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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtatttgtttttatttttctattcaatattgcattctggttagcgctcttttctaaaaataccaagatgcattcaaggttcacacttttattatgcagCCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCTAGGATTGTAGGTGCTAGTGGTGCGGTATCAGAGTGACAGATAAAGGGGG

Basic information

species Zea mays
transcript GRMZM2G335638_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G335638_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os02g07960.2 (Oryza sativa), 3'ss of exon 16
------ttgtatttgtttttatttttctattcaatattgcattctggttagcgctcttttctaaaaataccaagatgcattcaaggttcacacttttattatgcagCCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCTAGGATTGTAGGTGCTAGTGGTGCGGTATCAGAGTGACAGATAAAGGGGG
       | |  |||| ||  ||||  | |   | |   ||  |   | ||     |||   ||||||     |||  ||  | | |    | |||  |||||||||||| |||||||||||| ||| |||||||  | || ||||||||||||||||||||| || ||| ||   ||| || |||||||| ||  | | |    |
gctctgctctgcttgtgttgtttttcttttctgaga--acagccatatgagatggattt---aaaaatcatgtgattgatgaatgatctgaaatttc-ttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCTAGGATTATAAGTGTTACCAGTGAGGAATCAGAGTAACGAAGAGATCAAG
















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|148967602|gb|EE018855.2|EE018855
EST:     TTGTGATACTGTTGTCACGTTTTGCAGACATCATCAGTCAGTGTATTCAG                         CCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCT
genomic: CTGTGATACTGTTGTCACGTTTTGCAGACATCATCAGTCAGTGTATTCAGgtaattctaa ... tattatgcagCCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCT
EST: gi|166572471|gb|EG142025.1|EG142025
EST:     GTCACGTTTTGCAGACATCATCAGTCAGTGTATTCAG                         CCGGGACCAGAATTCAGGCCAGCAATGTCTCAAAATCGTCCAAGACCTAGC
genomic: GTCACGTTTTGCAGACATCATCAGTCAGTGTATTCAGgtaattctaa ... tattatgcagCCGGGACCAGAATTCAGGCCAGCAATGTCTCAAA-TCGTCCAAGACCTAGC
EST: gi|33097433|gb|CF057393.1|CF057393
EST:     CTGTGATACTGTTGTCACGTTTTGCAGACATCATCAGTCAGTGTGTTCAG                         CCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCT
genomic: CTGTGATACTGTTGTCACGTTTTGCAGACATCATCAGTCAGTGTATTCAGgtaattctaa ... tattatgcagCCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCT
EST: gi|4681241|gb|AI629911.1|AI629911
EST:     CTGTGATACTGTTGTCACGTTTTGCAGACATCATCAGTCAGTGTATTCAG                         CCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCT
genomic: CTGTGATACTGTTGTCACGTTTTGCAGACATCATCAGTCAGTGTATTCAGgtaattctaa ... tattatgcagCCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCT
EST: gi|32850663|gb|CD990344.1|CD990344
EST:     CTGTGATACTGTTGTCACGTTTTGCAGACATCATCAGTCAGTGTATTCAG                         CCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCT
genomic: CTGTGATACTGTTGTCACGTTTTGCAGACATCATCAGTCAGTGTATTCAGgtaattctaa ... tattatgcagCCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCT
EST: gi|44682246|gb|CK787294.1|CK787294
EST:     CTGTGATACTGTTGTCACGTTTTGCAGACATCGTCAGTCAGTGTATTCAG                         TCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGAACCTAGC
genomic: CTGTGATACTGTTGTCACGTTTTGCAGACATCATCAGTCAGTGTATTCAGgtaattctaa ... tattatgcagCCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGA-CCTAGC
EST: gi|60345562|gb|DN212535.1|DN212535
EST:     CTGTGATACTGTTGTCACGTTTTGCAGACATCATCAGTCAGTGTATTCAG                         CCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCT
genomic: CTGTGATACTGTTGTCACGTTTTGCAGACATCATCAGTCAGTGTATTCAGgtaattctaa ... tattatgcagCCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCT
EST: gi|40302989|gb|CK347376.1|CK347376
EST:     CTGTGATACTGTTGTCACGTTTTGCAGACATCATCAGTCAGTGTATTCAG                         CCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCT
genomic: CTGTGATACTGTTGTCACGTTTTGCAGACATCATCAGTCAGTGTATTCAGgtaattctaa ... tattatgcagCCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCT

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), 46 (downstream exon)
Score: 45

CATGGAGTCCCTGTCAAAGATGGTTGATCCTTCTATCCGAGGAGAGTGTTCTGTGATACTGTTGTCACGTTTTGCAGACATCATCAGTCAGTGTATTCAGgtaattctaa ... tattatgcagCCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCTAGGATTGTAGGTGCTAGTGGTGCGGTATCAGAGTGACAGATAAAGGGGG


Block sizes: 45 (upstream exon), 44 (downstream exon)
Score: 12

CATGGAGTCCCTGTCAAAGATGGTTGATCCTTCTATCCGAGGAGAGTGTTCTGTGATACTGTTGTCACGTTTTGCAGACATCATCAGTCAGTGTATTCAGgtaattctaa ... tattatgcagCCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCTAGGATTGTAGGTGCTAGTGGTGCGGTATCAGAGTGACAGATAAAGGGGG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 17

CATGGAGTCCCTGTCAAAGATGGTTGATCCTTCTATCCGAGGAGAGTGTTCTGTGATACTGTTGTCACGTTTTGCAGACATCATCAGTCAGTGTATTCAGgtaattctaa ... tattatgcagCCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCTAGGATTGTAGGTGCTAGTGGTGCGGTATCAGAGTGACAGATAAAGGGGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 33

CATGGAGTCCCTGTCAAAGATGGTTGATCCTTCTATCCGAGGAGAGTGTTCTGTGATACTGTTGTCACGTTTTGCAGACATCATCAGTCAGTGTATTCAGgtaattctaa ... tattatgcagCCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCTAGGATTGTAGGTGCTAGTGGTGCGGTATCAGAGTGACAGATAAAGGGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctcttttctaaaaataccaagatgcattcaaggttcacacttttattatgcagCCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCTAGGATTGTAGGTGCTAGTGGTGCGGTATCAGAGTGACAGATAAAGGGGG
       ttctaaa  putative branch site (score: 33)
                                         cttttatt  putative PPT
     ttttctaaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtatttgtttttatttttctattcaatattgcattctggttagcgctcttttctaaaaataccaagatgcattcaaggttcacacttttattatgcagCCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCTAGGATTGTAGGTGCTAGTGGTGCGGTATCAGAGTGACAGATAAAGGGGG

- - - -tgttttt
- - - - - - - - - - - - - - - -tgcattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaata