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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattctcttttggtctgagtcagtagttgacctttagaaatcttaattttgctgtccagcgacgatctcacttttgctctggtgcttgtaacttgtttagGTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACTCATCTTACTGCACCCACGCAAAGTGGACTGTTTAGCAAGTACTATGAAA

Basic information

species Zea mays
transcript GRMZM2G178227_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178227_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g50850.2 (Oryza sativa), 3'ss of exon 1
-cattctcttttggtctgagtcagtagttgacctttagaaatcttaattttgctgtccagcgacgatctcacttttgctctggtgcttgtaacttgtttagGTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACTCATCTTACTGCACCCACGCAAAGTGGACTGTTTAGCAAGTACTATGAAA
   || |||    ||| || | ||   |  |   |   | |  |     ||  | | | |  || || |  ||||||||   |||  |  |  ||   ||||||||||| |||||||||||||| |||||||||||||||||||||  ||  ||||||| | |  |   ||||  || | | |||   |||| |||||| |
atgttgtctgactgtccgactgagagatgcataatggcataattagtcatttttatgcggttac-attttgcttttgctaatgtgactacattttacatagGTGGAAATCTACGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAACCATCTTAGTTCCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACA
















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|60393978|gb|DN226848.1|DN226848
EST:     CGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTC                         GTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
genomic: CGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTCgtacgtgcca ... acttgtttagGTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
EST: gi|76290494|gb|DV030062.1|DV030062
EST:     ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTC                         GTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
genomic: ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTCgtacgtgcca ... acttgtttagGTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
EST: gi|31353537|gb|CD437894.1|CD437894
EST:     ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTC                         GTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
genomic: ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTCgtacgtgcca ... acttgtttagGTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
EST: gi|211186070|gb|FL219844.1|FL219844
EST:     ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTC                         GTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
genomic: ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTCgtacgtgcca ... acttgtttagGTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
EST: gi|78087329|gb|DV515722.1|DV515722
EST:     ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTC                         GTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
genomic: ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTCgtacgtgcca ... acttgtttagGTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
EST: gi|211324079|gb|FL420998.1|FL420998
EST:     ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTC                         GTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
genomic: ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTCgtacgtgcca ... acttgtttagGTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
EST: gi|149106278|gb|EE291979.2|EE291979
EST:     ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTC                         GTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
genomic: ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTCgtacgtgcca ... acttgtttagGTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
EST: gi|76285477|gb|DV025045.1|DV025045
EST:     ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTC                         GTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
genomic: ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTCgtacgtgcca ... acttgtttagGTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
EST: gi|211048309|gb|FL397306.1|FL397306
EST:     ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTC                         GTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
genomic: ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTCgtacgtgcca ... acttgtttagGTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
EST: gi|211186071|gb|FL219845.1|FL219845
EST:     ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTC                         GTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
genomic: ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTCgtacgtgcca ... acttgtttagGTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
EST: gi|9742974|gb|BE519122.1|BE519122
EST:     ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTC                         GCGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT
genomic: ACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTCgtacgtgcca ... acttgtttagGTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACT

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: 187

CGAGCTGCAACGGGAGCCCGCTAACCCGCGTGACCGCCTCTTTCAGTCCCACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTCgtacgtgcca ... acttgtttagGTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACTCATCTTACTGCACCCACGCAAAGTGGACTGTTTAGCAAGTACTATGAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 132

CGAGCTGCAACGGGAGCCCGCTAACCCGCGTGACCGCCTCTTTCAGTCCCACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTCgtacgtgcca ... acttgtttagGTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACTCATCTTACTGCACCCACGCAAAGTGGACTGTTTAGCAAGTACTATGAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 152

CGAGCTGCAACGGGAGCCCGCTAACCCGCGTGACCGCCTCTTTCAGTCCCACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTCgtacgtgcca ... acttgtttagGTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACTCATCTTACTGCACCCACGCAAAGTGGACTGTTTAGCAAGTACTATGAAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 64

CGAGCTGCAACGGGAGCCCGCTAACCCGCGTGACCGCCTCTTTCAGTCCCACCGCGTCCGCCACATGCTCGACCTCGTCGTCTCCACCTCCGGCAAGCTCgtacgtgcca ... acttgtttagGTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACTCATCTTACTGCACCCACGCAAAGTGGACTGTTTAGCAAGTACTATGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttgctgtccagcgacgatctcacttttgctctggtgcttgtaacttgtttagGTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACTCATCTTACTGCACCCACGCAAAGTGGACTGTTTAGCAAGTACTATGAAA
                                        ttgtaac  putative branch site (score: 64)
                                              cttgttt  CT-rich tract
                                               ttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattctcttttggtctgagtcagtagttgacctttagaaatcttaattttgctgtccagcgacgatctcacttttgctctggtgcttgtaacttgtttagGTGGAAATTTACGAGGACAAGGACAATGCTAGGAAGGATGAGATCAACACTCATCTTACTGCACCCACGCAAAGTGGACTGTTTAGCAAGTACTATGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
cattctc
- - - -ttttggt
- - - - - - - - - - - - - - - - - - - - - - - - -tgctgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttgt