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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtgatactgatagatgctctgaacatgcaagaaagcaataagaaacaaaagagtcacatgtcacctattcacaggattttgtacccttttttatttcagGAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTTGTGTTAATGTCTGTCTGGTCATTGTTCTTGGTGCTGCAAGTTCTCAAG

Basic information

species Zea mays
transcript GRMZM2G149576_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149576_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g51650.1 (Oryza sativa), 3'ss of exon 6
ggtgatactgatagatgctctgaacatgcaagaaagcaataagaaacaaaaga------gtcacatgtcacctattcacaggattttgtacccttttttatttcagGAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTTGTGTTAATGTCTGTCTGGTCATTGTTCTTGGTGCTGCAAGTTCTCAAG
        || ||||| || |||||||||||||||||||||  |||||||  |      |||  ||| |   |  |||| | |||   |    ||||| ||| |||||||||||| |||||||| ||||||||||||||||||| ||  | ||| |||| ||||| |  ||||||||||||||| |  |||||
-----cgttggtagatactatgaacatgcaagaaagcaatataaaacaaagtacagtttgtcctatgccctgtgctcactg-attcgatgttatttttaattccagGAGACTTTCTTGTTCAATTTGAGGTGGAAGAATATCCTAGTTCTCATGACTGTATGGTCGTCTTTCTTGGTGCTGCAAATCTTCAAG
















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|93282425|gb|EB674689.1|EB674689
EST:     GTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGG                         GAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTTTGTGTTAAT
genomic: GTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGGgtaagctaca ... tttatttcagGAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTT-GTGTTAAT
EST: gi|32841700|gb|CD981381.1|CD981381
EST:     GTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGG                         GAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTTGTGTTAATGTCT
genomic: GTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGGgtaagctaca ... tttatttcagGAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTTGTGTTAATGTCT
EST: gi|71763997|gb|DR961934.1|DR961934
EST:     GTTATGGGGAGCCCCTCCTGACTCTACCTCAGCCCAAGAAGTCTGCATGG                         GAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTTGTGTTAATGTCT
genomic: GTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGGgtaagctaca ... tttatttcagGAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTTGTGTTAATGTCT
EST: gi|76013549|gb|DT940719.1|DT940719
EST:     GTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGG                         GAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCTTTGTGTTAATGTCT
genomic: GTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGGgtaagctaca ... tttatttcagGAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTTGTGTTAATGTCT
EST: gi|13237072|gb|BG355086.1|BG355086
EST:     GTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGG                         GAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTTGTGTTAATGTCT
genomic: GTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGGgtaagctaca ... tttatttcagGAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTTGTGTTAATGTCT
EST: gi|71772906|gb|DR970829.1|DR970829
EST:     GTTATGGGGAGCCCCTCCTGACTCACCCTCAGCCCAAGAAGTCTGCATGG                         GAGACTTTCATGTTCAATCTGA
genomic: GTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGGgtaagctaca ... tttatttcagGAGACTTTCATGTTCAATCTGA
EST: gi|78104608|gb|DV523026.1|DV523026
EST:     GTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGG                         GAGACTTTCATGTTCAATCTGANGTGGAAGAATATCCCTTGTGT-AATGTC
genomic: GTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGGgtaagctaca ... tttatttcagGAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCC-TTGTGTTAATGTC
EST: gi|71769874|gb|DR967811.1|DR967811
EST:     GTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGG                         GAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCCTTGTGT-AATGTC
genomic: GTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGGgtaagctaca ... tttatttcagGAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCC-TTGTGTTAATGTC
EST: gi|13237258|gb|BG355272.1|BG355272
EST:     GTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGG                         GAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTTGTGTTAATGTCT
genomic: GTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGGgtaagctaca ... tttatttcagGAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTTGTGTTAATGTCT
EST: gi|211074549|gb|FL187269.1|FL187269
EST:     GTTATGGGGAGCCCCTCCTGACTCAAC-TCAGCC-AAGAAANCTGCATGG                         GAGACTT-CATGTTCAATCTGAAGTGGAAGA-TAACCTTGTGT-AATG
genomic: GTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGGgtaagctaca ... tttatttcagGAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTTGTGTTAATG

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), 42 (downstream exon)
Score: 107

TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGGgtaagctaca ... tttatttcagGAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTTGTGTTAATGTCTGTCTGGTCATTGTTCTTGGTGCTGCAAGTTCTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 422

TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGGgtaagctaca ... tttatttcagGAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTTGTGTTAATGTCTGTCTGGTCATTGTTCTTGGTGCTGCAAGTTCTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 292

TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGGgtaagctaca ... tttatttcagGAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTTGTGTTAATGTCTGTCTGGTCATTGTTCTTGGTGCTGCAAGTTCTCAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 115

TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGGgtaagctaca ... tttatttcagGAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTTGTGTTAATGTCTGTCTGGTCATTGTTCTTGGTGCTGCAAGTTCTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaaagagtcacatgtcacctattcacaggattttgtacccttttttatttcagGAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTTGTGTTAATGTCTGTCTGGTCATTGTTCTTGGTGCTGCAAGTTCTCAAG
                                ttttgtaccctttttt  CT-rich tract
                                          ttttttatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtgatactgatagatgctctgaacatgcaagaaagcaataagaaacaaaagagtcacatgtcacctattcacaggattttgtacccttttttatttcagGAGACTTTCATGTTCAATCTGAGGTGGAAGAATATCCTTGTGTTAATGTCTGTCTGGTCATTGTTCTTGGTGCTGCAAGTTCTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- -gatactg
- - - - - - -gatgctc
- - - - - - - - - - - -acatgca
- - - - - - - - - - - - - - - -gaaagcaa
- - - - - - - - - - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cacatgt