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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacccctgcttccggcacggacggacgggcgatctgttctctagatagacctcatgcgtgtccgtgtgttgatcttgacactttctttctcttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAGCTCCGCGGGCAGCCCAAGGTGGTGGAGGACCGCCAGTGGTCTCTCATGA

Basic information

species Zea mays
transcript GRMZM2G033117_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033117_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g41930.2 (Oryza sativa), 3'ss of exon 1
cacccctgcttccggcacggacggacgggcgatctgttctctagatagacctcatgcgtgtccgtgtgttgatcttgac----actttctttctcttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAGCTCCGCGGGCAGCCCAAGGTGGTGGAGGACCGCCAGTGGTCTCTCATGA
  | | |  || | || |   |  |      ||       | || | ||  |  |  ||  ||  || | ||||  | |        | | | ||||||   |||||       |   | |||||||||||| | |||||||||| ||||| ||| |||| |||||| | ||||| ||||||||||| ||||||||||||||||
tcctcttaatttcagcgc---cttaaccttaatacaagtaccagtttgagtttgtttgttcccaagt-tggatccggccctgggtaatttctttcttgctgaagGTGGAGAGACTGAGCTGAGCTATGGACAACTTGTGGCATCTCGGGGATGAGTTCCGTGGGCAGTCGAAGGTAGTGGAGGACCGTCAGTGGTCTCTCATGA
















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|87156037|gb|DY400826.1|DY400826
EST:     CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
genomic: CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
EST: gi|148949364|gb|EC894819.2|EC894819
EST:     CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
genomic: CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
EST: gi|211392146|gb|FL138784.1|FL138784
EST:     CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGRGCACCACCAG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTG
genomic: CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTG
EST: gi|88755431|gb|DY539572.1|DY539572
EST:     CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
genomic: CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
EST: gi|149043151|gb|EE047296.2|EE047296
EST:     CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
genomic: CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
EST: gi|87156661|gb|DY401450.1|DY401450
EST:     CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
genomic: CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
EST: gi|149071591|gb|EE159982.2|EE159982
EST:     CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
genomic: CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
EST: gi|22935447|gb|BU571722.1|BU571722
EST:     CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
genomic: CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
EST: gi|211394771|gb|FL138798.1|FL138798
EST:     CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
genomic: CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
EST: gi|31998268|gb|CD662002.1|CD662002
EST:     AAGTGCCCAGGTCATCTNTCGGGCCATTCGCCGGCGACGAGCACCACCAG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
genomic: AAGTGCCCAGGTCATCT-TCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
EST: gi|149102652|gb|EE288009.2|EE288009
EST:     CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
genomic: CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
EST: gi|211362524|gb|FL119618.1|FL119618
EST:     CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
genomic: CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
EST: gi|211394768|gb|FL138795.1|FL138795
EST:     CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCNG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
genomic: CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
EST: gi|78077999|gb|DV506414.1|DV506414
EST:     CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
genomic: CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
EST: gi|22935928|gb|BU572203.1|BU572203
EST:     CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
genomic: CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
EST: gi|148932942|gb|EE285770.2|EE285770
EST:     CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
genomic: CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
EST: gi|26560072|gb|CA832307.1|CA832307
EST:     CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
genomic: CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
EST: gi|149079919|gb|EE168929.2|EE168929
EST:     CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
genomic: CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
EST: gi|101384187|gb|EB814138.1|EB814138
EST:     CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
genomic: CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
EST: gi|5268422|gb|AI770386.1|AI770386
EST:     CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAG                         GTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG
genomic: CAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAG

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: 151

GACTCCCGTAGGCCGTGGTGCCGCCGCCGACTGCTGGGACTGCCCTACACCAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAGCTCCGCGGGCAGCCCAAGGTGGTGGAGGACCGCCAGTGGTCTCTCATGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 99

GACTCCCGTAGGCCGTGGTGCCGCCGCCGACTGCTGGGACTGCCCTACACCAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAGCTCCGCGGGCAGCCCAAGGTGGTGGAGGACCGCCAGTGGTCTCTCATGA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 51

GACTCCCGTAGGCCGTGGTGCCGCCGCCGACTGCTGGGACTGCCCTACACCAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAGCTCCGCGGGCAGCCCAAGGTGGTGGAGGACCGCCAGTGGTCTCTCATGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 56

GACTCCCGTAGGCCGTGGTGCCGCCGCCGACTGCTGGGACTGCCCTACACCAAGTGCCCAGGTCATCTTCGGGCCATTCGCCGGCGACGAGCACCACCAGgtacgcccac ... cttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAGCTCCGCGGGCAGCCCAAGGTGGTGGAGGACCGCCAGTGGTCTCTCATGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagacctcatgcgtgtccgtgtgttgatcttgacactttctttctcttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAGCTCCGCGGGCAGCCCAAGGTGGTGGAGGACCGCCAGTGGTCTCTCATGA
                           tcttgac  putative branch site (score: 56)
                           tcttgacactttcttt  CT-rich tract
                                    tttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacccctgcttccggcacggacggacgggcgatctgttctctagatagacctcatgcgtgtccgtgtgttgatcttgacactttctttctcttgcaacagGTGTGCCAGGTTGACCGAGCTATGGACAGCCTGTGGCATCTTGGGGACGAGCTCCGCGGGCAGCCCAAGGTGGTGGAGGACCGCCAGTGGTCTCTCATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - -ctgcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - -atgcgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgat