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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtatatatacttgattggttgatgccatggactctctccctatctttctgcgcctagcctaatgacaattcagtaggatgtatgccaattgatgagtatagcgtagatcgatgttggccctgaatgcagcatgccctaatgtggtattgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCATTGATCAGCTCCGTGACCAGCGCGTTGTGGCTGTTACACAG

Basic information

species Zea mays
transcript GRMZM2G034143_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 2
gtccgtatatatacttgattggttgatgccatggactctctccctatctttctgcgcctagcctaatgacaattcagtaggatgtatgccaattgatgagtatagcgtagatcgatgttggccctgaatgcagcatg-----ccctaatgtggtattgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCATTGATCAGCTCCGTGACCAGCGCGTTGTGGCTGTTACACAG
                  || ||   || |  |  |  ||  | || || | ||               ||| | |  |||  ||||  | || | |||  |||  ||||  |  | |   |||  ||||   ||||     || | || | || | |  | |||| || |||||||||||||| ||||| |||||||| || ||||||||||| ||||||||||| ||||| ||||| || || | |||||| |||
-----------------gttagtacctgtcgagtgccgtcgtcttacctatttgtttt----------gcaagtaatcagggagtat--cgatcgctgaacataatgtagcccttt-tgccccccaaatgtgtcatgtcgttccatgattttgtttggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAATTGATCAGCTACGTGATCAGCGTGTGGTTGTTGTTACTCAG

upper sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 3'ss of exon 2
gtccgtatatatacttgattggttgatgccatggactctctccctatctttctgcgcctagcctaatgacaattcagtaggatgtatgccaattgatgagtatagcgtagatcgatgttggccctgaatgcagcatgccctaatgtggtattgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCATTGATCAGCTCCGTGACCAGCGCGTTGTGGCTGTTACACAG
                     |||  |   |    |||  | | | | ||| |  |  ||   |      ||| |||||      ||  | | || ||   |||  ||||  |  | ||| | |   |||   ||| |||| || |||| | |  |||||| ||||| ||||||||||| |||||||||||||| || ||||| ||||| || |||||||| ||||| ||||| || || | |||||| |||
---------------------gttagtagtacttgctcagtgc-tgtttttgtctgtttattttgcaagtaat-cagtaa-----atatcgactgttgtacataatgtagccc--ttttgcctcccgatgtttcattccctgatttggtttggattacagGTGTTGCCGGGGGTGCATCTTCAGGCAAAAGTACTGTATGCAAAATGATAATCGATCAGCTACGTGATCAGCGTGTAGTTGTTGTTACTCAG
















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|211489871|gb|FL134685.1|FL134685
EST:     ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTG                         GCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
genomic: ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
EST: gi|78113249|gb|DV531643.1|DV531643
EST:     ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTG                         GCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
genomic: ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
EST: gi|211492747|gb|FL134690.1|FL134690
EST:     ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTG                         GCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
genomic: ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
EST: gi|211492748|gb|FL134691.1|FL134691
EST:     ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTG                         GCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
genomic: ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
EST: gi|71439660|gb|DR820710.1|DR820710
EST:     ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTG                         GCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
genomic: ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
EST: gi|148995152|gb|EE034432.2|EE034432
EST:     ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTG                         GCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
genomic: ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
EST: gi|211489870|gb|FL134684.1|FL134684
EST:     ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTG                         GCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
genomic: ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
EST: gi|211489869|gb|FL134683.1|FL134683
EST:     ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTG                         GCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
genomic: ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
EST: gi|211492744|gb|FL134687.1|FL134687
EST:     ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTG                         GCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
genomic: ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
EST: gi|211489866|gb|FL134680.1|FL134680
EST:     ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTG                         GCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
genomic: ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
EST: gi|31359325|gb|CD443682.1|CD443682
EST:     ACCAACGACGGGTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTG                         GCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
genomic: ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
EST: gi|149020749|gb|EE045750.2|EE045750
EST:     ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTG                         GCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
genomic: ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
EST: gi|211492749|gb|FL134692.1|FL134692
EST:     ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTG                         GCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
genomic: ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
EST: gi|148943394|gb|EC888453.2|EC888453
EST:     ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTG                         GCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
genomic: ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
EST: gi|149088610|gb|EE177727.2|EE177727
EST:     ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTG                         GCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
genomic: ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
EST: gi|211492751|gb|FL134694.1|FL134694
EST:     ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTG                         GCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA
genomic: ACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCA

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: 133

CTCCGTCTGGACGGTCCCAACGTCCAGTTTTCCGCCTCCTCCGAGGAAGAACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCATTGATCAGCTCCGTGACCAGCGCGTTGTGGCTGTTACACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 66

CTCCGTCTGGACGGTCCCAACGTCCAGTTTTCCGCCTCCTCCGAGGAAGAACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCATTGATCAGCTCCGTGACCAGCGCGTTGTGGCTGTTACACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

CTCCGTCTGGACGGTCCCAACGTCCAGTTTTCCGCCTCCTCCGAGGAAGAACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCATTGATCAGCTCCGTGACCAGCGCGTTGTGGCTGTTACACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 139

CTCCGTCTGGACGGTCCCAACGTCCAGTTTTCCGCCTCCTCCGAGGAAGAACCAACGACGTCTGGCCTGGAGAATGGCCATCAGGAGCCCTTTGTTATTGgtccgtatat ... ttgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCATTGATCAGCTCCGTGACCAGCGCGTTGTGGCTGTTACACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtagatcgatgttggccctgaatgcagcatgccctaatgtggtattgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCATTGATCAGCTCCGTGACCAGCGCGTTGTGGCTGTTACACAG
                                ccctaat  putative branch site (score: 139)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgtatatatacttgattggttgatgccatggactctctccctatctttctgcgcctagcctaatgacaattcagtaggatgtatgccaattgatgagtatagcgtagatcgatgttggccctgaatgcagcatgccctaatgtggtattgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCATTGATCAGCTCCGTGACCAGCGCGTTGTGGCTGTTACACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT