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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGAGCCGAAGCGCCGGGCGCCGCGGCTGAACGAGCGCATCCTGTCGTCGCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctcttcctctgacttgttcgggtcgaggagatagatatgtagcgcgctataataaccgacgccttcgccttcgttcgtctctgctctgcag

Basic information

species Zea mays
transcript GRMZM2G026470_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026470_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os05g36260.1 (Oryza sativa), 5'ss of exon 1
GTGGAGCCGAAGCGCCGGGCGCCGCGGCTGAACGAGCGCATCCTGTCGTCGCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctcttcctctgacttgttcgg-gtcgaggagatagatatgtagcgcgctataataaccgacgccttcgccttcgttcgtctctgctctgcag---------------------------------------------------------------
                             ||||||| | ||||| ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||    |   | |  | | | |||||   ||||       |      |       |  |    ||  |  || |  |||  ||  ||  | || ||| |                                                               
-----------------------------GAACGAGAGGATCCTCTCGTCGCTGTCGCGGAGGTCCGTCGCCGCGCACCCGTGGCACGACCTCGAGATCGGCC--CTGATGCTCCCGCCGTGTTCAACGTCgtaagtgcacgccc-tgttcttttgcatcctcctccagctccagcttaattattccgttctttgccgcccggccgctggcgatgatgacagctttgttgcgatgtgtcccgtggtggatttttggcacag

upper sequence: GRMZM2G026470_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ33488 (Selaginella moellendorffii), 5'ss of exon 1
GTGGAGCCGAAGCGCCGGGCGCCGCGGCTGAACGAGCGCATCCTGTCGTCGCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctcttcctctgacttgttcgggtcgaggagatagatatgtagcgcgctataataaccgacgccttcgccttcgttcgtctctgctctgcag-------
                                                 || || ||    | | |||||| ||||| ||||||||||||||||| ||||||  || || ||   ||  || |   | |      | |     ||       ||      | ||||    | |  |||||   | | ||| |   |        
------------------------------------------------GCGATGGCGGACCGATTCGTCGCGGCGCATCCCTGGCACGACCTCGAAATCGgtacgc-tcgtctcgtg--ttctcttgattctcaggctgttcttgcgatcttctcacgcgatcgaccgtcttgt-ttcgtggat-tttgccccaaaaccccaag

upper sequence: GRMZM2G026470_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ27219 (Selaginella moellendorffii), 5'ss of exon 1
GTGGAGCCGAAGC--GCCGGGCGCCGCGGCTGAACGAGCGCATCCTGTCGTCGCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctcttcctctgacttgttcgggtcgaggagatagatatgtagcgcgctataataaccgacgccttcgccttcgttcgtctctgctctgcag
| | |  ||      |||    |||   ||| ||| |||||||||| |||||||| || ||  | |||||||| ||||| ||||||||||| ||||| |||||| |  || | | |||   ||| |    || |  |   ||  | | | ||| |    | |  | | |  ||  |||| |                  
GCGAACTCGGGTTCTGCCAAAAGCCC--GCTTAACAAGCGCATCCTCTCGTCGCTCTCCCGCCGCTCCGTCGCGGCGCATCCCTGGCACGATCTCGAAATCGgtaaagct-tgcgtctttgttgcttctttcaa--atgcaggaaggaatcgctc----acacacaatgttttttccttag------------------

upper sequence: GRMZM2G026470_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ33440 (Selaginella moellendorffii), 5'ss of exon 1
GTGGAGCCGAAGC--GCCGGGCGCCGCGGCTGAACGAGCGCATCCTGTCGTCGCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctcttcctctgacttgttcgggtcgaggagatagatatgtagcgcgctataataaccgacgccttcgccttcgttcgtctctgctctgcag
| | |  ||      |||    |||   ||| ||| |||||||||| |||||||| || ||  | |||||||| ||||| ||||||||||| ||||| |||||| |  || | | |||   ||| |    || |  |   ||  | | | ||| |    | |  | | |  ||  |||  |                  
GCGAACTCGGGTTCTGCCAAAAGCCC--GCTTAACAAGCGCATCCTCTCGTCGCTCTCCCGCCGCTCCGTCGCGGCGCATCCCTGGCACGATCTCGAAATCGgtaaagct-tgcgtctttgttgcttctttcaa--atgcaggaaggaaccgctc----acacacaatgttttttcctcag------------------

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|71331881|gb|DR802819.1|DR802819
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTC
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC
EST: gi|18964263|gb|BM660906.1|BM660906
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGC-CGACCTCGAGATCG                         GTCCTGAAGC-CCGGCCGTCTTCAACGTC
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC
EST: gi|19272573|gb|BM888829.1|BM888829
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTC
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC
EST: gi|101385554|gb|EB814824.1|EB814824
EST:     GCTGACGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGCC
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC
EST: gi|60352307|gb|DN219280.1|DN219280
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTC
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC
EST: gi|22490296|gb|BU050219.1|BU050219
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTC
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC
EST: gi|18964037|gb|BM660771.1|BM660771
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTC
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC
EST: gi|19821815|gb|BQ047839.1|BQ047839
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTC
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC
EST: gi|18964956|gb|BM661307.1|BM661307
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTC
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC
EST: gi|87153912|gb|DY398701.1|DY398701
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTCGTCGTG
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTCGTCGTG
EST: gi|211434006|gb|FL392555.1|FL392555
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTC
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC
EST: gi|60400572|gb|DN233379.1|DN233379
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTC
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC
EST: gi|19351415|gb|BM895962.1|BM895962
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTC-AGATCG                         GTCCTGAAGCCCCGGCCGTCTTCAACGTC
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC
EST: gi|19057948|gb|BM736615.1|BM736615
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCC-GGCACGACCTCGAGATCG                         GTCCTGAAGC-CCGGCCGTCTTCAACGTC
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC
EST: gi|211493592|gb|FL394893.1|FL394893
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTC
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC
EST: gi|18964261|gb|BM660905.1|BM660905
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTC
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC
EST: gi|211063429|gb|FL406496.1|FL406496
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTC
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC
EST: gi|60344571|gb|DN211544.1|DN211544
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTC
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC
EST: gi|20300766|gb|BQ163709.1|BQ163709
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTC
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC

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), 29 (downstream exon)
Score: 21

GTGGAGCCGAAGCGCCGGGCGCCGCGGCTGAACGAGCGCATCCTGTCGTCGCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 324

GTGGAGCCGAAGCGCCGGGCGCCGCGGCTGAACGAGCGCATCCTGTCGTCGCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 337

GTGGAGCCGAAGCGCCGGGCGCCGCGGCTGAACGAGCGCATCCTGTCGTCGCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 46

GTGGAGCCGAAGCGCCGGGCGCCGCGGCTGAACGAGCGCATCCTGTCGTCGCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTC


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGAGCCGAAGCGCCGGGCGCCGCGGCTGAACGAGCGCATCCTGTCGTCGCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctcttcctctgacttgttcgggtcgaggagatagatatgtagcgcgctataataaccgacgccttcgccttcgttcgtctctgctctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC