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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccctttggcctatcgaatgcagagagtagcatacttcaaagtaaactatgagtatatgtagagatatcctgtttcctgacataatattcattccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGATGAACGAACAACTAAAATCTGCTAACTCGGAATTTCCGAAAACAGATTTG

Basic information

species Zea mays
transcript GRMZM2G048804_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048804_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g07100.1 (Oryza sativa), 3'ss of exon 8
------tccctttggcctatcgaatgcagagagtagcatacttcaaagtaaactatgagtatatgtagagatatcctgtttcctgacataatat-tcattccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGATGAACGAACAACTAAAATCTGCTAACTCGGAATTTCCGAAAACAGATTTG
          ||| |  ||| | ||| | | | ||  | | ||    | |||     |  |  ||   ||||      ||| |||| ||| |   |  ||  |||||||| ||||| ||||||||  | || ||||||||||| || ||||| ||| |||| || ||||||||||||||| ||| |||| | || ||||||||||| 
taagaaagtgtttcgt-tataggatgaataaa-taagaaatttttggggaaa-----aagacgtgctcagatgcttgtttttctgatatactgcatttttatttaagGTATCTATCACAAGGGAATCTTAGGGATGCAAATTTGCTCATGGACGAGCTGAAGGATCAACTAAAATCTGCTGACTTGGAAATCCCCAAAACAGATTTA
















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|31558703|gb|CD527915.1|CD527915
EST:     TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAAT                         GTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
genomic: TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAATgtaagatatc ... attccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
EST: gi|33771157|gb|CF272818.1|CF272818
EST:     TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAAT                         GTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
genomic: TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAATgtaagatatc ... attccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
EST: gi|94472950|gb|EB701908.1|EB701908
EST:     TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAAT                         GTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
genomic: TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAATgtaagatatc ... attccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
EST: gi|71773197|gb|DR971110.1|DR971110
EST:     TGTTACCCTGGTGAAAATGATACCTGCA-TTGCACGTGGGGTCCTAAT                         GTACCTATCTCAAGGG
genomic: TGTTACCCTGGTGAAGATGATAC-TGCAATTGCACGTGGGGTCCTAATgtaagatatc ... attccttaagGTACCTATCTCAAGGG
EST: gi|113704317|gb|EE681821.1|EE681821
EST:     TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAAT                         GTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
genomic: TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAATgtaagatatc ... attccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
EST: gi|37379196|gb|CF626330.1|CF626330
EST:     TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAAT                         GTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
genomic: TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAATgtaagatatc ... attccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
EST: gi|71773196|gb|DR971109.1|DR971109
EST:     TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAAT                         GTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
genomic: TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAATgtaagatatc ... attccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
EST: gi|74236760|gb|DT644674.1|DT644674
EST:     TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAAT                         GTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
genomic: TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAATgtaagatatc ... attccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
EST: gi|211155842|gb|FL114458.1|FL114458
EST:     TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAAT                         GTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
genomic: TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAATgtaagatatc ... attccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
EST: gi|32911197|gb|CF016009.1|CF016009
EST:     TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAAT                         GTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
genomic: TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAATgtaagatatc ... attccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
EST: gi|78021285|gb|DV489672.1|DV489672
EST:     GATGATACTGCAATTGCACGTGGGGTCCTAAT                         GTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
genomic: GATGATACTGCAATTGCACGTGGGGTCCTAATgtaagatatc ... attccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
EST: gi|31349428|gb|CD433785.1|CD433785
EST:     TGTTACCCTGGTGAAGATGATACTGNCA-TTGCACGTGGGGTCCTAAT                         GTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
genomic: TGTTACCCTGGTGAAGATGATACTG-CAATTGCACGTGGGGTCCTAATgtaagatatc ... attccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
EST: gi|113702828|gb|EE680332.1|EE680332
EST:     CTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAAT                         GTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT
genomic: CTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAATgtaagatatc ... attccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGAT

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: 46 (upstream exon), 49 (downstream exon)
Score: 138

TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAATgtaagatatc ... attccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGATGAACGAACAACTAAAATCTGCTAACTCGGAATTTCCGAAAACAGATTTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 156

TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAATgtaagatatc ... attccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGATGAACGAACAACTAAAATCTGCTAACTCGGAATTTCCGAAAACAGATTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 191

TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAATgtaagatatc ... attccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGATGAACGAACAACTAAAATCTGCTAACTCGGAATTTCCGAAAACAGATTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 256

TGTTACCCTGGTGAAGATGATACTGCAATTGCACGTGGGGTCCTAATgtaagatatc ... attccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGATGAACGAACAACTAAAATCTGCTAACTCGGAATTTCCGAAAACAGATTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actatgagtatatgtagagatatcctgtttcctgacataatattcattccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGATGAACGAACAACTAAAATCTGCTAACTCGGAATTTCCGAAAACAGATTTG
                             tcctgac  putative branch site (score: 256)
                                          ttcattcctt  putative PPT
                                  acataatattcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccctttggcctatcgaatgcagagagtagcatacttcaaagtaaactatgagtatatgtagagatatcctgtttcctgacataatattcattccttaagGTACCTATCTCAAGGGAACTTGAGAGATGCAAATTTACTTATGGATGAGATGAACGAACAACTAAAATCTGCTAACTCGGAATTTCCGAAAACAGATTTG

- - - - - - - -gaatgca
- - - - - - - - - - - - - - -gcatact
- - - - - - - - - - - - - - - - - - -caaagtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - atatgta