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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttctgcaaatgcttttagtaatggaaactactgcttgacaattgtgtttgttaccataatgtaattctttctctacagGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGCAAAAGCCGTAGCAGGAGAAGCAGAAGTCCCATTCATAAGTTGCTCTGCTAGTGAATTTGTTGAGC

Basic information

species Zea mays
transcript GRMZM2G072865_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G072865_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 4
gttggttctgcaaatgcttttagtaatggaaactactgcttgacaattgtgtttgttaccataatgtaattctttctctacagGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGCAAAAGCCGTAGCAGGAGAAGCAGAAGTCCCATTCATAAGTTGCTCTGCTAGTGAATTTGTTGAGC
||  ||||||||     ||| |||||||   | |  |||| ||| |  || ||||| || || ||||||||| || | |||||||||| |||||||| ||||||||||| |||||||||||||| || ||||| ||||| |||||||||||||||||||||||||| ||||||||||| ||| 
gtcagttctgcagtca-tttaagtaatgatgaatgttgctggactagagtttttgt-actatgatgtaattcattatttacagGTGGGCCTTCCAGGAACTGGAAAGACGCTTCTTGCAAAAGCTGTCGCAGGGGAAGCTGAAGTCCCATTCATAAGTTGCTCTGCAAGTGAATTTGTGGAGT

upper sequence: GRMZM2G072865_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G39040.1 (Glycine max), 3'ss of exon 5
----------gttggttctgcaaatgctt-ttagtaatggaaactactgct-tgacaatt----gtgtttgttaccataatgtaattctttctct-acagGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGCAAAAGCCGTAGCAGGAGAAGCAGAAGTCCCATTCATAAGTTGCTCTGCTAGTGAATTTGTTGAGC
          || | || |  | |  |   ||| |  |  | | || |  | |   ||||      ||  ||    |  ||  | |  ||| ||| ||||||||||||||| ||||| || |||||  | || ||||| || || ||||| ||||| || || ||||| |||||||| ||||||||||| ||||| ||| 
ctcatcgtatgtggattatttatagccaagttactttttcatattattattgttttaatttgaaacgtaggtagtaaatatccactgttttatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTTTACTGGCAAAGGCTGTGGCAGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTTGTAGAGT

upper sequence: GRMZM2G072865_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA0028S00210.2 (Glycine max), 3'ss of exon 4
--------------gttggttctgcaaatgcttttagtaatggaaactactgcttgacaattgtgtttgttaccataatgtaattcttt----ctctacagGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGCAAAAGCCGTAGCAGGAGAAGCAGAAGTCCCATTCATAAGTTGCTCTGCTAGTGAATTTGTTGAGC
               |||  | |||       |||    ||    | || || || |   |    | |        ||| |   ||||     |  |||||||||||||||| || || || |||||  | |||||||| || || || || ||||| || || ||||| |||||||| ||||||||||| || || ||  
gaaatgttttcacttttgtctttgctg-catgtttgaggatttttaatattgttttaggttgacatctaggctgtgaatatctctcttgattaccttacagGTGGGTCTTCCTGGCACAGGTAAGACTTTACTTGCAAAGGCTGTGGCTGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTCGTAGAAT

upper sequence: GRMZM2G072865_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G37090.1 (Glycine max), 3'ss of exon 5
--------------gttggttctgcaaatgcttttagtaatggaaactactgcttgacaat--tgtgtttgttaccataatgtaattctttctct-acagGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGCAAAAGCCGTAGCAGGAGAAGCAGAAGTCCCATTCATAAGTTGCTCTGCTAGTGAATTTGTTGAGC
               ||  || |    | | |     |       | || || || |   |    |||  ||    |  ||  | |  ||| ||| ||||||||||||||| ||||| || |||||  | || ||||| || || ||||| ||||| || || ||||| |||||||| ||||||||||| ||||| ||| 
cacagtgtatgtggattatttatagccaagttaccttttcatattattattgttttaatttgacatgtaggtagtaaatatccactgttttatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTTTACTGGCAAAGGCTGTGGCAGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTTGTAGAGT

upper sequence: GRMZM2G072865_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------gttggttctgcaaatgctttta-gtaatgga--aactactgcttgacaattgtgtttgttaccataatgt-------aattctttctctac-agGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGCAAAAGCCGTAGCAGGAGAAGCAGAAGTCCCATTCATAAGTTGCTCTGCTAGTGAATTTGTTGAGC
                        ||  ||||   | | | | ||  | ||||   |||   || ||   |    | |   |||  || || |       | | |||||| | | |||| |||||||| || || || || || ||||||||||| || || || || ||||| |||||||| ||||||||||||||||| ||||| ||||| ||||
gtgagttttatcatttgatttcactttattcttatattacgtatatatcatggtttaacgtttggttacaagagctctcctttagaatgatatgcctttgactcctttcttttccagGTTGGTCTTCCCGGAACAGGGAAAACCCTTCTTGCAAAGGCTGTTGCTGGGGAAGCTGAAGTCCCCTTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGC

upper sequence: GRMZM2G072865_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------gttggttctgcaaatgcttttagtaatggaaac-tactgcttgacaattgtgtttg----ttaccataatgtaattctttctctacagGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGCAAAAGCCGTAGCAGGAGAAGCAGAAGTCCCATTCATAAGTTGCTCTGCTAGTGAATTTGTTGAGC
                         || ||   ||   ||  ||  |  |  |  | || |||   | | | |||     |||      | |    || | |    |||| |||||||| || || || || || |||||||||||||| || || || ||| | || || |||||||||||||||||||| ||||| ||||| ||||
gtgagtttaataatgtagttacaacttatggccatttcttaggtggtttatgcgcaatgtttggttactatctttagaatttatggctttatttccctgttttggtagGTCGGTCTTCCTGGAACAGGGAAAACCCTTCTTGCAAAAGCTGTTGCTGGGGAATCTGATGTTCCATTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGC

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|32868282|gb|CF007964.1|CF007964
EST:     CGTGGTGTCTTATTG                         GTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGCAAAAGCCGTAGCAGGA
genomic: CGTGGTGTCTTATTGgttggttctg ... ttctctacagGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGCAAAAGCCGTAGCAGGA
EST: gi|32925296|gb|CF030108.1|CF030108
EST:     GAAATTGTGGCGTGGTGTCTTATTG                         GTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGC
genomic: GAAATTGTGGCGTGGTGTCTTATTGgttggttctg ... ttctctacagGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGC
EST: gi|32867768|gb|CF007450.1|CF007450
EST:     CGTGGTGTCTTATTG                         GTGGGTCTTCCAGGGACTGGGAAAGACACTTCTTGCAAAAGCCGTAGCAGG
genomic: CGTGGTGTCTTATTGgttggttctg ... ttctctacagGTGGGTCTTCCAGGGACT-GGAAAGACACTTCTTGCAAAAGCCGTAGCAGG
EST: gi|32925381|gb|CF030193.1|CF030193
EST:     TCGTGGTGTCTTATTG                         GTGGGTCTTCCAGGGACTGGAAAGACACTTCTTG
genomic: -CGTGGTGTCTTATTGgttggttctg ... ttctctacagGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTG

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), 49 (downstream exon)
Score: 55

CGTGGTGTCTTATTGgttggttctg ... ttctctacagGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGCAAAAGCCGTAGCAGGAGAAGCAGAAGTCCCATTCATAAGTTGCTCTGCTAGTGAATTTGTTGAGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 77

CGTGGTGTCTTATTGgttggttctg ... ttctctacagGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGCAAAAGCCGTAGCAGGAGAAGCAGAAGTCCCATTCATAAGTTGCTCTGCTAGTGAATTTGTTGAGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 57

CGTGGTGTCTTATTGgttggttctg ... ttctctacagGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGCAAAAGCCGTAGCAGGAGAAGCAGAAGTCCCATTCATAAGTTGCTCTGCTAGTGAATTTGTTGAGC


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 54

CGTGGTGTCTTATTGgttggttctg ... ttctctacagGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGCAAAAGCCGTAGCAGGAGAAGCAGAAGTCCCATTCATAAGTTGCTCTGCTAGTGAATTTGTTGAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaactactgcttgacaattgtgtttgttaccataatgtaattctttctctacagGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGCAAAAGCCGTAGCAGGAGAAGCAGAAGTCCCATTCATAAGTTGCTCTGCTAGTGAATTTGTTGAGC
         gcttgac  putative branch site (score: 54)
                                         ttctttctctac  putative PPT
                                ataatgtaattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttctgcaaatgcttttagtaatggaaactactgcttgacaattgtgtttgttaccataatgtaattctttctctacagGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGCAAAAGCCGTAGCAGGAGAAGCAGAAGTCCCATTCATAAGTTGCTCTGCTAGTGAATTTGTTGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT