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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttaatgagtatatagacatgcagtcacatatttttagttaaatgattggacatcttatactgcttactctaactctagacatgattcatattcataatttactcaaccatttgtgtgcaacaactttggctgttagataacatatacatatggatggattagGTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATACTATGGAAAGAGTTCTCCTTTTAACAGTTTGACAACAGAAAATCTACAGT

Basic information

species Zea mays
transcript GRMZM2G031572_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031572_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g36760.1 (Oryza sativa), 3'ss of exon 2
gtaagtttaat-gagtatatagacatgcagtcacatatttttagttaaatgattggacatcttatactgcttactctaactctagac-atgattcatattcataatt-tactcaaccatttgtgtgcaacaactttggctgttagataacatatacat-atggatggattagGTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATACTATGGAAAGAGTTCTCCTTTTAACAGTTTGACAACAGAAAATCTACAGT
|| ||| |  |  |||||||||   | ||||      ||   | |  |   ||| |||||  | |  | |  | ||||  | |   | ||  || |     ||  || || |  ||      |||      |   |     |  |||    | |   | |||  ||   |||||| |||||||||| |||||||| ||| |||| || ||||||||||| ||||| ||||||||||| |||||| | ||||||||||| |||||||||  ||
gtgagtatgctcaagtatatagttgtacagt------ttccaactggagcaattagacattatttgttacacattctaggtgtgatctatactttaagcatatggttatattttacttcacctgttttgataacatacacatgggatggtttgtgtgtgatgtgtg---tagGTGATGGCAAAGAAGTTTGGTGCGGCAGTGGTCTCCCCTGAGCATCGGTACTACGGAAAGAGTTCCCCTTTTGAGAGTTTGACAACGGAAAATCTAAGGT

upper sequence: GRMZM2G031572_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G24270.1 (Glycine max), 3'ss of exon 3
gtaagtttaatgagtatatagacatgcagtcacatatttttagttaaatgattggacatcttatactgcttactctaactctagacatgattcatattcataatttactcaaccatttgtgtgcaacaactttggctgttagataacatatacatatggatggattagGTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATACTATGGAAAGAGTTCTCCTTTTAACAGTTTGACAACAGAAAATCTACAGT
                                                    |  | |   | | ||      ||| | |   ||  ||  || | |  | ||       |   | |  | |  |  || ||   |  |  | ||   |||              |||||  |||||||||| ||||| || ||  ||||| ||| ||| ||||| ||||||||||||||||| || |||||   ||||   ||||||||| |  | |
----------------------------------------------------taaagagtgt-tgctagcatttctcaataatgatgtggctcttgtcaagaaa------agataataatataaactaattt---ccatgcgttattttattttctcta------tagGTACTGGCAAAGAAGTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTACTATGGAAAGAGTTCCCCATTTAATTCTTTGGAGACAGAAAATTTGAAAT

upper sequence: GRMZM2G031572_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0023g03020.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtttaatgagtatatagacatgcagtcacatatttttagttaaatgattggacatcttatactgcttactctaactctagacatgattcatattcataatttactcaaccatttgtgtgcaacaactttggctgttagataacatatacatatggatggattagGTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATACTATGGAAAGAGTTCTCCTTTTAACAGTTTGACAACAGAAAATCTACAGT
                                                    |  | |   || | | | | |||  | | |||     |     | |  | | ||    ||| |  |   || || || | ||    ||   |||  |       ||||  | ||      |||||||||||||||| || ||  ||||||||| ||||||||| ||||||||||||||||| || |||     | ||| ||||||||||||  | |
---------------------------------------------------ctcaaaa--ctaaaatccatcctcagattgtaggagcaaggaggagtt-ttacttgtataacaaacttgctgaaaaaattctgaaccttg--taatgt-------tggacagGTTT-----TGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTACTATGGAAAGAGTTCCCCCTTTCGGTCTCTGAGAACAGAAAATCTGAAAT

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|71441298|gb|DR822348.1|DR822348
EST:     ACATCTGTGGAGAATCTACGTGCAATGGGATTGGCAATAACTACTTAGCT                         GTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATAC
genomic: ACATCTGTGGAGAATCTACGTGCAATGGGATTGGCAATAACTACTTAGCTgtaagtttaa ... gatggattagGTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATAC
EST: gi|31357650|gb|CD442007.1|CD442007
EST:     ACATCTGTGGAGAATCTACGTGCAATGGGATTGGCAATAACTACTTAGCT                         GTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATAC
genomic: ACATCTGTGGAGAATCTACGTGCAATGGGATTGGCAATAACTACTTAGCTgtaagtttaa ... gatggattagGTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATAC
EST: gi|93011649|gb|EB637169.1|EB637169
EST:     ACATCTGTGGAGAATCTACGTGCAATGGGATTGGCAATAACTACTTAGCT                         GTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCCCCGATAC
genomic: ACATCTGTGGAGAATCTACGTGCAATGGGATTGGCAATAACTACTTAGCTgtaagtttaa ... gatggattagGTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATAC
EST: gi|211493121|gb|FL031303.1|FL031303
EST:     ACATCTGTGGAGAATCTACGTGCAATGGGATTGGCAATAACTACTTAGCT                         GTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATAC
genomic: ACATCTGTGGAGAATCTACGTGCAATGGGATTGGCAATAACTACTTAGCTgtaagtttaa ... gatggattagGTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATAC
EST: gi|211493120|gb|FL031302.1|FL031302
EST:     ACATCTGTGGAGAATCTACGTGCAATGGGATTGGCAATAACTACTTAGCT                         GTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATAC
genomic: ACATCTGTGGAGAATCTACGTGCAATGGGATTGGCAATAACTACTTAGCTgtaagtttaa ... gatggattagGTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATAC
EST: gi|211469990|gb|FL213489.1|FL213489
EST:     ACATCTGTGGAGAATCTACGTGCAATGGGATTGGCAATAACTACTTAGCT                         GTGGTGGCAAAGAAATTTGGTGCTGCAATTGGTTTCTCCTGAGCATCGATA
genomic: ACATCTGTGGAGAATCTACGTGCAATGGGATTGGCAATAACTACTTAGCTgtaagtttaa ... gatggattagGTGGTGGCAAAGAAATTTGGTGCTGCA-TTGGTTTCTCCTGAGCATCGATA

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: 102

CTACGAATTTCTCGACTACTACCGAGCTCCAAATGGCCCGATCTTCCTATACATCTGTGGAGAATCTACGTGCAATGGGATTGGCAATAACTACTTAGCTgtaagtttaa ... gatggattagGTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATACTATGGAAAGAGTTCTCCTTTTAACAGTTTGACAACAGAAAATCTACAGT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 110

CTACGAATTTCTCGACTACTACCGAGCTCCAAATGGCCCGATCTTCCTATACATCTGTGGAGAATCTACGTGCAATGGGATTGGCAATAACTACTTAGCTgtaagtttaa ... gatggattagGTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATACTATGGAAAGAGTTCTCCTTTTAACAGTTTGACAACAGAAAATCTACAGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 124

CTACGAATTTCTCGACTACTACCGAGCTCCAAATGGCCCGATCTTCCTATACATCTGTGGAGAATCTACGTGCAATGGGATTGGCAATAACTACTTAGCTgtaagtttaa ... gatggattagGTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATACTATGGAAAGAGTTCTCCTTTTAACAGTTTGACAACAGAAAATCTACAGT


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 83

CTACGAATTTCTCGACTACTACCGAGCTCCAAATGGCCCGATCTTCCTATACATCTGTGGAGAATCTACGTGCAATGGGATTGGCAATAACTACTTAGCTgtaagtttaa ... gatggattagGTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATACTATGGAAAGAGTTCTCCTTTTAACAGTTTGACAACAGAAAATCTACAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttgtgtgcaacaactttggctgttagataacatatacatatggatggattagGTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATACTATGGAAAGAGTTCTCCTTTTAACAGTTTGACAACAGAAAATCTACAGT
                           agataac  putative branch site (score: 83)
                             ataacatatacatat  TA-rich tract