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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggactatctattttactactattgcaaacttttattattaacattgtgcactcttcaggtttaactaagattgtacactctagcgatcagatca...

Basic information

species Zea mays
transcript GRMZM2G087095_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087095_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g54170.1 (Oryza sativa), 5'ss of exon 2
TCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggact--atctattttac----tactattgcaaacttttattattaacattgtgcactcttcaggtttaactaagattgtacactctagcgatcagatca
  |||||||||| || ||| | |||||||||||||| ||||||||    |||||||| |  ||| |||||||| ||||||||||  ||  | |  ||  | ||||      | ||||      | || ||||| ||||  | || | ||   |  |||       |  | | | || | ||||| |  
CATGCTTAAGACGCTTGAGAGATACCAGAGGTACATTTATGCTTCGCAAGATGCTGCCGCACCAACTAGCGATGAGATGCAGgtttgataattttattcagtttatggcacattatttgttgatgtttttattgacataat-cattttt---gcataatgtcccctagaaaat-taaccatcaggta-
















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|71315310|gb|DR794267.1|DR794267
EST:     ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
genomic: ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
EST: gi|6695990|gb|AW289098.1|AW289098
EST:     ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
genomic: ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
EST: gi|50331176|gb|CO526302.1|CO526302
EST:     ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
genomic: ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
EST: gi|74236437|gb|DT644351.1|DT644351
EST:     ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
genomic: ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
EST: gi|32838769|gb|CD978450.1|CD978450
EST:     ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
genomic: ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
EST: gi|78112771|gb|DV531165.1|DV531165
EST:     ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
genomic: ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
EST: gi|91870871|gb|EB401123.1|EB401123
EST:     ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
genomic: ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
EST: gi|8368837|gb|BE051782.1|BE051782
EST:     ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
genomic: ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
EST: gi|76285512|gb|DV025080.1|DV025080
EST:     ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
genomic: ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
EST: gi|71425166|gb|DR806565.1|DR806565
EST:     ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
genomic: ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
EST: gi|71421466|gb|DR805441.1|DR805441
EST:     TCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
genomic: TCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
EST: gi|71330056|gb|DR801767.1|DR801767
EST:     ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
genomic: ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
EST: gi|32847296|gb|CD986977.1|CD986977
EST:     ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
genomic: ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
EST: gi|71421467|gb|DR805442.1|DR805442
EST:     ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
genomic: ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
EST: gi|76285511|gb|DV025079.1|DV025079
EST:     ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
genomic: ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
EST: gi|211463199|gb|FL126648.1|FL126648
EST:     ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCATATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
genomic: ACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
EST: gi|71425163|gb|DR806564.1|DR806564
EST:     TTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG
genomic: TTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAG

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

TCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAGCACTCACAAAG


Block sizes: 35 (upstream exon), 15 (downstream exon)
Score: 2

TCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAGCACTCACAAAG


Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 94

TCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggac ... gaaagtgcagAATAACTATCAAGAATATGTGAAGCTGAAGGCACGAGTTGAGGTTTTACAGCACTCACAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAGgtgcgaggactatctattttactactattgcaaacttttattattaacattgtgcactcttcaggtttaactaagattgtacactctagcgatcagatca

- - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG