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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGTTCAACTTTGTTAATGGTATCGAGCTAGTTTGCCGGGCTCACCAGCTGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACTgtgagttctcgttcacatatagattgacacccagatattgtgtagtattctactatagtagtatacatttgtatttcagtgtgaccatattgaattgttatgatgcccatattaacgtatcttttgttctccag

Basic information

species Zea mays
transcript GRMZM2G518717_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G518717_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 8
GCAGTTCAACTTTGTTAATGGTATCGAGCTAGTTTGCCGGGCTCACCAGCTGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACTgtgagttctcgttcacatatagattgacacccagatattgtgtagtattctactatagtagtatacatttgtatttcagtgtgaccatattgaattgttatgatgcccatattaacgtatcttttgttctccag
    ||||||  | ||||   | |||| ||||||||||| |||||||||||||| ||||||||||||||||||||||| ||||| || |||||||||||||| ||||   |||||||| |   |      ||||||| |   ||| ||| |||||   | ||||   |||   ||||| |      |||||||  || |   || |||    |    || |||||    |||||
----TTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttctgttcacatgtcagt------ccagataat-catagcattgtactaagcttgtatttcttt---tttcaatactgttatattga--tgctcacataccc----tgcaatacctttt---ttccag

upper sequence: GRMZM2G518717_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT3G19980.1 (Arabidopsis thaliana), 5'ss of exon 8
GCAGTTCAACTTTGTTAATGGTATCGAGCTAGTTTGCCGGGCTCACCAGCTGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACTgtgagttctcgttcacatatagattgacacccagatattgtgtagtattctactatagtagtatacatttgt--atttcagtgtgaccatattgaattgttatgatgcccatattaacgtatcttttgttctccag
    || |||  | | ||     | || ||||| ||||| || ||||| || || || |||||  | |||||||||||||| || || ||||||||||||||||||   |     |  ||  ||||| |      ||||     |  || |   |   |  |      ||||  ||||   | ||    |   |                                          
----TTTAACCATATCAACAAGCTGGATCTAGTATGCCGCGCGCACCAACTTGTACAAGAAGGTCTTAAGTACATGTTCCAAGATAAAGGCCTTGTAACTgtgagtgtcctgcttctaatgaattgatattttt-tattagtgggcgttttgaaactctgcttagtgattgttaattttgttttgtttgtgaag------------------------------------------
















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|60342747|gb|DN209720.1|DN209720
EST:     TGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACT                         GTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATA
genomic: TGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACTgtgagttctc ... tgttctccagGTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATA
EST: gi|15100292|gb|BI396083.1|BI396083
EST:     GGGCCTTGTAACT                         GTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATA
genomic: GGGCCTTGTAACTgtgagttctc ... tgttctccagGTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATA
EST: gi|13198328|gb|BG354266.1|BG354266
EST:     CAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACT                         GTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATA
genomic: CAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACTgtgagttctc ... tgttctccagGTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATA
EST: gi|37390257|gb|CF632357.1|CF632357
EST:     TGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACT                         GTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATA
genomic: TGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACTgtgagttctc ... tgttctccagGTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATA
EST: gi|15079375|gb|BI388689.1|BI388689
EST:     TGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACT                         GTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATA
genomic: TGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACTgtgagttctc ... tgttctccagGTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATA
EST: gi|32938506|gb|CF043325.1|CF043325
EST:     ACATGTTCCAGGAGAAGGGCCTTGTAACT                         GTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATA
genomic: ACATGTTCCAGGAGAAGGGCCTTGTAACTgtgagttctc ... tgttctccagGTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATA
EST: gi|211507416|gb|FL430849.1|FL430849
EST:     TGGTCCTGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACT                         GTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATA
genomic: TGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACTgtgagttctc ... tgttctccagGTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATA
EST: gi|5791300|gb|AI978092.1|AI978092
EST:     TGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACT                         GTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATA
genomic: TGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACTgtgagttctc ... tgttctccagGTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATA
EST: gi|6056953|gb|AW091358.1|AW091358
EST:     TGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACT                         GTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATA
genomic: TGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACTgtgagttctc ... tgttctccagGTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATA

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: 48 (upstream exon), 48 (downstream exon)
Score: 139

GCAGTTCAACTTTGTTAATGGTATCGAGCTAGTTTGCCGGGCTCACCAGCTGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACTgtgagttctc ... tgttctccagGTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATATTAAGCTTCGATGAGAAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 148

GCAGTTCAACTTTGTTAATGGTATCGAGCTAGTTTGCCGGGCTCACCAGCTGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACTgtgagttctc ... tgttctccagGTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATATTAAGCTTCGATGAGAAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

GCAGTTCAACTTTGTTAATGGTATCGAGCTAGTTTGCCGGGCTCACCAGCTGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACTgtgagttctc ... tgttctccagGTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATATTAAGCTTCGATGAGAAGATG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 82

GCAGTTCAACTTTGTTAATGGTATCGAGCTAGTTTGCCGGGCTCACCAGCTGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACTgtgagttctc ... tgttctccagGTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATATTAAGCTTCGATGAGAAGATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGTTCAACTTTGTTAATGGTATCGAGCTAGTTTGCCGGGCTCACCAGCTGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACTgtgagttctcgttcacatatagattgacacccagatattgtgtagtattctactatagtagtatacatttgtatttcagtgtgaccatattgaattgttatgatgcccatattaacgtatcttttgttctccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA