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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaaaccaaacacgtagttacgccttttatgaacctctgtctatgatgctatcaatagttgtaaaattagtgatccttatttttctgtttaccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACAAGCAAAAAG

Basic information

species Zea mays
transcript AC195874.2_FGT002
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC195874.2_FGT002 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G40430.2 (Glycine max), 3'ss of exon 4
-----taaaaaccaaacacgtagttacgccttttatgaacctctgtctatgatgctatcaatagttgtaaaattagtgatccttatttttctgtttaccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACAAGCAAAAAG
       |  |||| |    | ||  |  |||   | |   | |   ||  ||  | | |||  ||      ||| | ||  |  |||  |  | |  ||||||||| || || ||||| |||||||| ||||| || || || ||||||||||||||||| |||
gatcaccattaccatattgatcgtaccctcttcctttagattattattactatttttttaatgtttcc----ttactcata-tagtttacccatatgtcttgaagGTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACAAGCAAGAAG

upper sequence: AC195874.2_FGT002 (Zea mays), 3'ss of exon 4
lower sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 4
---taaaaaccaaacacgtagttacgcc--ttttatgaacctctgtctatgatgctatc--aatagttgtaaaattagtgatccttatttttctgtttaccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACAAGCAAAAAG
   |       | | | | || | |  |  | ||   |   |   ||| || |  ||    |||| |||  ||  ||||  ||| |||   |    | | ||  ||||| ||| ||||||| ||||| || ||||||||||||||||| |||||||||||||||| |
tatttgtgtttatatatgcagatgctacagtgtttctagatttgatctgtgtttgtactctaataattgctaa-ctagt--tccctatgact----taaactgaaagGTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAGG

upper sequence: AC195874.2_FGT002 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 5
taaaaaccaaacacgtagttacgcctttta---tgaacctctgtctatgatgctatcaatagttgtaaaattag----tgatccttatttttctgtttacct--tgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACAAGCAAAAAG
            | ||  ||  || |  |    || |  |  || |||  |  |    ||  || ||   ||      |    | |     | |||||  ||  | |||||||| || ||||| || ||||| ||||||||||||||||| ||||||||||||||||||
---------tgtatgtgtttgggcttgctgacgtgtagtttggtgtatattattgctcatcattatattctttcctttttgctcatggaactgtgtttgtctgataaagGTTTATCTTATACTTGACGAATTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAAG

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|10191604|gb|BE761680.1|BE761680
EST:     TTTAGTGTTTAATTTTCCCAAG                         GTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
genomic: TTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
EST: gi|60336636|gb|DN203609.1|DN203609
EST:     ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAG                         GTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
genomic: ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
EST: gi|32909659|gb|CF014471.1|CF014471
EST:     ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAG                         GTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
genomic: ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
EST: gi|211264888|gb|FL091722.1|FL091722
EST:     ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAG                         GTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
genomic: ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
EST: gi|211262443|gb|FL091703.1|FL091703
EST:     ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAG                         GTTTACCTGATACTAGATGAATTTATT
genomic: ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATT
EST: gi|16916618|gb|BM072921.1|BM072921
EST:     ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAG                         GTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
genomic: ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
EST: gi|33103150|gb|CF063110.1|CF063110
EST:     ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAG                         GTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
genomic: ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
EST: gi|166583021|gb|EG238440.1|EG238440
EST:     TTTCTTTAGCAAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAG                         GTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGC
genomic: TTTCTTTAGC-AATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGC
EST: gi|32909660|gb|CF014472.1|CF014472
EST:     ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAG                         GTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
genomic: ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
EST: gi|22545654|gb|BU098013.1|BU098013
EST:     ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAG                         GTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
genomic: ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
EST: gi|211264887|gb|FL091721.1|FL091721
EST:     ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAG                         GTTTAC-TGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCA
genomic: ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCA
EST: gi|60346385|gb|DN213358.1|DN213358
EST:     ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAG                         GTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
genomic: ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
EST: gi|211267313|gb|FL091727.1|FL091727
EST:     ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAG                         GTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
genomic: ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
EST: gi|78025572|gb|DV493959.1|DV493959
EST:     ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAG                         GTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
genomic: ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
EST: gi|166627380|gb|EG231513.1|EG231513
EST:     ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAG                         GTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGC
genomic: ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGC
EST: gi|4827606|gb|AI668298.1|AI668298
EST:     ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGGGTTTAATTTTCCCAAG                         GTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
genomic: ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
EST: gi|211262451|gb|FL091711.1|FL091711
EST:     TTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAAATTTTCACAAG                         GTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCA
genomic: TTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAA-TTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCA
EST: gi|71422803|gb|DR805854.1|DR805854
EST:     ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAG                         GTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA
genomic: ATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACA

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: 266

TGAATTGGCATACTTGGAATGCATTCACTTGTTTGTCGAGATATTGGACCATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACAAGCAAAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 655

TGAATTGGCATACTTGGAATGCATTCACTTGTTTGTCGAGATATTGGACCATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACAAGCAAAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 387

TGAATTGGCATACTTGGAATGCATTCACTTGTTTGTCGAGATATTGGACCATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACAAGCAAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 352

TGAATTGGCATACTTGGAATGCATTCACTTGTTTGTCGAGATATTGGACCATTTCTTTAGCAATGTTTGTGAGCTCGATTTAGTGTTTAATTTTCACAAGgtacagattc ... taccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACAAGCAAAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgctatcaatagttgtaaaattagtgatccttatttttctgtttaccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACAAGCAAAAAG
                             tccttatttttctgtt  CT-rich tract
         aatagttgtaaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaaaccaaacacgtagttacgccttttatgaacctctgtctatgatgctatcaatagttgtaaaattagtgatccttatttttctgtttaccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACAAGCAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - ccaaaca
- - - - - - - - - - - - - - - - - - - - - - tgatgct