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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatcttctcttatctttcaagctcgcacagcatggtagcttttttttttcctaatcgcgattcatatggcctggccctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGATGAACGGCTACCAGTTAGGCGGTAAAAAGCTCAAGGTACAACTGAAGAG

Basic information

species Zea mays
transcript GRMZM2G005459_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005459_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g71200.1 (Oryza sativa), 3'ss of exon 8
------------gtaagatcttctcttatctttcaagctcgcaca-gcatg-gtagcttttttttttcctaatcgcgattcatatggcctggccctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGATGAACGGCTACCAGTTAGGCGGTAAAAAGCTCAAGGTACAACTGAAGAG
                  |||     | ||| |||  | | ||||  ||     |        |||| || || |      | || |  |      || |||||||||||| |||||||| |||||||| ||||| |||||||||||      ||||||||| | ||| |||||| ||||||| ||||| |||||||| |||||
gtaatctctctctctctctctctctctctctctcacacacacacacacacacacacacacacattttgcttatagtctgcta-attgttttctaacgggtgcagGTTTTGTAAGCTACGATTCTCCTGCTTCCGCACAGGCAGCCATTGGTGTGATGAACGGTTTCCAATTAGGCAGTAAAAAACTCAAAGTACAACTCAAGAG
















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|211119732|gb|FL458408.1|FL458408
EST:     AAGCGCTAAGGTGTTCGTGGACAAAGCAACGGGCGTGAGCAAATGCTTCG                         GTTTCGTGAGCTACGACTYTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
genomic: AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCGgtaagatctt ... ctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
EST: gi|60337356|gb|DN204329.1|DN204329
EST:     AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCG                         GTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
genomic: AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCGgtaagatctt ... ctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
EST: gi|37383165|gb|CF628572.1|CF628572
EST:     GGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCG                         GTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
genomic: GGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCGgtaagatctt ... ctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
EST: gi|13178538|gb|BG349796.1|BG349796
EST:     AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCG                         GTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
genomic: AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCGgtaagatctt ... ctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
EST: gi|60394696|gb|DN227566.1|DN227566
EST:     AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCG                         GTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
genomic: AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCGgtaagatctt ... ctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
EST: gi|83278898|gb|DV942906.1|DV942906
EST:     AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCG                         GTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
genomic: AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCGgtaagatctt ... ctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
EST: gi|148934647|gb|EC878698.2|EC878698
EST:     AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCG                         GTTTTGTGAGTTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
genomic: AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCGgtaagatctt ... ctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
EST: gi|5713840|gb|AI943825.1|AI943825
EST:     AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCG                         GTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
genomic: AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCGgtaagatctt ... ctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
EST: gi|13178260|gb|BG349518.1|BG349518
EST:     AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCG                         GTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
genomic: AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCGgtaagatctt ... ctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
EST: gi|76011818|gb|DT938988.1|DT938988
EST:     AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCG                         GTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
genomic: AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCGgtaagatctt ... ctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
EST: gi|211198530|gb|FL470721.1|FL470721
EST:     AAGCGCTAAGGTGTTCGTGGACAAAGCAACGGGCGTGAGCAAATGCTTCG                         GTTTCGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
genomic: AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCGgtaagatctt ... ctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
EST: gi|149074525|gb|EE162923.2|EE162923
EST:     AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCG                         GTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA
genomic: AAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCGgtaagatctt ... ctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGA

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: 48 (upstream exon), 49 (downstream exon)
Score: 92

TACGGTGACCAGGAGCTTTCCAGCGCCTTCCAGAGTTTCGGAAGAGTAGTAAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCGgtaagatctt ... ctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGATGAACGGCTACCAGTTAGGCGGTAAAAAGCTCAAGGTACAACTGAAGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 24

TACGGTGACCAGGAGCTTTCCAGCGCCTTCCAGAGTTTCGGAAGAGTAGTAAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCGgtaagatctt ... ctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGATGAACGGCTACCAGTTAGGCGGTAAAAAGCTCAAGGTACAACTGAAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 19

TACGGTGACCAGGAGCTTTCCAGCGCCTTCCAGAGTTTCGGAAGAGTAGTAAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCGgtaagatctt ... ctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGATGAACGGCTACCAGTTAGGCGGTAAAAAGCTCAAGGTACAACTGAAGAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 20

TACGGTGACCAGGAGCTTTCCAGCGCCTTCCAGAGTTTCGGAAGAGTAGTAAGCGCTAAGGTGTTCGTAGATAAAGCAACGGGCGTGAGCAAATGCTTCGgtaagatctt ... ctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGATGAACGGCTACCAGTTAGGCGGTAAAAAGCTCAAGGTACAACTGAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtagcttttttttttcctaatcgcgattcatatggcctggccctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGATGAACGGCTACCAGTTAGGCGGTAAAAAGCTCAAGGTACAACTGAAGAG
                 tcctaat  putative branch site (score: 20)
        ttttttttttcctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatcttctcttatctttcaagctcgcacagcatggtagcttttttttttcctaatcgcgattcatatggcctggccctggctgcagGTTTTGTGAGCTACGACTCTCCTGCCTCCGCGCAGGCAGCCATCAACAGGATGAACGGCTACCAGTTAGGCGGTAAAAAGCTCAAGGTACAACTGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA