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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcggcattctgaatcccctctttcccgcccagctagattgctttgtcaaggtcatagaagtcagcaactgcgtgaaacgttgagttactattaatgattttgagtccgacag

Basic information

species Zea mays
transcript GRMZM2G155543_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155543_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g45190.3 (Oryza sativa), 5'ss of exon 1
-----------------------------TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcggcattctgaatcccctctttcccgcccagctagattgctttgtcaaggtcatagaagtcagcaactgcgtgaaacgtt-----gagttactattaatgattttgagtccgacag--------------------------------
                             ||||||| |||||||||||||| ||||| |||||| |||| ||| |||||||||||||||||| |||||||||||    || ||  |    |||| |         |||| |  | | ||     ||  ||||||  |  | || |  |  |||         ||   |   |||||||  ||     ||  |                                 
CTGATTCTTTTGCTGTTTGGATTGAGCAGTCGAGACGAAGAAGCAGATCTCATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAGgtaa--ctggaatctttttcccccacgaagaaattcagcaatttggtttcacggag--catagagcttgggaattctgcaaaaaaaaaaaaagaaaaaaagttaatgagatttgacgcgctaacgctaaatttggtgaaatgttgtgctccttag

upper sequence: GRMZM2G155543_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g45190.1 (Oryza sativa), 5'ss of exon 2
TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcggcattctgaatcccctctttcccgcccagctagattgctttgtcaaggtcatagaagtcagcaactgcgtgaaacgtt-----gagttactattaatgattttgagtccgacag--------------------------------
||||||| |||||||||||||| ||||| |||||| |||| ||| |||||||||||||||||| |||||||||||    || ||  |    |||| |         |||| |  | | ||     ||  ||||||  |  | || |  |  |||         ||   |   |||||||  ||     ||  |                                 
TCGAGACGAAGAAGCAGATCTCATGCTCCATGCAGCTGACGAACAGAACAGATGACTACATCGCCTTTAAGgtaa--ctggaatctttttcccccacgaagaaattcagcaatttggtttcacggag--catagagcttgggaattctgcaaaaaaaaaaaaagaaaaaaagttaatgagatttgacgcgctaacgctaaatttggtgaaatgttgtgctccttag
















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|211414035|gb|FK970738.1|FK970738
EST:     CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
EST: gi|211416583|gb|FK970749.1|FK970749
EST:     CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
EST: gi|211419127|gb|FK970761.1|FK970761
EST:     CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
EST: gi|211416592|gb|FK970758.1|FK970758
EST:     CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
EST: gi|211416589|gb|FK970755.1|FK970755
EST:     CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
EST: gi|211414037|gb|FK970740.1|FK970740
EST:     CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
EST: gi|211414040|gb|FK970743.1|FK970743
EST:     CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
EST: gi|76935292|gb|DV174281.1|DV174281
EST:     CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
EST: gi|211416580|gb|FK970746.1|FK970746
EST:     CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
EST: gi|211416586|gb|FK970752.1|FK970752
EST:     CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
EST: gi|211416590|gb|FK970756.1|FK970756
EST:     CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
EST: gi|89252124|gb|DY623910.1|DY623910
EST:     CGTGCTCCATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAACAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
EST: gi|211414038|gb|FK970741.1|FK970741
EST:     CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAAACAGCGGCAT
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAA-CAGCGGCAT
EST: gi|211416582|gb|FK970748.1|FK970748
EST:     CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGACCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
EST: gi|211419126|gb|FK970760.1|FK970760
EST:     CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
EST: gi|29543772|gb|CB604152.1|CB604152
EST:     CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
EST: gi|149109099|gb|EE190008.2|EE190008
EST:     CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
EST: gi|211414039|gb|FK970742.1|FK970742
EST:     CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
EST: gi|94478824|gb|EB707782.1|EB707782
EST:     CGTGCTCTATGCAGTTGACAAACCCAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
EST: gi|149104621|gb|EE290069.2|EE290069
EST:     CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
EST: gi|211416578|gb|FK970744.1|FK970744
EST:     CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAG                         GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC
genomic: CGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATC

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), 42 (downstream exon)
Score: 285

TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATCGTGCCACCTCGGTCCACCAGCGATGTCATTG


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 109

TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATCGTGCCACCTCGGTCCACCAGCGATGTCATTG


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 127

TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATCGTGCCACCTCGGTCCACCAGCGATGTCATTG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 124

TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcgg ... agtccgacagGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATCGTGCCACCTCGGTCCACCAGCGATGTCATTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGAGACAAAGAAGCAGATCTCGTGCTCTATGCAGTTGACAAACCGAACAGATGACTACATCGGCTTTAAGgtaagctcggcattctgaatcccctctttcccgcccagctagattgctttgtcaaggtcatagaagtcagcaactgcgtgaaacgttgagttactattaatgattttgagtccgacag

- - - - - - - - - - - - - - - - - - - - - - - - CAGATG