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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgtttagcaatacagttactttcatgcattttcttttcctttatttcttcgttatcatgtgttttgtgtgttgtgtgttgcatttcatcttttttcagGTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG

Basic information

species Zea mays
transcript GRMZM2G088397_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088397_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g45390.2 (Oryza sativa), 3'ss of exon 5
tatgtttagcaatacagttactttcatgcattttcttttcctttatttcttcgttatcatgtgttttgtgt-gttgtgtgttgcatttcatcttttttcagGTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG
  ||     ||   || ||    |  |   | || |  | || ||||| |||  |||  |        | |     | | ||| ||||  |  |||| |||||||||||||| ||||| ||| | |||||||||||||
-ctggggcacatctcatttgtccttttctttgttttcattctctatttattcactatggttcaagggattttaccatttcttgtatttacttgttttgcagGTGGAAATGATACTTCAAGCACTAGAATATGAGAAAG
















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|37398538|gb|CF636584.1|CF636584
EST:     ATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAA                         GTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG
genomic: ATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAAgtaagaaggc ... cttttttcagGTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG
EST: gi|211216465|gb|FL469136.1|FL469136
EST:     TGAGAACAAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAA                         GTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG
genomic: TGAGAAC-AATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAAgtaagaaggc ... cttttttcagGTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG
EST: gi|37383541|gb|CF628790.1|CF628790
EST:     ATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAA                         GTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG
genomic: ATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAAgtaagaaggc ... cttttttcagGTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG
EST: gi|32808293|gb|CD960527.1|CD960527
EST:     ATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAA                         GTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG
genomic: ATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAAgtaagaaggc ... cttttttcagGTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG
EST: gi|32840843|gb|CD980524.1|CD980524
EST:     ATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAA                         GTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG
genomic: ATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAAgtaagaaggc ... cttttttcagGTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG
EST: gi|194717181|gb|FK934334.1|FK934334
EST:     ATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAA                         GTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG
genomic: ATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAAgtaagaaggc ... cttttttcagGTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG
EST: gi|32945555|gb|CF050374.1|CF050374
EST:     ATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAA                         GTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG
genomic: ATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAAgtaagaaggc ... cttttttcagGTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG

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: 45 (upstream exon), 38 (downstream exon)
Score: 38

CTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAAgtaagaaggc ... cttttttcagGTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG


Block sizes: 45 (upstream exon), 38 (downstream exon)
Score: 40

CTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAAgtaagaaggc ... cttttttcagGTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG


Block sizes: 48 (upstream exon), 38 (downstream exon)
Score: 30

CTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAAgtaagaaggc ... cttttttcagGTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG


Block sizes: 46 (upstream exon), 38 (downstream exon)
Score: 65

CTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAAgtaagaaggc ... cttttttcagGTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttcgttatcatgtgttttgtgtgttgtgtgttgcatttcatcttttttcagGTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG
                                     catttcatcttttttc  CT-rich tract
                                      atttcatctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgtttagcaatacagttactttcatgcattttcttttcctttatttcttcgttatcatgtgttttgtgtgttgtgtgttgcatttcatcttttttcagGTGGAAATGATTCTTCAGGCATTGGAATATGAGAAAG

- - - - - - - - - - - ttcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgca