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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtacgaaactatcatagtagtgcggttttgaaaactgcggtctttcaaagttctcagagctattctattactttggtgaccaacgcatcacactgtgcagGATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGTCCAAAG

Basic information

species Zea mays
transcript GRMZM2G101596_T01
intron # 4
splice site 3'
intron type U2

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|93282402|gb|EB674666.1|EB674666
EST:     TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAG                         GATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
genomic: TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAGgtatcagttg ... cactgtgcagGATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
EST: gi|13125936|gb|BG316611.1|BG316611
EST:     TGGTTTTACAATTCCCAGGAGTGTCAACAGGCTGCAAATCTTTTCAGCAG                         GATTCTGAATG
genomic: TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAGgtatcagttg ... cactgtgcagGATTCTGAATG
EST: gi|91056521|gb|EB166939.1|EB166939
EST:     TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAG                         GATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
genomic: TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAGgtatcagttg ... cactgtgcagGATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
EST: gi|211391326|gb|FK987375.1|FK987375
EST:     TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAG                         GATTCTGAATGCTTTCT
genomic: TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAGgtatcagttg ... cactgtgcagGATTCTGAATGCTTTCT
EST: gi|76928738|gb|DV171746.1|DV171746
EST:     TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAG                         GATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
genomic: TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAGgtatcagttg ... cactgtgcagGATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
EST: gi|93281394|gb|EB673658.1|EB673658
EST:     TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAG                         GATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
genomic: TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAGgtatcagttg ... cactgtgcagGATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
EST: gi|211393955|gb|FK987391.1|FK987391
EST:     TGGTTTTACATTTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAG                         GATTCTGAATGCTTTCCTCAAAGGTGGCACCAAAGCCGAAAAATTCCTTCT
genomic: TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAGgtatcagttg ... cactgtgcagGATTCTGAATGCTTTC-TCAAAGGTGGCACCAAAGCCGAAAA-TTCCTTCT
EST: gi|76010496|gb|DT937666.1|DT937666
EST:     TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAG                         GATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
genomic: TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAGgtatcagttg ... cactgtgcagGATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
EST: gi|76909432|gb|DV163378.1|DV163378
EST:     TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAG                         GATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
genomic: TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAGgtatcagttg ... cactgtgcagGATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
EST: gi|91048464|gb|EB158882.1|EB158882
EST:     TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAG                         GATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
genomic: TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAGgtatcagttg ... cactgtgcagGATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
EST: gi|76011730|gb|DT938900.1|DT938900
EST:     TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAG                         GATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
genomic: TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAGgtatcagttg ... cactgtgcagGATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
EST: gi|89758076|gb|DY687416.1|DY687416
EST:     TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAG                         GATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
genomic: TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAGgtatcagttg ... cactgtgcagGATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
EST: gi|148999366|gb|EE036307.2|EE036307
EST:     TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAG                         GATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
genomic: TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAGgtatcagttg ... cactgtgcagGATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
EST: gi|211393950|gb|FK987386.1|FK987386
EST:     TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAG                         GATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
genomic: TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAGgtatcagttg ... cactgtgcagGATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
EST: gi|78114665|gb|DV533053.1|DV533053
EST:     TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAG                         GATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT
genomic: TGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAGgtatcagttg ... cactgtgcagGATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGT

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: 59

AAGCTCCTTATATAATGTACCGCAATGCTGCTCAAGAAGTTATAGGAATCTGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAGgtatcagttg ... cactgtgcagGATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGTCCAAAG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 60

AAGCTCCTTATATAATGTACCGCAATGCTGCTCAAGAAGTTATAGGAATCTGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAGgtatcagttg ... cactgtgcagGATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGTCCAAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 48

AAGCTCCTTATATAATGTACCGCAATGCTGCTCAAGAAGTTATAGGAATCTGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAGgtatcagttg ... cactgtgcagGATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGTCCAAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 63

AAGCTCCTTATATAATGTACCGCAATGCTGCTCAAGAAGTTATAGGAATCTGGTTTTACAATTCCCAGGAGTGTCAACAGGTTGCAAATCTTTTCAGCAGgtatcagttg ... cactgtgcagGATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGTCCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaagttctcagagctattctattactttggtgaccaacgcatcacactgtgcagGATTCTGAATGCTTTCTCAAAGGTGGCACCAAAGCCGAAAATTCCTTCTGTCCAAAG
               tattctattacttt  TA-rich tract