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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCATGCTGGTCTTCTGAATCTATGCATTGTTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAGgtttattactttctttcttttttcattttcctcaccttcatttacagatccctcaatccatctccttctgaaatacatctggtcttcttcctgcgcatttgtctagtgtaaatctgacacattctgtgttttatttaaattggctggtgcag

Basic information

species Zea mays
transcript GRMZM2G169089_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169089_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g36800.1 (Oryza sativa), 5'ss of exon 2
AGCCATGCTGGTCTTCTGAATCTATGCATTGTTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAGgtttattac--tttctttcttttttcattttcctcaccttcatttacagatccctcaatccatctccttctgaaatacatctggtcttcttcctgcgcatttgtctagtgtaaatctgacacattctgtgttttatttaaattggctggtgcag
|||||||| || |||||||| |||||||||||||| ||| | || |||||||||||||| |||||||||||||||||||||||| ||||   |||||| || | || ||||||| ||        ||    |  || | |  ||    ||||           |   | | || ||   |||    ||||    || | || ||||||     |||| |  ||| || | |||||
AGCCATGCAGGCCTTCTGAACCTATGCATTGTTGTGCTGGTTGCTGTGAACAGCAGACTTATTATTGAGAATTTAATGAAGgttcattatcatttcttgctctctttattttccccagggagtagtagcatttacttattatatgcttttct----------cgacatgcctcttgtctatta---tagttctgatttaactcattct---cattatctgtatttgccgctgcag

upper sequence: GRMZM2G169089_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA09G07520.1 (Glycine max), 5'ss of exon 2
AGCCATGCTGGTCTTCTGAATCTATGCATTGTTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAGgtttattactttctttcttttttcattttcctcaccttcatttacagatccctcaatccatctccttctgaaatacatctggtcttcttcctgcgcatttgtctagtgtaaatctgacacattctgtgttttatttaaattggctggtgcag
|| ||||| || ||  | ||||| ||||| || || ||  | || |||||||||||||| || ||||||||||||||||||||||    |  |||| | | |   ||||| |    ||    |   | ||       |  || |||  ||   || |||      || |   || |||  ||| |    ||| | |       || ||||   |||||  ||     |     
AGTCATGCAGGACTGTTCAATCTCTGCATAGTAGTGCTTGTTGCCGTGAACAGCAGACTTATCATTGAGAATTTAATGAAGgtttgc--ccctcttccctct---atttttcatgtctatcctgcaaaatt------tggatttccaacttgtatgcatgca--tttatctgtgtgcagctgttt----taacttttttgtcatcggtgtgc-atttatgttttgcag-----

upper sequence: GRMZM2G169089_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA13G16560.1 (Glycine max), 5'ss of exon 2
AGCCATGCTGGTCTTCTGAATCTATGCATTGTTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAGgtttattactttctttcttttttcattttcctcaccttcatttacagatccctcaatccatctccttctgaaatacatctggtcttcttcctgcgcatttgtctagtgtaaatctgacacattctgtgttttatttaaattggctggtgcag
|| || || || ||  | || || || || || || ||  | || ||||| ||| ||||||| ||||||||||||||||||||||  | | | ||| | | ||| ||| |     | ||||  | ||        | |   | | ||| |    ||  | ||  |||  |  ||    || |  |  |||   ||||    | |  |||||||||||   |  || |      
AGTCACGCGGGCCTCTTCAACCTCTGTATAGTAGTCCTTGTTGCTGTGAATAGCCGACTCATCATTGAGAATTTAATGAAGgttt--tgcct-cttccatgtttaattgt----gcattcacctgcaa-----caattttctgttctttt----tatttatgaccttgattttgacggttcgggttttgttg-tctgctttaatgagtgttttatttgt-tctgcag------

upper sequence: GRMZM2G169089_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA17G06120.1 (Glycine max), 5'ss of exon 2
AGCCATGCTGGTCTTCTGAATCTATGCATTGTTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAGgtttattactttctttcttttttcattttcctcaccttcatttacagatccctcaatccatctccttctgaaatacatctggtcttcttcctgcgcatttgtctagtgtaaatctgacacattctgtgttttatttaaattggctggtgcag
|| || || || ||  | || || || || || || ||  | || ||||| ||| ||||||| ||||||||||||||||||||||  | |||  |   | |||  ||| |    || ||||  | ||       ||||   |||  |  |    ||  | |||||||  |  ||    ||    |  | |   ||||    | |  |||||||||||   |  || |      
AGTCACGCGGGCCTCTTCAACCTTTGTATAGTAGTCCTTGTTGCTGTGAATAGCCGACTCATCATTGAGAATTTAATGAAGgttt--tgcttcttccatgtttaaattgt----acattcacctgcaa------caatttttctgttcttt---tatttatggtcttgattttgacggttcaggttttattg-tctgctttaatgagtgttttatttgt-tctgcag------

upper sequence: GRMZM2G169089_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S131_22V6.1 (Physcomitrella patens), 5'ss of exon 2
AGCCATGCTGGTCTTCTGAATCTATGCATTGTTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAGgtttattactttctttcttttttcattttcctcaccttcatttacagatccctcaatccatctccttctgaaatacatctggtcttcttcctgcgcatttgtctagtgtaaatctgacacattctgtgttttatttaaattggctggtgcag
|| ||||||||  |  | ||||| || ||||||||| |||| || || |||||| | || ||||||||||| |||||||||||   | ||           ||| ||      ||   |  ||||   |    |   |     |  ||    |   ||||    |||  || ||  | || |   |||||| |  |                                     
AGTCATGCTGGGTTGTTCAATCTCTGTATTGTTGTTTTGATAGCTGTTAACAGCCGGCTTATTATTGAGAACTTAATGAAGgtgagtaacc----------tttgatgactagcattgttgtttatgaagttgtatcttggaatttttggtcagagcatcg---cttactcgtggtctttcg--aagtgtagacat-------------------------------------

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|71768082|gb|DR966019.1|DR966019
EST:     TTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAG                         TATGGCCTGTTGATAAGAGCTGGATTTTGGTTTAGTGCAAGATCGCTGGGT
genomic: TTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAGgtttattact ... gctggtgcagTATGGCCTGTTGATAAGAGCTGGATTTTGGTTTAGTGCAAGATCGCTGGGT
EST: gi|89248515|gb|DY620301.1|DY620301
EST:     TTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAG                         TATGGCCTGTTGATAAGAGCTGGATTTTGGTTTAGTGCAAGATCGCTGGGT
genomic: TTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAGgtttattact ... gctggtgcagTATGGCCTGTTGATAAGAGCTGGATTTTGGTTTAGTGCAAGATCGCTGGGT
EST: gi|101391387|gb|EB817628.1|EB817628
EST:     TTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAG                         TATGGCCTGTTGATAAGAGCTGGATTTTGGTTTAGTGCAAGATCGCTGGGT
genomic: TTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAGgtttattact ... gctggtgcagTATGGCCTGTTGATAAGAGCTGGATTTTGGTTTAGTGCAAGATCGCTGGGT
EST: gi|93015559|gb|EB641079.1|EB641079
EST:     TTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAG                         TATGGCCTGTTGATAAGAGCTGGATTTTGGTTTAGTGCAAGATCGCTGGGT
genomic: TTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAGgtttattact ... gctggtgcagTATGGCCTGTTGATAAGAGCTGGATTTTGGTTTAGTGCAAGATCGCTGGGT
EST: gi|149037287|gb|EE155331.2|EE155331
EST:     TTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAG                         TATGGCCTGTTGATAAGAGCTGGATTTTGGTTTAGTGCAAGATCGCTGGGT
genomic: TTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAGgtttattact ... gctggtgcagTATGGCCTGTTGATAAGAGCTGGATTTTGGTTTAGTGCAAGATCGCTGGGT

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), 48 (downstream exon)
Score: 84

AGCCATGCTGGTCTTCTGAATCTATGCATTGTTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAGgtttattact ... gctggtgcagTATGGCCTGTTGATAAGAGCTGGATTTTGGTTTAGTGCAAGATCGCTGGGTGACTGGCCCCTTCTAATGTGCTG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 58

AGCCATGCTGGTCTTCTGAATCTATGCATTGTTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAGgtttattact ... gctggtgcagTATGGCCTGTTGATAAGAGCTGGATTTTGGTTTAGTGCAAGATCGCTGGGTGACTGGCCCCTTCTAATGTGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

AGCCATGCTGGTCTTCTGAATCTATGCATTGTTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAGgtttattact ... gctggtgcagTATGGCCTGTTGATAAGAGCTGGATTTTGGTTTAGTGCAAGATCGCTGGGTGACTGGCCCCTTCTAATGTGCTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 95

AGCCATGCTGGTCTTCTGAATCTATGCATTGTTGTTCTGATCGCAGTGAACAGCAGACTCATTATTGAGAATTTAATGAAGgtttattact ... gctggtgcagTATGGCCTGTTGATAAGAGCTGGATTTTGGTTTAGTGCAAGATCGCTGGGTGACTGGCCCCTTCTAATGTGCTG