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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaaataatggaatacctgccgattgccaacaaatctgtggagaaaattaaatatattgtttttatcatgtaagttatcctattatattatctggtgcagACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTGAAAGAAGGGTTTTTACTGTAACTGGTAATCGTCCTGATGAAGAG

Basic information

species Zea mays
transcript GRMZM2G330772_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G330772_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g07000.1 (Oryza sativa), 3'ss of exon 7
gtaaataatggaatacctgccgattgccaacaaatctgtggagaaaattaaatatattgt--ttttatcatgtaagttatcctattatattatctggtgcagACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTGAAAGAAGGGTTTTTACTGTAACTGGTAATCGTCCTGATGAAGAG
    || ||  ||| | |    | |   ||||  |    |||  |    ||      |    |  |  | ||| ||| || |   | ||   |||| || ||   ||||||||||||||| |||| |||||||| || || |||||||||||||| ||||| |||||||||| ||||||||||||||||
--ctatgattcaattcttagtcactatgaacacctgctaggactagtgcaatgcccctaaagtggtgacttgtgagtaatgcccctttaccctctgatgtagGTTTTGAGAGAAGCAATCCGGCAGGAGTATCGTGATGTCGTTGAAAGAAGGGTGTTTACAGTAACTGGTAGTCGTCCTGATGAAGAG
















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|211110807|gb|FL361656.1|FL361656
EST:     AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG                         ACCTTGAGAGAAGCAATCAGG-AAGAGTATCGGGAGGGTGTTGAAA
genomic: AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAGgtactgtgtt ... tctggtgcagACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTGAAA
EST: gi|211495566|gb|FL127190.1|FL127190
EST:     AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG                         ACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTGAAAGAAGG
genomic: AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAGgtactgtgtt ... tctggtgcagACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTGAAAGAAGG
EST: gi|60359751|gb|DN226724.1|DN226724
EST:     AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG                         ACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTGAAAGAAGG
genomic: AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAGgtactgtgtt ... tctggtgcagACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTGAAAGAAGG
EST: gi|67020224|gb|CO448973.1|CO448973
EST:     AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG                         ACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTTAAAGAAGG
genomic: AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAGgtactgtgtt ... tctggtgcagACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTGAAAGAAGG
EST: gi|211425646|gb|FL363236.1|FL363236
EST:     AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG                         ACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTGAAAGAAGG
genomic: AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAGgtactgtgtt ... tctggtgcagACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTGAAAGAAGG
EST: gi|211262997|gb|FL346818.1|FL346818
EST:     AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG                         ACCTTGAGAGAAGCAATCAGGCA-GAGGTATCGGGAGGTTGTTGAAAAGAA
genomic: AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAGgtactgtgtt ... tctggtgcagACCTTGAGAGAAGCAATCAGGCAAGAG-TATCGGGAGGTTGTTGAAA-GAA
EST: gi|67020710|gb|CO449459.1|CO449459
EST:     AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG                         ACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTGAAAGAAGG
genomic: AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAGgtactgtgtt ... tctggtgcagACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTGAAAGAAGG
EST: gi|9732911|gb|BE511663.1|BE511663
EST:     AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG                         ACCTTGAGAGAAGCAATTAGGCAAGAGTATCGGGAGGTTGTTGAAAGAAGG
genomic: AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAGgtactgtgtt ... tctggtgcagACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTGAAAGAAGG
EST: gi|211531082|gb|FL312439.1|FL312439
EST:     AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAG                         ACCTTGAGAGAA-CAATCAGGCAAGAAGTATCGGGAGGTTGTTGAAAGAAG
genomic: AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAGgtactgtgtt ... tctggtgcagACCTTGAGAGAAGCAATCAGGCAAGA-GTATCGGGAGGTTGTTGAAAGAAG

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: 43 (upstream exon), 47 (downstream exon)
Score: 315

AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAGgtactgtgtt ... tctggtgcagACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTGAAAGAAGGGTTTTTACTGTAACTGGTAATCGTCCTGATGAAGAG


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 278

AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAGgtactgtgtt ... tctggtgcagACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTGAAAGAAGGGTTTTTACTGTAACTGGTAATCGTCCTGATGAAGAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 341

AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAGgtactgtgtt ... tctggtgcagACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTGAAAGAAGGGTTTTTACTGTAACTGGTAATCGTCCTGATGAAGAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 329

AGCAGTGAAAAAGAAATTGAAGGAGCGGATGGATGACTTTCAGgtactgtgtt ... tctggtgcagACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTGAAAGAAGGGTTTTTACTGTAACTGGTAATCGTCCTGATGAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattaaatatattgtttttatcatgtaagttatcctattatattatctggtgcagACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTGAAAGAAGGGTTTTTACTGTAACTGGTAATCGTCCTGATGAAGAG
     aatatattgtttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaataatggaatacctgccgattgccaacaaatctgtggagaaaattaaatatattgtttttatcatgtaagttatcctattatattatctggtgcagACCTTGAGAGAAGCAATCAGGCAAGAGTATCGGGAGGTTGTTGAAAGAAGGGTTTTTACTGTAACTGGTAATCGTCCTGATGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - -cctgccg
- - - - - - - - - - - - - -caacaaa
- - - - - - - - - - - - - - - - - - - -ggagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtaa