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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatttacattctcttaacatccaactgccagtacttaagaaacttattttatgcaattaaagcagggcaaactataactgttctttttcctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA

Basic information

species Zea mays
transcript GRMZM2G094978_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094978_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g36750.1 (Oryza sativa), 3'ss of exon 4
agatttacattctcttaacatccaactgccagtacttaagaaacttattttatgcaattaaa-gcagggcaaactataactgttctttttcctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA
|  |     || ||  |   |  || |   ||||| |    |   ||  |  || | ||  | ||  |  |    | |  | |    ||  |||| | |||||||| |||||||| || |  ||| |||| |||||| | || || || |||||||||||||||||||||||||||||||  ||||||||||| |||
atgtactatttttcacactttttaaatagtagtacatgttgatagtagct-gtgaacttgtatgccagatagctcacatatttatgcttgactgaatgcagGTTTCGGCAATAGTTTCATGTTTACTGGGCCCTGATCGTGCAGAAAAAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCA
















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|211136606|gb|FL156037.1|FL156037
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCGATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|91056651|gb|EB167069.1|EB167069
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|149014075|gb|EE043602.2|EE043602
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|88753379|gb|DY537520.1|DY537520
EST:     GCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: GCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|86467368|gb|DY233738.1|DY233738
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|149112364|gb|EE295251.2|EE295251
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|211329033|gb|FL456230.1|FL456230
EST:     TTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGSCCTGATAGAGCTGATAAGATT
genomic: TTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|50333792|gb|CO528918.1|CO528918
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|71764323|gb|DR962260.1|DR962260
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|93011639|gb|EB637159.1|EB637159
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|71300514|gb|DR786312.1|DR786312
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|60352425|gb|DN219398.1|DN219398
EST:     TCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|71766391|gb|DR964328.1|DR964328
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|101382873|gb|EB813490.1|EB813490
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|60357150|gb|DN224123.1|DN224123
EST:     GCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: GCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|71448345|gb|DR829395.1|DR829395
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|71300530|gb|DR786320.1|DR786320
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|50327117|gb|CO522243.1|CO522243
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|101388003|gb|EB816016.1|EB816016
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|71766392|gb|DR964329.1|DR964329
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT

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

GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 347

GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA


Block sizes: 23 (upstream exon), 43 (downstream exon)
Score: 3

GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 75

GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttatgcaattaaagcagggcaaactataactgttctttttcctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA
                                           tcctgat  putative branch site (score: 75)
                                 ctgttctttttcct  CT-rich tract
                        aaactataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatttacattctcttaacatccaactgccagtacttaagaaacttattttatgcaattaaagcagggcaaactataactgttctttttcctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG