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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcgatctcttagcacccatttcactcgtgaaaaatgccgccgaactgcatttcaaccttgttctcttcctgtttcctcag

Basic information

species Zea mays
transcript GRMZM2G155384_T01
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155384_T01 (Zea mays), 5'ss of exon 22
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 5'ss of exon 22
-----AATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcgatctcttagcacccatttcactcgtgaaaaatgccgccgaactgcatttcaaccttgttctcttcctgtttcctcag
     |||||| || || ||||| ||||| || ||||| |||||||| || |||||||||||||| ||  | ||||| || ||||||||||| | |      |||  |   || ||          ||  |    ||    | | |  |  | || | ||   || |      
GTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTCTCTCCATACCATTCTGACCGGTTTCTACTTTCCCCgtgagtatag-----ctagtgctatttacatctactgtttattgcattcaatattaatccttcaattttttgtttgggtgtag----
















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|32929670|gb|CF034482.1|CF034482
EST:     GGCTTGGTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
EST: gi|32926108|gb|CF030920.1|CF030920
EST:     GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
EST: gi|32841969|gb|CD981650.1|CD981650
EST:     GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
EST: gi|211100368|gb|FL070846.1|FL070846
EST:     GGCTTGTTGACCCTTTCCCCATACCATTCCGATAGATTTCTTCTCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
EST: gi|32926755|gb|CF031567.1|CF031567
EST:     GGCTTGGTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGGTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
EST: gi|211100372|gb|FL070850.1|FL070850
EST:     GGCTTGTTGACCCTTTCCCCATACCATTCCGATAGATTTCTTCTCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
EST: gi|32925375|gb|CF030187.1|CF030187
EST:     GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
EST: gi|32867559|gb|CF007241.1|CF007241
EST:     GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
EST: gi|32925086|gb|CF029898.1|CF029898
EST:     GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
EST: gi|211100371|gb|FL070849.1|FL070849
EST:     GGCTTGTTGACCCYTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
EST: gi|32925553|gb|CF030365.1|CF030365
EST:     GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
EST: gi|60347371|gb|DN214344.1|DN214344
EST:     GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
EST: gi|32926620|gb|CF031432.1|CF031432
EST:     GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
EST: gi|211100370|gb|FL070848.1|FL070848
EST:     GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
EST: gi|32849654|gb|CD989335.1|CD989335
EST:     GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
EST: gi|32908274|gb|CF013087.1|CF013087
EST:     GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC                         GATGGCACTTGGGGGCCTT
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTT
EST: gi|32928954|gb|CF033766.1|CF033766
EST:     GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCCCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGGTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
EST: gi|32841970|gb|CD981651.1|CD981651
EST:     GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
EST: gi|32925292|gb|CF030104.1|CF030104
EST:     GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
EST: gi|32928817|gb|CF033629.1|CF033629
EST:     GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
EST: gi|32925632|gb|CF030444.1|CF030444
EST:     GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC                         GATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA
genomic: GGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAA

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: 47 (upstream exon), 49 (downstream exon)
Score: 223

AATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAAGTCCACCATCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 131

AATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAAGTCCACCATCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 74

AATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAAGTCCACCATCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

AATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcg ... gtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAAGTCCACCATCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCCgtgagtgtcgatctcttagcacccatttcactcgtgaaaaatgccgccgaactgcatttcaaccttgttctcttcctgtttcctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC