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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcttcattagcgatgtataatgcattacctaaaaaaagaataacaccttcaggcagcaagggctgagttaactaagttatatttccttttcacttgcagAAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG

Basic information

species Zea mays
transcript GRMZM2G163713_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G163713_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g12600.1 (Oryza sativa), 3'ss of exon 2
-------------------------------------------------------------------------------ctcttcattagcgatgtataat-gcattacctaa---aaaaagaataacaccttcaggcagcaagggctgagttaactaagttatatttccttttcacttgcagAAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG
                                                                                | ||||   |  |  | || |       | |||     ||   | || |||| || |  ||||    | |  | |||        |||  |||  ||||||||||||| || ||||| ||||  |||||| |||||||||||||||||||||||
gtcagttagacacttcgtatgttgtgatggaataatggaattgaattccttctttgtgtacagtattgttatctgtgtggtgttcacatgttagctttagtcatgcctcttaagttgcaacatagaatacctgcatggtgcaaaacatcaactgact--------ttttttttcaacttgcagAAACAGGAAGAATTAGTTTTCGTGACTGCCTATGACATTCTCTTTGGTCAG
















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|71442759|gb|DR823809.1|DR823809
EST:     TTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAG                         AAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG
genomic: TTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAGgtgagccaac ... tcacttgcagAAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG
EST: gi|78075306|gb|DV503740.1|DV503740
EST:     TTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAG                         AAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG
genomic: TTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAGgtgagccaac ... tcacttgcagAAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG
EST: gi|101389847|gb|EB816854.1|EB816854
EST:     TTCTTAAAGAGGTTT-AGCATCGAGTGAAATACTGAGCAGCAAATGGAAG                         AAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG
genomic: TTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAGgtgagccaac ... tcacttgcagAAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG
EST: gi|211084459|gb|FL146410.1|FL146410
EST:     TTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAG                         AAACAAGAGGAATTGGTTTATGTGACTA
genomic: TTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAGgtgagccaac ... tcacttgcagAAACAAGAGGAATTGGTTTATGTGACTA
EST: gi|149085197|gb|EE174704.2|EE174704
EST:     TTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAG                         AAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG
genomic: TTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAGgtgagccaac ... tcacttgcagAAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG
EST: gi|149069618|gb|EE158000.2|EE158000
EST:     TTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAG                         AAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG
genomic: TTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAGgtgagccaac ... tcacttgcagAAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG
EST: gi|148940057|gb|EC884801.2|EC884801
EST:     TTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAG                         AAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG
genomic: TTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAGgtgagccaac ... tcacttgcagAAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG
EST: gi|78118872|gb|DV537256.1|DV537256
EST:     TTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAA                         AAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG
genomic: TTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAGgtgagccaac ... tcacttgcagAAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG
EST: gi|71442758|gb|DR823808.1|DR823808
EST:     TTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAG                         AAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG
genomic: TTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAGgtgagccaac ... tcacttgcagAAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG
EST: gi|91048771|gb|EB159189.1|EB159189
EST:     TTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAG                         AAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG
genomic: TTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAGgtgagccaac ... tcacttgcagAAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG

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: 47 (upstream exon), 48 (downstream exon)
Score: 44

ACCTACCAATTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAGgtgagccaac ... tcacttgcagAAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG


Block sizes: 23 (upstream exon), 47 (downstream exon)
Score: 11

ACCTACCAATTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAGgtgagccaac ... tcacttgcagAAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 25

ACCTACCAATTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAGgtgagccaac ... tcacttgcagAAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG


Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 15

ACCTACCAATTCTTAAAGAGGTTTTAGCATCGAGTGAAATACTGAGCAGCAAATGGAAGgtgagccaac ... tcacttgcagAAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttcaggcagcaagggctgagttaactaagttatatttccttttcacttgcagAAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG
                     agttaac  putative branch site (score: 15)
                                   tatttccttttcactt  putative PPT
                       ttaactaagttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcttcattagcgatgtataatgcattacctaaaaaaagaataacaccttcaggcagcaagggctgagttaactaagttatatttccttttcacttgcagAAACAAGAGGAATTGGTTTATGTGACTACCTATGACATTCTCTTTGGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - atgcatt
- - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - -aataaca
- - - - - - - - - - - - - - - - - - - - - - - - - - -gcagcaa