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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCAACAGCCTCCCAGGCTACAAGACCAGATACGATGATGTTAACCTTGTGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattcttaaagagatgttgcttcaattattgtcagtttgtcagcatgattctttttcaccctgtcctagtttcgctccag

Basic information

species Zea mays
transcript GRMZM2G404855_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G404855_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 5'ss of exon 4
TTGCAACAGCCTCCCAGGCTACAAGACCAGATACGATGATGTTAACCTTGTGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattcttaaa-gagatgttgcttcaattattgtcagtttgtcagcatgattctttttcaccctgtcctagtttcgctccag
|||||||||||||||||| ||||||||  |||| |||||||| ||||||||||| |||||||||||||| || |||||||||||||| ||||||||||||||||||||||||||| |  || |   ||  |||  |      |||| ||||| |||| |   |||  ||| ||| ||   ||||||
TTGCAACAGCCTCCCAGGATACAAGACTCGATATGATGATGTGAACCTTGTGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattcttaaaagcaatatcattttcattggt-----cttgttagcattattcat---cactgtgtgctatttattctccag

upper sequence: GRMZM2G404855_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G06590.2 (Glycine max), 5'ss of exon 2
TTGCAACAGCCTCCCAGGCTACAAGACCAGATACGATGATGTTAACCTTGTGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattctta-aagagatgttgctt-caattattgtcagtttg-tcagcatgattctttttcaccctgtcctagtttcgctccag
|||| |||| || ||||||||||| ||  |||| ||| |||| || ||  | ||||||||||||||||| ||||| || || ||||| ||||| ||||||||||   |    | ||  |||||| | | | || ||| | | | || |||  || |||  | || | | | |    || ||       
TTGCTACAGTCTTCCAGGCTACAAAACTCGATATGATAATGTCAATCTAATTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttcacaacaattgatgttacatactatcattttaattctgatcaatataatt--tgtttagcatttatgggtctcag-----

upper sequence: GRMZM2G404855_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA13G20790.1 (Glycine max), 5'ss of exon 2
TTGCAACAGCCTCCCAGGCTACAAGACCAGATACGATGATGTTAACCTTGTGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattcttaaagagatgttgcttcaattattgtcag----tttgtcagcatgattctttttcaccctgtcctagtttcgctccag
|||| |||| || ||||||||||| ||  | || ||| |||| || ||  | ||||||||||||||||| ||||| || || ||||| ||||| ||||||||||  |||    || |  |  |||    | |||  || |     |  |||  || |||  | || | | | |    |||||       
TTGCTACAGTCTTCCAGGCTACAAAACTCGGTATGATAATGTCAATCTAATCACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaa--atttcacaacaatttatgcacgtactatcatctgaattctgatcaatataatt--tgtttagcatttttgggtttcag-----

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|6166676|gb|AW144940.1|AW144940
EST:     TGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGT
genomic: TGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... ttcgctccagGTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGT
EST: gi|60354405|gb|DN221378.1|DN221378
EST:     TGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGT
genomic: TGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... ttcgctccagGTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGT
EST: gi|6166632|gb|AW144896.1|AW144896
EST:     TGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGT
genomic: TGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... ttcgctccagGTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGT
EST: gi|6952333|gb|AW424401.1|AW424401
EST:     TGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGT
genomic: TGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... ttcgctccagGTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGT
EST: gi|6166631|gb|AW144895.1|AW144895
EST:     TGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGT
genomic: TGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... ttcgctccagGTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGT
EST: gi|6195048|gb|AW147152.1|AW147152
EST:     TGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGT
genomic: TGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... ttcgctccagGTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGT
EST: gi|6827805|gb|AW331448.1|AW331448
EST:     TGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGT
genomic: TGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... ttcgctccagGTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGT

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), 47 (downstream exon)
Score: 60

TTGCAACAGCCTCCCAGGCTACAAGACCAGATACGATGATGTTAACCTTGTGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... ttcgctccagGTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGTTTGAGAGTGGCAGAATATGCTTTTCATTATGCCAAGGCCAATGGCCGGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 112

TTGCAACAGCCTCCCAGGCTACAAGACCAGATACGATGATGTTAACCTTGTGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... ttcgctccagGTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGTTTGAGAGTGGCAGAATATGCTTTTCATTATGCCAAGGCCAATGGCCGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 80

TTGCAACAGCCTCCCAGGCTACAAGACCAGATACGATGATGTTAACCTTGTGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... ttcgctccagGTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGTTTGAGAGTGGCAGAATATGCTTTTCATTATGCCAAGGCCAATGGCCGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

TTGCAACAGCCTCCCAGGCTACAAGACCAGATACGATGATGTTAACCTTGTGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... ttcgctccagGTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGTTTGAGAGTGGCAGAATATGCTTTTCATTATGCCAAGGCCAATGGCCGGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCAACAGCCTCCCAGGCTACAAGACCAGATACGATGATGTTAACCTTGTGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattcttaaagagatgttgcttcaattattgtcagtttgtcagcatgattctttttcaccctgtcctagtttcgctccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA