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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactggaaacacattaagacccactgaacttttcccatgcagaggtttttaaactggaatttttgttctgtgatgttagGATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG

Basic information

species Zea mays
transcript GRMZM2G081682_T02
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081682_T01 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 16
gtaactggaaacacattaagacccactgaacttttcccatgcagaggtttttaaactggaatttttgt---tctgtgatgttagGATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG
||||||||||   |||||   ||  || || ||||   || ||| | | |  |   |    ||||| |   | | || ||||||||||||||||| ||||| ||||| |||||||| |||||||| |||||||||||||| ||||||||||| |||
gtaactggaa---cattacagccttctaaagttttt--attcagggatctagatg-taatctttttatctctttctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGTGAGATCGGTGCCTTGATTGAG
















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|21389890|gb|BQ527939.1|BQ527939
EST:     GAATGGACACCCTGGCACGTGGCCTTCGTAACGTTGCCAAGCTGATTGAG                         GATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGGgtaactggaa ... gtgatgttagGATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|33101487|gb|CF061447.1|CF061447
EST:     GAATGGACACCCTGGCACGTGGCCTTCGTAACGTTGCCAAGCTGATTGAG                         GATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGGgtaactggaa ... gtgatgttagGATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|5739589|gb|AI947384.1|AI947384
EST:     CCTGGCACGTGGCCTTCGTAACGTTGCCAAGCTGATTGAG                         GATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: CCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGGgtaactggaa ... gtgatgttagGATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|60347665|gb|DN214638.1|DN214638
EST:     GAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGG                         GATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGGgtaactggaa ... gtgatgttagGATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|21331635|gb|BQ487016.1|BQ487016
EST:     GAATGGACACCCTGGCACGTGGCCTTCGTAACGTTGCCAAGCTGATTGAG                         GATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGGgtaactggaa ... gtgatgttagGATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|32909378|gb|CF014190.1|CF014190
EST:     GAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGG                         GATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGGgtaactggaa ... gtgatgttagGATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|22715088|gb|BU197571.1|BU197571
EST:     GAATGGACACCCTGGCACGTGGCCTTCGTAACGTTGCCAAGCTGATTGAG                         GATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGGgtaactggaa ... gtgatgttagGATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|60397236|gb|DN230052.1|DN230052
EST:     GAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGG                         GATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGGgtaactggaa ... gtgatgttagGATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|6095640|gb|AW120307.1|AW120307
EST:     GAATGGACACCCTGGCACGTGGCCTTCGTAACGTTGCCAAGCTGATTGAG                         GATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGGgtaactggaa ... gtgatgttagGATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|9794851|gb|BE553159.1|BE553159
EST:     GAATGGACACCCTGGCACGTGGCCTTCGTAACGTTGCCAAGCTGATTGAG                         GATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGGgtaactggaa ... gtgatgttagGATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|5804468|gb|AI979438.1|AI979438
EST:     GAATGGCCCCCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGG                         GATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGGgtaactggaa ... gtgatgttagGATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGT

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), 49 (downstream exon)
Score: 819

GCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGGAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGGgtaactggaa ... gtgatgttagGATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1095

GCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGGAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGGgtaactggaa ... gtgatgttagGATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 795

GCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGGAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGGgtaactggaa ... gtgatgttagGATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1330

GCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGGAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGGgtaactggaa ... gtgatgttagGATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaacttttcccatgcagaggtttttaaactggaatttttgttctgtgatgttagGATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG
                     tttttaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactggaaacacattaagacccactgaacttttcccatgcagaggtttttaaactggaatttttgttctgtgatgttagGATGGTTCCCTAGATGATCTTGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT