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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtacacaaccgttgtaacactacttttatgagttggaataaaaatccatatctggtatcgtgctggtactgatgctttctgttattcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGATAATACTTAGATATTGCTGATTTATCAGCATTGATTAACTCTTTGGCAT

Basic information

species Zea mays
transcript GRMZM5G824597_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824597_T02 (Zea mays), 3'ss of exon 6
lower sequence: 13113.m00164 (Oryza sativa), 3'ss of exon 5
-----gttgtacacaaccgttgtaacactacttttatgagttggaataaaaatccatatctggtatcgtgctggtactgatgctttctgttattcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGATAATACTTAGATATTGCTGATTTATCAGCATTGATTAACTCTTTGGCAT
     |||||||       ||| | | |||||||||   |     | |        |||||| |      |  |  ||||  ||| || || ||||     ||||| ||||| |||||||||||||||||||||||||| ||| |||  || ||  ||| | |||||||||   ||| || | ||||||||            
cggaggttgtacggttttcttgaatcgctacttttacatgaaaagaaattttattgtatctgattgtagaccagctctgactcttgctatttttctc---cagGGCGAGAGTGCGAGGAGCTTTGTTGCAAGATACTGAGGAAGATGTCGAAGA--ATAGTCAGATATTGCCT-TTTCTCTGTATTGATTAG-----------
















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|37377388|gb|CF625291.1|CF625291
EST:     AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG                         GGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
genomic: AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAGgttgtacaca ... tcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
EST: gi|93012148|gb|EB637668.1|EB637668
EST:     AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG                         GGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
genomic: AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAGgttgtacaca ... tcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
EST: gi|76283432|gb|DV023000.1|DV023000
EST:     AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG                         GGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
genomic: AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAGgttgtacaca ... tcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
EST: gi|78180984|gb|DV551357.1|DV551357
EST:     AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG                         GGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
genomic: AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAGgttgtacaca ... tcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
EST: gi|94476028|gb|EB704986.1|EB704986
EST:     AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG                         GGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
genomic: AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAGgttgtacaca ... tcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
EST: gi|7844188|gb|AW787410.1|AW787410
EST:     AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG                         GGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
genomic: AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAGgttgtacaca ... tcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
EST: gi|7844190|gb|AW787412.1|AW787412
EST:     AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG                         GGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
genomic: AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAGgttgtacaca ... tcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
EST: gi|94476019|gb|EB704977.1|EB704977
EST:     AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG                         GGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
genomic: AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAGgttgtacaca ... tcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
EST: gi|12046853|gb|BF729005.1|BF729005
EST:     AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG                         GGCAAGAGTACGAGGAGCTTTGGTGCAAGATACTGAAGAAAATGCTGATGA
genomic: AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAGgttgtacaca ... tcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
EST: gi|15177373|gb|BI398312.1|BI398312
EST:     AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG                         GGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGGTGATGA
genomic: AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAGgttgtacaca ... tcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
EST: gi|7844189|gb|AW787411.1|AW787411
EST:     AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG                         GGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
genomic: AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAGgttgtacaca ... tcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
EST: gi|94479639|gb|EB708597.1|EB708597
EST:     AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG                         GGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
genomic: AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAGgttgtacaca ... tcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
EST: gi|60350072|gb|DN217045.1|DN217045
EST:     AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG                         GGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
genomic: AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAGgttgtacaca ... tcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
EST: gi|71326414|gb|DR799890.1|DR799890
EST:     AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG                         GGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA
genomic: AAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAGgttgtacaca ... tcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGA

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), 41 (downstream exon)
Score: 31

TGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAGgttgtacaca ... tcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGATAATACTTAGATATTGCTGATTTATCAGCATTGATTAACTCTTTGGCAT


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 17

TGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAGgttgtacaca ... tcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGATAATACTTAGATATTGCTGATTTATCAGCATTGATTAACTCTTTGGCAT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 11

TGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAGgttgtacaca ... tcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGATAATACTTAGATATTGCTGATTTATCAGCATTGATTAACTCTTTGGCAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 10

TGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAGgttgtacaca ... tcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGATAATACTTAGATATTGCTGATTTATCAGCATTGATTAACTCTTTGGCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatccatatctggtatcgtgctggtactgatgctttctgttattcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGATAATACTTAGATATTGCTGATTTATCAGCATTGATTAACTCTTTGGCAT
                          tactgat  putative branch site (score: 10)
                                  ctttctgttattctt  CT-rich tract
                                         ttattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtacacaaccgttgtaacactacttttatgagttggaataaaaatccatatctggtatcgtgctggtactgatgctttctgttattcttgattagGGCAAGAGTACGAGGAGCTTTGTTGCAAGATACTGAAGAAAATGCTGATGATAATACTTAGATATTGCTGATTTATCAGCATTGATTAACTCTTTGGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT