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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGGAGAAGAACGAGAACCACACGCTTTGCCTCAATTCTGCCAAAGCGATCGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGAGGgtaaagaatctcgcctcatttctctcggattttgatgagttacggcaagagatcatcagagcagagctgtcatgaatgtttgcttcattcctttttatag...

Basic information

species Zea mays
transcript GRMZM2G081380_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081380_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g33080.1 (Oryza sativa), 5'ss of exon 3
TTGGGAGAAGAACGAGAACCACACGCTTTGCCTCAATTCTGCCAAAGCGATCGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGAGGgtaaag-------aatctcgcctcatttctctcgg--attttgatgagttacggcaagagatcatcagagcagagctgtcatgaatgtttgcttcattcctttttatag
 ||||||||||||||||||||||| || ||||||||||||||||| || ||||||||||||||||| ||||||||||| || ||||||||||| || ||||||             |||  |   ||||| |     | ||   ||   |       | ||||| || |  ||  |  | | |  | ||| |  || |           
GTGGGAGAAGAACGAGAACCACACCCTCTGCCTCAATTCTGCCAAGGCCATCGGCTGCACTGTCGTGAACATCGGCACGCAGGACCTCGCCGAGGGAAGGgtaggactgcactggactctgcctgtttctttaattcaattccttgtcctcttttgtgtgatcaccacattagtacattaacg--tatttacgacagtatga-------

upper sequence: GRMZM2G081380_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv00s1365g00010.t01 (Vitis vinifera), 5'ss of exon 2
TTGGGAGAAGAACGAGAACCACACGCTTTGCCTCAATTCTGCCAAAGCGATCGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGAGGgtaaagaatctcgcctcatttctctcggattttgatgagttacggcaagagatcatcagagcagagctgtcatgaatgtttgcttcattcctttttatag--
|||||||| ||| || || ||||| || |||||||| ||||||||||| || || || ||||| ||||| ||||| ||||| ||| ||   ||||| |||||| |    |  ||||          | ||  |  |   ||  |    ||  |  | | | |     ||   |     |  | || ||    |  |||    
TTGGGAGAGGAATGAAAATCACACCCTCTGCCTCAACTCTGCCAAAGCTATTGGATGTACTGTGGTCAATATCGGGACACAGGACTTCATTGAAGGAAGGgtatatttgcatgcctttccatatatgaatgct--ttgtttgggagttgaatttttgatatcttgaatgatgttttgatgggttttatcgggtaatatgtct

upper sequence: GRMZM2G081380_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S271_37V6.1 (Physcomitrella patens), 5'ss of exon 1
TTGGGAGAAGAACGAGAACCACACGCTTTGCCTCAATTCTGCCAAAGCGATCGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGAGGgtaaagaatctcgcctcatttctctcggattttgatg-agttacggcaagaga------tcatcagagcagagctgtcat-gaatgtttgcttcattc--ctttttatag-------------------------------------------
 ||||||   |  ||||| ||||| ||||| ||||||||||| ||||| || || ||| |||| |||||||| ||||| |||||| | | ||| || ||||||| || |   ||   |||| |        | |||| |   |  | | ||        |  |  |     |||||   | | |  |||   |  |    |  |  ||||                                           
GTGGGAGCGAATAGAGAATCACACCCTTTGTCTCAATTCTGCTAAAGCTATTGGTTGCTCTGTTGTCAACATTGGCACTCAAGACTTGGGCGACGGAAGGgtaatgactagtgcacgatttttactaaggatagatgtaacgaatgtacgaagcttgtgttgttggttgttagctgatgttggacattttaatggtgtgaccatccatagttggtgcttgatctcattagtcatgatgtgtgggttggtgcag

upper sequence: GRMZM2G081380_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S314_45V6.1 (Physcomitrella patens), 5'ss of exon 4
TTGGGAGAAGAACGAGAACCACACGCTTTGCCTCAATTCTGCCAAAGCGATCGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGAGGgtaaagaatctcgc-ctcatttctctcggat---tttgatgagt-tacggcaagagatcatcagagcagagctgtcatgaatgtttgcttcattcctttttatag----------------------------------------------------------------
 |||||    |  ||||| ||||| |||||||||||||| || ||||| || || ||| |||| |||||||| ||||| || ||| | | ||| || ||||||| ||     || |   ||| | | ||||     | | || | || |  |     |     ||   |  |  | |    ||||   ||| |   ||| |||                                                                  
ATGGGAACGAATAGAGAATCACACACTTTGCCTCAATTCCGCTAAAGCCATTGGATGCTCTGTAGTCAACATTGGCACTCAGGACTTAGGCGACGGAAGGgtaatgacaagtgcacgtctttgtttaggatgaacgtaacgaatatatgaaactttgtatgttgatgtggacaataagacgtgttcttttcgtgaatttgtattagaatgagatggtaaaacacacttcttgcttaattttgtgagtcattttgtgtgggtgaatgcag

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|71313366|gb|DR793232.1|DR793232
EST:     CGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGAAGG                         C-TCATCTGGTCCTGGGCTTAATATCTC
genomic: CGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGA-GGgtaaagaatc ... ttgcttgcagCCTCATCTGGTCCTGGGCTTAATATCTC
EST: gi|148970201|gb|EE021132.2|EE021132
EST:     TCGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGAGG                         CCTCATCTGGTCCTGGGCTTAATATCTCAAATAATCAAG
genomic: TCGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGAGGgtaaagaatc ... ttgcttgcagCCTCATCTGGTCCTGGGCTTAATATCTCAAATAATCAAG

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 17 (downstream exon)
Score: 18

TTGGGAGAAGAACGAGAACCACACGCTTTGCCTCAATTCTGCCAAAGCGATCGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGAGGgtaaagaatc ... ttgcttgcagCCTCATCTGGTCCTGGGCTTAATATCTCAAATAATCAAG


Block sizes: 49 (upstream exon), 29 (downstream exon)
Score: 4

TTGGGAGAAGAACGAGAACCACACGCTTTGCCTCAATTCTGCCAAAGCGATCGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGAGGgtaaagaatc ... ttgcttgcagCCTCATCTGGTCCTGGGCTTAATATCTCAAATAATCAAG


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 9

TTGGGAGAAGAACGAGAACCACACGCTTTGCCTCAATTCTGCCAAAGCGATCGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGAGGgtaaagaatc ... ttgcttgcagCCTCATCTGGTCCTGGGCTTAATATCTCAAATAATCAAG