||||||||||| |||||||||||||||||||    ||| |
gtaggtatta-gttcgattcagcattaatttcctaaacacaacgatttcaattcattagctaatcatgtagccctgttcttttgcagACAACTTATGAGAACTTCAGGTATCGCTACGATAGACGGGCTAACCCGTATAACAGAGGCGTTCTGAACAACTTTCTAGAGATATTCTGCAGCCGTATTC

upper sequence: GRMZM5G821611_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G07190.1 (Glycine max), 3'ss of exon 4
----------gtaggtccaacattcattccaattcttatctcattgatgccgtaaccgcagttcagtagct--aatcctttacccatttttatt-----tgtagACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATATAACAAAGGTGTTCTGAACAATTTTCTAGAGATATTCTGCACTGCTATCC
           |   |  ||  || ||         ||  | |  | |    || |     | ||| |  |  ||   | ||    | || |||     |  |||| ||||||||||| |||||||| || |||||||| || |  ||||| |||||||| || ||  | || |||||  ||||||||||||||||    || |
gtaatcattcctttttaaaatctttatatagtagtataatttaaagttaagctatctatcctacaggacttgcaactttatatttgtgttcattactgttacagACTACATATGAGAACTTCAGATACCGATATGATCGACGGGCCAACCCGTATAACAAGGGAGTGTTCAATAATTTCTTAGAGATATTCTGCACCAGCATTC

upper sequence: GRMZM5G821611_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA19G27160.1 (Glycine max), 3'ss of exon 4
gtaggtccaacattcattccaattcttatctcattgatgccgtaaccgcagttcagtagctaatcctttacccatttttatttgtagACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATATAACAAAGGTGTTCTGAACAATTTTCTAGAGATATTCTGCACTGCTATCC
||| |  ||   ||| ||  ||| |  ||    | | ||       |  |  |   | |||     ||| | |  || |  ||| |||| |||||||| || |||||||| || ||||||||||| |  |||||||||||  |||| ||  |||| |||||   ||||||||||||||     || |
gtaagcaca--gttctttttaatccgcatgctctagctgtt-----cagatgtatatggcttcatatttgctccattattcttgcagACTACATATGAAAACTTCAGATACCGATATGATCGGCGAGCCAACCCATATAATGAAGGAGTGTTGAATAATTTCAAAGAGATATTCTGCATCAGCATTC

upper sequence: GRMZM5G821611_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G05670.2 (Glycine max), 3'ss of exon 4
gtaggtccaacattcattccaattcttatctcattgatgccgtaaccgcagttcagtagctaatcctttacccatttttatttgtagACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATATAACAAAGGTGTTCTGAACAATTTTCTAGAGATATTCTGCACTGCTATCC
||| | ||    ||| ||  ||| |  ||  |  |        |   | | | |||    | ||  ||   ||||| ||  ||| |||| |||||||| || |||||||| || ||||||||||| |  || |||||||| ||||| ||  |||| |||||   ||||||||||||||     ||  
gtaagccc--tgttcgttttaatccacatg-ctctagcttttcagatgta-tacagc--ttcatatttgctccattatt-cttgcagACTACATATGAAAACTTCAGATACCGATATGATCGGCGAGCCAATCCATATAATAAAGGAGTGTTGAATAATTTCAAAGAGATATTCTGCATCAGCATTT

upper sequence: GRMZM5G821611_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G26140.2 (Glycine max), 3'ss of exon 4
----------------gtaggtccaacatt-cattccaattcttatctcattgatgccgtaaccgcagttcagtagctaatcctttacccatttttatttgtagACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATATAACAAAGGTGTTCTGAACAATTTTCTAGAGATATTCTGCACTGCTATCC
                  |      | ||   | |  ||||   |  | | |         || | | ||       ||    | |  |||||  | ||   |||| ||||||||||| |||||||| || |||||||| || |  ||||| ||||||| ||| ||  | || |||||  ||||||||||||||||    || |
gtaatcagtcctttttaaaatctttatatagtagtataatttaaaattaagtatctatcctactggacttgcaactttatatttgtgtccattactgtt-acagACTACATATGAGAACTTCAGATACCGATATGATCGACGGGCCAACCCGTATAACACAGGAGTGTTCAATAATTTCTTAGAGATATTCTGCACCAGCATTC

upper sequence: GRMZM5G821611_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G41060.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaggtccaacattcattccaattcttatctcattgatgccgtaaccgcagttcagtagctaatccttt-acccatttttatt-tgtagACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATATAACAAAGGTGTTCTGAACAATTTTCTAGAGATATTCTGCACTGCTATCC
    || |   | |||||    |  || |   |      |  | |    |  |  ||   ||||| ||| | |  | |||||| ||||||| ||||||||||||||||||||  | ||||||||||     |||||| |||||||||| ||  |  | || ||   ||| || || |   || | || |
----gtaccctaatcatttgcctctttctgaaaaaacctctctcattcgatatgcgtgtttaatcgtttgatctttctttattctgtagACTACATATGAGAATTTCAGATACAGTTATGATCGGCATAGCAACCCACATAACAAAGGAGTGGTTGATAACTTCAAAGAAATCTTTTTTTCTCCAATAC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|9255011|gb|BE345479.1|BE345479
EST:     TTGTGGGTGGTTTATCTGTCTTCCATTTATACCTGATGAGCACTAACCAG                         ACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATAT
genomic: TTGTGGGTGGTTTATCTGTCTTCCATTTATACCTGATGAGCACTAACCAGgtaggtccaa ... ttatttgtagACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATAT
EST: gi|60348094|gb|DN215067.1|DN215067
EST:     TTGTGGGTGGTTTATCTGTCTTCCATTTATACCTGATGAGCACTAACCAG                         ACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATAT
genomic: TTGTGGGTGGTTTATCTGTCTTCCATTTATACCTGATGAGCACTAACCAGgtaggtccaa ... ttatttgtagACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATAT
EST: gi|60356386|gb|DN223359.1|DN223359
EST:     TTGTGGGTGGTTTATCTGTCTTCCATTTATACCTGATGAGCACTAACCAG                         ACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATAT
genomic: TTGTGGGTGGTTTATCTGTCTTCCATTTATACCTGATGAGCACTAACCAGgtaggtccaa ... ttatttgtagACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATAT
EST: gi|89758330|gb|DY687546.1|DY687546
EST:     TTGTGGGTGGTTTATCTGTCTTCCATTTATACCTGATGAGCACTAACCAG                         ACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATAT
genomic: TTGTGGGTGGTTTATCTGTCTTCCATTTATACCTGATGAGCACTAACCAGgtaggtccaa ... ttatttgtagACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATAT

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), 46 (downstream exon)
Score: 493

GACACCAGCATCAGTTGCTCTGATTATCTACTGTTTTCTCTGTGTATGGTTTGTGGGTGGTTTATCTGTCTTCCATTTATACCTGATGAGCACTAACCAGgtaggtccaa ... ttatttgtagACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATATAACAAAGGTGTTCTGAACAATTTTCTAGAGATATTCTGCACTGCTATCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 676

GACACCAGCATCAGTTGCTCTGATTATCTACTGTTTTCTCTGTGTATGGTTTGTGGGTGGTTTATCTGTCTTCCATTTATACCTGATGAGCACTAACCAGgtaggtccaa ... ttatttgtagACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATATAACAAAGGTGTTCTGAACAATTTTCTAGAGATATTCTGCACTGCTATCC


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 633

GACACCAGCATCAGTTGCTCTGATTATCTACTGTTTTCTCTGTGTATGGTTTGTGGGTGGTTTATCTGTCTTCCATTTATACCTGATGAGCACTAACCAGgtaggtccaa ... ttatttgtagACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATATAACAAAGGTGTTCTGAACAATTTTCTAGAGATATTCTGCACTGCTATCC


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 839

GACACCAGCATCAGTTGCTCTGATTATCTACTGTTTTCTCTGTGTATGGTTTGTGGGTGGTTTATCTGTCTTCCATTTATACCTGATGAGCACTAACCAGgtaggtccaa ... ttatttgtagACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATATAACAAAGGTGTTCTGAACAATTTTCTAGAGATATTCTGCACTGCTATCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgatgccgtaaccgcagttcagtagctaatcctttacccatttttatttgtagACAACATATGAGAATTTCAGATATCGCTATGATCGGCGCGATAACCCATATAACAAAGGTGTTCTGAACAATTTTCTAGAGATATTCTGCACTGCTATCC
                         agctaat  putative branch site (score: 839)
                               tcctttacccattttt  CT-rich tract
                                         atttttatttgta  TA-rich tract