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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttaactgtgctactatattctttcgacttatctggattgaccacatatttcttggtaaaacttgctttggaaagatcaagaatgttctatataagctaatactaccatatgttatcggtgttgttgaatacaattttaatccctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA

Basic information

species Zea mays
transcript GRMZM2G073054_T01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA19G37750.2 (Glycine max), 3'ss of exon 18
gtaagtttaactgtgctactatattctttcgacttatctggattgaccacatatttcttggtaaaacttgct-ttggaaagatcaagaatgttctatataagctaatactaccatatgttatcggtgttgttgaatacaattttaatccctttt--tcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA
                                                    |||   |      ||||  | | |||||    || |   || | || |||  |||| |           ||   |||    ||   |  ||   | | | ||  |||||| ||||| || ||||| |||||||  || |||||||| ||||| ||||| ||||||||||| || | ||| | ||  
-------------------------------------------------agcattcagtacatgtacttattatcggaaaagagaaaagaattatttacaaggcaatagt-----------tcaaagttacaaaacttatcttctgtacttcttaatcagGGCGATGCGGACTATCTAAGATATCAAGGGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGT

upper sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 18
lower sequence: Vv08s0007g03750.t01 (Vitis vinifera), 3'ss of exon 18
gtaagtttaactgtgctactatattctttcgacttatctggattgaccacatatttcttggtaaaacttgctttggaaagatcaagaatgttctatataagctaatactaccatatgttatcggtgttgttgaatacaattttaatcccttttt---cagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA
                                                     |||| | |||     |  |   ||||   || |  | | ||   |   |   | ||      |||| |   |    || || | |||| | ||   | | |   ||||| |||||||| ||||| || ||||||||  ||||||| ||||| |||||||||||||| ||||| | ||||||||  
-----------------------------------------------------tttcctagtatggggttgtagagaaaatacatggctttccttctt---ccttttctttttcttgtttttaat----tttaaaataattattatttatgtataaccagGGGGATGCAGAGTATCTAAGGTATCGTGGACTGCAAGAATTTGATCAGGCAATGCAGCATCTTGAAGAAAAATATGGC
















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|32836879|gb|CD976557.1|CD976557
EST:     TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTT                         GGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
genomic: TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTTgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
EST: gi|60347950|gb|DN214923.1|DN214923
EST:     GTAGATTTGACCTT                         GGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
genomic: GTAGATTTGACCTTgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
EST: gi|32934500|gb|CF039312.1|CF039312
EST:     TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTT                         GGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
genomic: TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTTgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
EST: gi|60338294|gb|DN205267.1|DN205267
EST:     TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTT                         GGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
genomic: TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTTgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
EST: gi|32837113|gb|CD976791.1|CD976791
EST:     TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTT                         GGAGATGCAGATTATCTTAGACATCGTGGTATGCAAGAGTTTGACCAGGCA
genomic: TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTTgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
EST: gi|32920624|gb|CF025436.1|CF025436
EST:     TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTT                         GGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
genomic: TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTTgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
EST: gi|60394366|gb|DN227236.1|DN227236
EST:     TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTT                         GGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
genomic: TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTTgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
EST: gi|91878000|gb|EB407957.1|EB407957
EST:     TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTT                         GGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
genomic: TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTTgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
EST: gi|60345781|gb|DN212754.1|DN212754
EST:     TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTT                         GGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
genomic: TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTTgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
EST: gi|211026372|gb|FL004586.1|FL004586
EST:     TCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTAT                         GGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTNGACCAGGC
genomic: TCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCT-Tgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGC
EST: gi|32864974|gb|CF004656.1|CF004656
EST:     TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTT                         GGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
genomic: TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTTgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
EST: gi|32930900|gb|CF035712.1|CF035712
EST:     TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTT                         GGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
genomic: TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTTgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
EST: gi|32837751|gb|CD977429.1|CD977429
EST:     TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTT                         GGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
genomic: TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTTgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
EST: gi|32921787|gb|CF026599.1|CF026599
EST:     TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTT                         GGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
genomic: TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTTgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
EST: gi|32931179|gb|CF035991.1|CF035991
EST:     TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTT                         GCAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
genomic: TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTTgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
EST: gi|32933816|gb|CF038628.1|CF038628
EST:     TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTT                         GGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA
genomic: TTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTTgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCA

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: 1017

ATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCATTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTTgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 177

ATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCATTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTTgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 27

ATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCATTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTTgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 292

ATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCATTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCTTgtaagtttaa ... cctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatactaccatatgttatcggtgttgttgaatacaattttaatccctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA
                                     ttttaat  putative branch site (score: 292)
                                     ttttaatccctttttc  CT-rich tract
                           ttgaatacaattttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttaactgtgctactatattctttcgacttatctggattgaccacatatttcttggtaaaacttgctttggaaagatcaagaatgttctatataagctaatactaccatatgttatcggtgttgttgaatacaattttaatccctttttcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA