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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccgccgcctttgcttcccgcacgatctcgatctccgttttcccacctctaacgtctgctgccccgagcactagcctctgattcgatgccatctataccctgcccgcag

Basic information

species Zea mays
transcript GRMZM2G144372_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144372_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 2
TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccgccgcctttgcttcccgcacgatctcgatctccgttttcccacctctaacgtctgctgccccgagcactagcctctgattcgatgccatctataccctgcccgcag
||||||||||| ||||||||||||||||| |||||||| || ||||||||||||||||| |||||||||||  |||    |  || | || ||||    |||||||||||| ||  ||| |  ||  |    | | ||       |  ||| ||| | |                         
TTCAACGTCCCCGATCTCCGCGTCGGCACGCTCGACTCCCTCCTCGCCCTCAGCGACGATCTCGTCAAGgtaacccatctcttctcttctccccg----atctcgatctcccttgccccccagctctcacgcgattcctattattcctgccgctgctgcag-----------------------

upper sequence: GRMZM2G144372_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA16G26220.1 (Glycine max), 5'ss of exon 2
TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccgccgcct-ttgcttcccgcacgatctcgatctccgttttcccacctc-taacgtctgctgccccgagcactagc--ctctgattcgatgccatctataccctgcccgcag---------------------------------------------
|||||  ||||  ||||||| ||||| ||||| ||||| || ||| ||||||||||||| ||||||||||| |   |     ||  |  |       ||  || |  | | ||||      | |  ||  ||         ||   |   |    | || |  |    ||  |   || ||   |                                                
TTCAATATCCCCAATCTCCGGGTCGGAACCCTAGACTCCCTCCTCTCCCTCAGCGACGATCTCGTCAAGgtacgtacaattcccaatcacacgaaaaacattcaccgttttcgttgcgatccttgatattgtggaaaattgcggataaatgtggttatgttgtggctgcaattgcgccttgtttgtttattggtttcattttgcttgatctgtttgtgtgtgtgtgtgtgcag

upper sequence: GRMZM2G144372_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA19G27360.1 (Glycine max), 5'ss of exon 2
TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccgccgcctttgcttcccgcacgatctcgatctccgttttcccacctctaacgtctgctgccccgagcactagcctctgattcgatgccatctataccctgcccgcag
|||||| | ||  | ||||||||||| ||||| ||||| || ||| |||||||||| ||||||| ||||||       |   |||       ||  |  |      |||| | | |  |  |||||   ||   |        |||  || ||   |   |||| ||   ||            
TTCAACATTCCCAACCTCCGCGTCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAGgt-------gaatcctcattccgccaaattacacttttctctgatcttgcgtctcta---tccatttatttattcacctgcttcctctgtaatgc-attattag-----------

upper sequence: GRMZM2G144372_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G07260.1 (Glycine max), 5'ss of exon 2
TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccgccgcctttgcttcccgcacgatctcga---tctccgttt----tcccacctctaacgtctgctgccccgagcactagcctctgattcgatgccatctataccctgcccgcag----------------------------
|||||| ||||  ||||||||||||| ||||| ||||| || ||| |||||||||||||   ||||||||| |  |      ||  |    ||   ||  || |||   | | || ||    | ||    | | | |          ||  | ||       ||  |    ||  |  |   |||  |                               
TTCAACATCCCCAATCTCCGCGTCGGAACCCTAGACTCCCTCCTCTCCCTCAGCGACGATACCGTCAAGgtacgtcaaattcccaatcacaccaaaacattcgcgactatttacggttgcggttccgttgcgatccttgatattgtggaaaattacagataaatgtggctgcaatttcattatgcttgatctgttttctgtgtgtgtgtgttcgtgcag

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|211396453|gb|FL097334.1|FL097334
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGG-GGCAGATC
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATC
EST: gi|211396451|gb|FL097332.1|FL097332
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAG-CAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|71428528|gb|DR809578.1|DR809578
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|211396449|gb|FL097330.1|FL097330
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|67038589|gb|CO464901.1|CO464901
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|211396455|gb|FL097336.1|FL097336
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|13177876|gb|BG349059.1|BG349059
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|211419024|gb|FL311427.1|FL311427
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|89758156|gb|DY687449.1|DY687449
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|148982506|gb|EE028351.2|EE028351
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|211396448|gb|FL097329.1|FL097329
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTMACACAAGATCCGGAG-CAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|76012958|gb|DT940128.1|DT940128
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|67023340|gb|CO452089.1|CO452089
EST:     CGTCGGCACCCTCGACTAGATTGC-GGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: CGTCGGCACCCTCGACTCGCTT-CTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|9824919|gb|BE575016.1|BE575016
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|211396452|gb|FL097333.1|FL097333
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|116818640|gb|EC861688.1|EC861688
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|211396454|gb|FL097335.1|FL097335
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|211396456|gb|FL097337.1|FL097337
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAG-CAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|15312777|gb|BI478368.1|BI478368
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGA
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGA
EST: gi|33104344|gb|CF064304.1|CF064304
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
EST: gi|21987710|gb|BQ779238.1|BQ779238
EST:     GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG                         TCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAG

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), 49 (downstream exon)
Score: 231

TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAGGACCTCGAGCGCGCCGGAGGGGTCGAGAGTGGGACCCTCACCGTCGATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 324

TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAGGACCTCGAGCGCGCCGGAGGGGTCGAGAGTGGGACCCTCACCGTCGATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 295

TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAGGACCTCGAGCGCGCCGGAGGGGTCGAGAGTGGGACCCTCACCGTCGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 312

TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAGgttccccccg ... ctgcccgcagTCCAATGTTTTCGTGGAGGGCGTGTCACACAAGATCCGGAGGCAGATCGAGGACCTCGAGCGCGCCGGAGGGGTCGAGAGTGGGACCCTCACCGTCGATG