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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCAGAAGAGCCAGCAGGTCACCGACGCCGTCGTCTCCATACTCGGCTCCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcctcacccactcgttcgctcggcgccgccttcgtctctcttgatcttactgctagggctccccgcgtcactgcctctggattggtgctctgatgctgctgctgcttctgccgttgcttcgtctgggcgcag

Basic information

species Zea mays
transcript GRMZM2G046590_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046590_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 1
GCTGCAGAAGAGCCAGCAGGTCACCGACGCCGTCGTCTCCATACTCGGCTCCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcctcacccactcgttcgctcggcgccgccttcgtctctcttgatcttactgctagggctccccgcgtcactgcctctggattggtgctctgatgctgctgctgct--tctgccgttgctt---cgtctgggcgcag
||||||||||||||||   || |||||||||||||||||||| |||||||||||||||||||||||| ||||||||||| |||||||||||||||||||||| | ||| ||| |      | ||||||  |||| ||  |  ||| ||   || ||  | |     || |||  | | | | ||| |  || || |||||||| |||||  ||  ||||| | ||  |     | || | ||||
GCTGCAGAAGAGCCAGTCCGTGACCGACGCCGTCGTCTCCATCCTCGGCTCCTTCGACAGCCGCCTCTCCGCGCTCGACGCCGCCATGCGCCCCATCCAGgtacacctgctctctgctctgctcgctcctcgccccccccccctc-ctccctcctagggttc---ttcgccgtttgattccttctaggctgctgttctgatgccgctgcctctcctctgctgctgtgtgcatatgtgtgtgcag

upper sequence: GRMZM2G046590_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA10G23810.1 (Glycine max), 5'ss of exon 1
GCTGCAGAAGAGCCAGCAGGTCACCGACGCCGTCGTCTCCATACTCGGCTCCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcctcacccactcgttcgctcggcgccgccttcgtctctcttgatcttactgctagggctccccgcgtcactgcctctggattggtgctctgatgctgctgctgcttctgccgttgcttcgtctgggcgcag
 ||| |||  ||||||    |||| |||| |||||| || || ||||||||||||||   ||||||| |||| |||||  ||||||||||||||| ||||||    |||  ||| ||     ||| |          |  |||| |  |  | ||    | |         ||    ||   |   ||||    |  ||| |                                     
TCTGGAGAGAAGCCAGGCCATCACGGACGACGTCGTTTCGATTCTCGGCTCCTTCGATCACCGCCTCTCCGCCCTCGAAACCGCCATGCGCCCCACCCAGgtcgctctctccactca--aaatcggttcttttgaattgggtctttgctagtttt----cgaaaaaaaaaagctgttctttattgtgattttgaccgtgacgtcaa---------------------------------

upper sequence: GRMZM2G046590_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv08s0007g02340.t01 (Vitis vinifera), 5'ss of exon 1
GCTGCAGAAGAGCCAGCAGGTCACCGACGCCGTCGTCTCCATACTCGGCTCCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcctcacccactcgttcgctcggcgccgccttcgtctctcttgatcttactgctagggctccccgcgtcactgcctctggattg-gtgctctgatgctgctgctgcttctgccgttgcttcgtctgggcgcag
 ||||| |||||||||    |||| ||     | ||| |||| |||||||||||||||  ||||||| |||| |||||  |||||||||| ||||  ||||||    || |||    |||  ||| | ||           | ||  |  |   | | |  | ||    |      |  |      ||||| | ||| |     | ||| |  ||                         
TCTGCAAAAGAGCCAGACCATCACGGATAGTATGGTCGCCATTCTCGGCTCCTTCGACCACCGCCTCTCCGCTCTCGAAACCGCCATGCGTCCCACTCAGgtgt--ttcttcattttctc-ctcgtttgg-----------tttccgtgaaaaattcaggaaagga---caagaaaatggaaagaagattgcgggctttatgagttctgttttttga-----------------------

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|211425858|gb|FL143031.1|FL143031
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|71438744|gb|DR819794.1|DR819794
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|211425857|gb|FL143030.1|FL143030
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|211425849|gb|FL143022.1|FL143022
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|211428442|gb|FL143033.1|FL143033
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|160481670|gb|EY254240.1|EY254240
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|211425850|gb|FL143023.1|FL143023
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|211425855|gb|FL143028.1|FL143028
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|149098030|gb|EE183977.2|EE183977
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGACCATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|148983420|gb|EE029420.2|EE029420
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|211425851|gb|FL143024.1|FL143024
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|149103987|gb|EE289410.2|EE289410
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|211425859|gb|FL143032.1|FL143032
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|78117266|gb|DV535653.1|DV535653
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|211425854|gb|FL143027.1|FL143027
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|211428443|gb|FL143034.1|FL143034
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|211425856|gb|FL143029.1|FL143029
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|211425853|gb|FL143026.1|FL143026
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|211425852|gb|FL143025.1|FL143025
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|149089875|gb|EE179160.2|EE179160
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|149088666|gb|EE177784.2|EE177784
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
EST: gi|149090520|gb|EE179830.2|EE179830
EST:     CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAG                         GTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG
genomic: CCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTG

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: 254

GCTGCAGAAGAGCCAGCAGGTCACCGACGCCGTCGTCTCCATACTCGGCTCCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 206

GCTGCAGAAGAGCCAGCAGGTCACCGACGCCGTCGTCTCCATACTCGGCTCCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 145

GCTGCAGAAGAGCCAGCAGGTCACCGACGCCGTCGTCTCCATACTCGGCTCCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 254

GCTGCAGAAGAGCCAGCAGGTCACCGACGCCGTCGTCTCCATACTCGGCTCCTTCGACAGCCGCCTCACCGCGCTCGACTCCGCCATGCGCCCCATCCAGgtgcgcctcc ... ctgggcgcagGTGAGGACGCACGCCGTTCGGACCGCGCACGAGAACATCGACCGCACGCTGCGCTCCGCGGATGTGATCCTCACCCAGTTCGACAGGACCCGAGAG