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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGGTCACTTGGATGGGGCAGTGATGATGGTGAGGATGGCTCTGAAGAGTCCATTTTTGGAACCGGGGATGCAGATGATGTCAAGCCCAAGAGCTTTCCTgtaagttcccaacgcgtgaccagcccttttctcttgtggattgtctgttcatgatttaaattgtttgttttcttggttgcttag

Basic information

species Zea mays
transcript GRMZM2G067764_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G067764_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 5'ss of exon 2
ACGGTCACTTGGATGGGGCAGTGATG---ATGGTGAGGATGGCTCTGAAGAGTCCATTTTTGGAACCGGGGATGCAGATGATGTCAAGCCCAAGAGCTTTCCTgtaagttcccaacgcgtgaccagcccttttctcttgtggattgtctgttcatgatttaaattgtttgttttcttggttgcttag-------
    ||||| || ||||| |||||||   | ||||| || ||||| || |||||||| ||||| ||||| ||||||||||||||  ||| ||||||||||||||||||||  ||| | |||   ||   || | | || |   || | | ||  | || | |||   | |  |||||  ||  || |       
---CTCACTCGGGTGGGGAAGTGATGGGGACGGTGACGACGGCTCGGAGGAGTCCATATTTGGCACCGGTGATGCAGATGATGTTGAGCTCAAGAGCTTTCCTgtaagttatcaatgagtgggtagtatttgtttgtt-tattttctgtatttcttatgttaatc-ctggagttcttattttgttggtgtgaag
















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|89760976|gb|DY689173.1|DY689173
EST:     CCATTTTTGGAACCGGGGATGCAGATGATGTCAAGCCCAAGAGCTTTCCT                         GTGTGTGATGACCGGCACTCTGAACTGATCCCCTGCTTGGATAGGAACTTG
genomic: CCATTTTTGGAACCGGGGATGCAGATGATGTCAAGCCCAAGAGCTTTCCTgtaagttccc ... ggttgcttagGTGTGTGATGACCGGCACTCTGAACTGATCCCCTGCTTGGATAGGAACTTG
EST: gi|89250850|gb|DY622636.1|DY622636
EST:     CCATTTTTGGAACCGGGGATGCAGATGATGTCAAGCCCAAGAGCTTTCCT                         GTGTGTGATGACCGGCACTCTGAACTGATCCCCTGCTTGGATAGGAACTTG
genomic: CCATTTTTGGAACCGGGGATGCAGATGATGTCAAGCCCAAGAGCTTTCCTgtaagttccc ... ggttgcttagGTGTGTGATGACCGGCACTCTGAACTGATCCCCTGCTTGGATAGGAACTTG
EST: gi|74245364|gb|DT653278.1|DT653278
EST:     CCATTTTTGGAACCGGGGATGCAGATGATGTCAAGCCCAAGAGCTTTCCT                         GTGTGTGATGACCGGCACTCTGAACTGATCCCCTGCTTGGATAGGAACTTG
genomic: CCATTTTTGGAACCGGGGATGCAGATGATGTCAAGCCCAAGAGCTTTCCTgtaagttccc ... ggttgcttagGTGTGTGATGACCGGCACTCTGAACTGATCCCCTGCTTGGATAGGAACTTG
EST: gi|88752440|gb|DY536581.1|DY536581
EST:     CCATTTTTGGAACCGGGGATGCAGATGATGTCAAGCCCAAGAGCTTTCCT                         GTGTGTGATGACCGGCACTCTGAACTGATCC
genomic: CCATTTTTGGAACCGGGGATGCAGATGATGTCAAGCCCAAGAGCTTTCCTgtaagttccc ... ggttgcttagGTGTGTGATGACCGGCACTCTGAACTGATCC
EST: gi|149087020|gb|EE176561.2|EE176561
EST:     CCATTTTTGGAACCGGGGATGCAGATGATGTCAAGCCCAAGAGCTTTCCT                         GTGTGTGATGACCGGCACTCTGAACTGATCCCCTGCTTGGATAGGAACTTG
genomic: CCATTTTTGGAACCGGGGATGCAGATGATGTCAAGCCCAAGAGCTTTCCTgtaagttccc ... ggttgcttagGTGTGTGATGACCGGCACTCTGAACTGATCCCCTGCTTGGATAGGAACTTG
EST: gi|93011970|gb|EB637490.1|EB637490
EST:     CCATTTTTGGAACCGGGGATGCAGATGATGTCAAGCCCAAGAGCTTTCCT                         GTGTGTGATGACCGGCACTCTGAACTGATCCCCTGCTTGGATAGGAACTTG
genomic: CCATTTTTGGAACCGGGGATGCAGATGATGTCAAGCCCAAGAGCTTTCCTgtaagttccc ... ggttgcttagGTGTGTGATGACCGGCACTCTGAACTGATCCCCTGCTTGGATAGGAACTTG

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: 151

ACGGTCACTTGGATGGGGCAGTGATGATGGTGAGGATGGCTCTGAAGAGTCCATTTTTGGAACCGGGGATGCAGATGATGTCAAGCCCAAGAGCTTTCCTgtaagttccc ... ggttgcttagGTGTGTGATGACCGGCACTCTGAACTGATCCCCTGCTTGGATAGGAACTTGATATATCAAATGAGGCTGAAGCTGGATTTAAACCTGATGGAGCACTATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 130

ACGGTCACTTGGATGGGGCAGTGATGATGGTGAGGATGGCTCTGAAGAGTCCATTTTTGGAACCGGGGATGCAGATGATGTCAAGCCCAAGAGCTTTCCTgtaagttccc ... ggttgcttagGTGTGTGATGACCGGCACTCTGAACTGATCCCCTGCTTGGATAGGAACTTGATATATCAAATGAGGCTGAAGCTGGATTTAAACCTGATGGAGCACTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126

ACGGTCACTTGGATGGGGCAGTGATGATGGTGAGGATGGCTCTGAAGAGTCCATTTTTGGAACCGGGGATGCAGATGATGTCAAGCCCAAGAGCTTTCCTgtaagttccc ... ggttgcttagGTGTGTGATGACCGGCACTCTGAACTGATCCCCTGCTTGGATAGGAACTTGATATATCAAATGAGGCTGAAGCTGGATTTAAACCTGATGGAGCACTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 213

ACGGTCACTTGGATGGGGCAGTGATGATGGTGAGGATGGCTCTGAAGAGTCCATTTTTGGAACCGGGGATGCAGATGATGTCAAGCCCAAGAGCTTTCCTgtaagttccc ... ggttgcttagGTGTGTGATGACCGGCACTCTGAACTGATCCCCTGCTTGGATAGGAACTTGATATATCAAATGAGGCTGAAGCTGGATTTAAACCTGATGGAGCACTATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGGTCACTTGGATGGGGCAGTGATGATGGTGAGGATGGCTCTGAAGAGTCCATTTTTGGAACCGGGGATGCAGATGATGTCAAGCCCAAGAGCTTTCCTgtaagttcccaacgcgtgaccagcccttttctcttgtggattgtctgttcatgatttaaattgtttgttttcttggttgcttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT