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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgataatttcctctcttttcatcaattgtggccagtaatccagtataatcctatcttgacaatatattgacttacacagaattcattctacagATTGCTATGAGGTCTCCTCACACAAACTTAGCATTCCAGAAAATCTTTTCTTTGCCACCAGAAGAATTTCTTATCAATGATTTTACTTGTCACTTAAAGA

Basic information

species Zea mays
transcript GRMZM2G005195_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005195_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g19400.1 (Oryza sativa), 3'ss of exon 4
gtgataatttcctctcttttcatcaattgtggccagtaatccagtataatcctatcttgaca-atatattgacttacacagaattcattctacagATTGCTATGAGGTCTCCTCACACAAACTTAGCATTCCAGAAAATCTTTTCTTTGCCACCAGAAGAATTTCTTATCAATGATTTTACTTGTCACTTAAAGA
    ||||   ||    ||   || ||| | |   |   |  ||| | ||||||||||| |     | ||  ||||  || |||| |   | ||||||||| | |||||||| |||||||||| |||||||||||| ||||||||||||||||||||||||||||| |||||||||||||| |||||  ||||| 
---gtaatgcacttatcttc--tctatttttgagtgaggtgaagtgtcatcctatcttggcctgcctcttttcttatgca-aatttaccatgcagATTGCTGTAAGGTCTCCACACACAAACTCAGCATTCCAGAAGATCTTTTCTTTGCCACCAGAAGAATTTCTAATCAATGATTTTACCTGTCATCTAAAGC

upper sequence: GRMZM2G005195_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgataatttcctctcttttcatcaattgtggccagtaatcca-gtataatcctatcttgacaatatattgacttac--acagaattcattctacagATTGCTATGAGGTCTCCTCACACAAACTTAGCATTCCAGAAAATCTTTTCTTTGCCACCAGAAGAATTTCTTATCAATGATTTTACTTGTCACTTAAAGA
            | | |    |  | ||    |    |||| |  ||||| |   |  ||    |       ||||    | ||||  |   | ||||||  | || |||||||||| ||||| | ||| || |||||  |||||  | | |||| |||||||||||| |||||||| ||||| |||||||||||| 
-----------gtatgtggctacgactttgttctctcaatcaacatataaactggtagtgttgttgcgcgttcttatctgctgaatggaaatttcagATTAATGTGCGGTCTCCTCAAACAAATTCAGCTTTTCAGAAGCTCTTTGGTCTCCCACAAGAAGAATTTCTAATCAATGACTTTACATGTCACTTAAAGC

upper sequence: GRMZM2G005195_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 4
----gtgataatttcctctcttttca---tcaatt---gtggccagtaatccagtataatcctatcttgacaatatattgacttacacagaatt---------cattcta--cagATTGCTATGAGGTCTCCTCACACAAACTTAGCATTCCAGAAAATCTTTTCTTTGCCACCAGAAGAATTTCTTATCAATGATTTTACTTGTCACTTAAAGA
     |||  |  |  | |  | | |   ||| ||   | ||  | ||      | |  ||  |  ||        ||| |||| | ||  |||         |||| ||  |||||     ||||||||||||| ||||| |  ||||| |||||| |||||    | |||||||| |||||||| ||||||||||||||||||||||| ||  
gtaaatgactagcttttatggtcttaaattcactttgtgaggggactatgtttatgtgttctgactttcttgtctgatttacttgctcattatttcctgatgacattgtatgcagATAAACTTGAGGTCTCCTCAAACAAATTCGGCATTTCAGAAACTCTTTGGACTTCCACCAGAGGAATTTCTCATCAATGATTTTACTTGTCACTTGAAAC

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|211352921|gb|FL033082.1|FL033082
EST:     AAGTCGTGAAGGATTACCTGGATAAAGTGGAGAAAGAAGTTGGCAAAAAG                         ATTGCTATGAGGTCTCCTCACACAAACTTAGCATTCCAGAAAATCTTTTCT
genomic: AAGTCGTGAAGGATTACCTGGATAAAGTGGAGAAAGAAGTTGGCAAAAAGgtgataattt ... cattctacagATTGCTATGAGGTCTCCTCACACAAACTTAGCATTCCAGAAAATCTTTTCT
EST: gi|24934560|gb|CA452778.1|CA452778
EST:     AAGTCGTGAAGGATTACCTGGATAAAGTGGAGAAAGAAGTTGGCAAAAAG                         ATTGCTATGAGGTCTCCTCACACAAACTTAGCATTCCAGAAAATCTTTTCT
genomic: AAGTCGTGAAGGATTACCTGGATAAAGTGGAGAAAGAAGTTGGCAAAAAGgtgataattt ... cattctacagATTGCTATGAGGTCTCCTCACACAAACTTAGCATTCCAGAAAATCTTTTCT
EST: gi|211352922|gb|FL033083.1|FL033083
EST:     AAGTCGTGAAGGATTACCTGGATAAAGTGGAGAAAGAAGTTGGCAAAAAG                         ATTGCTATGAGGTCTCCTCACACAAACTTANCATTCCAGAAAATCTTTTCT
genomic: AAGTCGTGAAGGATTACCTGGATAAAGTGGAGAAAGAAGTTGGCAAAAAGgtgataattt ... cattctacagATTGCTATGAGGTCTCCTCACACAAACTTAGCATTCCAGAAAATCTTTTCT

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: 18 (upstream exon), 49 (downstream exon)
Score: 4

CCAGTCAAAATTGCATCTAAGAATCTTCTTAAACAATACAAGGGGTACTGAAGTCGTGAAGGATTACCTGGATAAAGTGGAGAAAGAAGTTGGCAAAAAGgtgataattt ... cattctacagATTGCTATGAGGTCTCCTCACACAAACTTAGCATTCCAGAAAATCTTTTCTTTGCCACCAGAAGAATTTCTTATCAATGATTTTACTTGTCACTTAAAGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 53

CCAGTCAAAATTGCATCTAAGAATCTTCTTAAACAATACAAGGGGTACTGAAGTCGTGAAGGATTACCTGGATAAAGTGGAGAAAGAAGTTGGCAAAAAGgtgataattt ... cattctacagATTGCTATGAGGTCTCCTCACACAAACTTAGCATTCCAGAAAATCTTTTCTTTGCCACCAGAAGAATTTCTTATCAATGATTTTACTTGTCACTTAAAGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 72

CCAGTCAAAATTGCATCTAAGAATCTTCTTAAACAATACAAGGGGTACTGAAGTCGTGAAGGATTACCTGGATAAAGTGGAGAAAGAAGTTGGCAAAAAGgtgataattt ... cattctacagATTGCTATGAGGTCTCCTCACACAAACTTAGCATTCCAGAAAATCTTTTCTTTGCCACCAGAAGAATTTCTTATCAATGATTTTACTTGTCACTTAAAGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 52

CCAGTCAAAATTGCATCTAAGAATCTTCTTAAACAATACAAGGGGTACTGAAGTCGTGAAGGATTACCTGGATAAAGTGGAGAAAGAAGTTGGCAAAAAGgtgataattt ... cattctacagATTGCTATGAGGTCTCCTCACACAAACTTAGCATTCCAGAAAATCTTTTCTTTGCCACCAGAAGAATTTCTTATCAATGATTTTACTTGTCACTTAAAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccagtataatcctatcttgacaatatattgacttacacagaattcattctacagATTGCTATGAGGTCTCCTCACACAAACTTAGCATTCCAGAAAATCTTTTCTTTGCCACCAGAAGAATTTCTTATCAATGATTTTACTTGTCACTTAAAGA
                              gacttac  putative branch site (score: 52)
                                           ttcattct  putative PPT
                      aatatattgactta  TA-rich tract