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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgacaagctgttgtctgatttaggaacttcacttagcagtgtgttcctttattctgtttttgttttctcttgtaaccttatgctttctccttttgaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCACCAGCATCCACTGCACCTGCAGCCAACCAAGAACCTACCACTGCTGCTCC

Basic information

species Zea mays
transcript GRMZM2G057158_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057158_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g03920.1 (Oryza sativa), 3'ss of exon 1
-tttgacaagctgttgtctgatttaggaacttcac--ttagcagtgtgttcctt---tattctgtttttgttttctcttgtaaccttatgctttctccttttgaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCACCAGCATCCACTGCACCT---GCAGCCAACCAAGAACCTACCACTGCTGCTCC
 ||||| | || |     | | |   | | | ||   ||| |  || ||  |     | |||    | || ||  |||| |   | |||   ||  ||| |||||||||| ||||| || || || || |||||||| ||||||||||| ||||||||||| || || ||||||   ||||||||| | | | || |  |   |     
ctttga-atgcagcaagtttactgctgcagtgcatgtttaaccttgagtcacaaagattttccaaatgtgcttattcttatg--cctat---tttccctcttgaagGTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCACCAGCGTCAACCGCACCTCCTGCAGCCAACAATGTAACTCCTGCCATTAA---
















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|23357630|gb|BU645279.1|BU645279
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ccttttgaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
EST: gi|148941332|gb|EC886240.2|EC886240
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ccttttgaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
EST: gi|211122355|gb|FL034206.1|FL034206
EST:     GATCTACAAGGGCCGGAWCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACWGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ccttttgaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
EST: gi|94480135|gb|EB709093.1|EB709093
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGACACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ccttttgaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
EST: gi|76929924|gb|DV172221.1|DV172221
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ccttttgaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
EST: gi|26457469|gb|CA829052.1|CA829052
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ccttttgaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
EST: gi|213174821|gb|FM189465.1|FM189465
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ccttttgaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
EST: gi|21432104|gb|BQ547594.1|BQ547594
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ccttttgaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
EST: gi|148940781|gb|EC885603.2|EC885603
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ccttttgaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
EST: gi|211122354|gb|FL034205.1|FL034205
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ccttttgaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCAC
EST: gi|211122356|gb|FL034207.1|FL034207
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGYGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCG
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ccttttgaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCG

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), 48 (downstream exon)
Score: 297

AAGGCGATCGTAGCCGATAGCTGCGACGTGCCGGCGCCGCAGCAGCGGCTGATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ccttttgaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCACCAGCATCCACTGCACCTGCAGCCAACCAAGAACCTACCACTGCTGCTCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 271

AAGGCGATCGTAGCCGATAGCTGCGACGTGCCGGCGCCGCAGCAGCGGCTGATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ccttttgaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCACCAGCATCCACTGCACCTGCAGCCAACCAAGAACCTACCACTGCTGCTCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 315

AAGGCGATCGTAGCCGATAGCTGCGACGTGCCGGCGCCGCAGCAGCGGCTGATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ccttttgaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCACCAGCATCCACTGCACCTGCAGCCAACCAAGAACCTACCACTGCTGCTCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 285

AAGGCGATCGTAGCCGATAGCTGCGACGTGCCGGCGCCGCAGCAGCGGCTGATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ccttttgaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCACCAGCATCCACTGCACCTGCAGCCAACCAAGAACCTACCACTGCTGCTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctttattctgtttttgttttctcttgtaaccttatgctttctccttttgaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCACCAGCATCCACTGCACCTGCAGCCAACCAAGAACCTACCACTGCTGCTCC
                          ttgtaac  putative branch site (score: 285)
                                ccttatgctttctcct  CT-rich tract
             tttttgtttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgacaagctgttgtctgatttaggaacttcacttagcagtgtgttcctttattctgtttttgttttctcttgtaaccttatgctttctccttttgaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGCGCCACCACCAGCATCCACTGCACCTGCAGCCAACCAAGAACCTACCACTGCTGCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - gctgttg
- - - - - - - - ctgattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctttc