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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attacatatacagggaacttgaccagccaacatttgctttaccttctacccattgagtcctgattattcttgctgtattcatgctttggaaattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTG

Basic information

species Zea mays
transcript GRMZM2G082330_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082330_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os11g24540.2 (Oryza sativa), 3'ss of exon 10
--attacatatacagggaacttgaccagccaacatttgctttaccttctacccattgagtcctgattattcttgctgtattcatgctttggaaattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTG
    ||  | ||     |  | || | | |    |  | | |||||| || | |||  |   || ||||  |    |   | || || |  | | | | ||||||||||||||||||||| |||||||| ||||||| |||||| |||| ||||| || |||||||||||||||||||| ||||| ||||||||||||||||
ttgatatgtgtatcttcagttagatctgtcc-tgtaagatataccttttatctattatgaagtg-ttatagtgttagatatgattctatccatactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTG

upper sequence: GRMZM2G082330_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT2G43070.1 (Arabidopsis thaliana), 3'ss of exon 10
attacatatacagggaacttgaccagccaacatttgctttaccttc-tacccattgagtcctgattattcttgc---tgtattcatgctttggaaattactc------agGTTGCTCGTGGTGATAACA---CTGGGGAATCAATTCCTATGCTCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTG
          ||   |  ||||  ||    |  |||   ||  |   ||      | | || ||  |     ||   | ||||| |  |||| || |  ||       ||||||| |  || || | ||   ||||||| || ||||| ||||| |||||||| || || ||||||||||| |||||||||||||| ||||| || ||||   
---------tcaataactttgaatagtagtcgattgtgataattgagtaattgaagggcccagagaagctcagccagtatattctta-tttgaaactcccttctttgtagGTTGCCCAAGGAGACAGCAGCACTGGGGAGTCCATTCCGATGCTACTAAGGATTCCTCGGTTCTTTGATCCTTGGGGTGGTTATGACATGATTGGTTTTG---

upper sequence: GRMZM2G082330_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 10
-------attacatatacagggaacttgaccagccaa-catttgctttaccttctacccattgagtcctgattattcttgctgtattcatgctttggaaattactcagGTTGCTCGTGGTGATAACACTGG---GGAATCAATTCCTATGCTCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTG
       |  || |||| |   |   |||| | | ||  ||||   ||  |  | |       | |      |||   | || |  |  ||   ||          |||||||||||||||| |||| |||    ||||| ||||| |||||  | ||  | || || ||||||||||| |||||||||||||||||||| |||||||   
ttctattaacacctataaattcagaatgacaacctaaatatttagattcaccacaattagacaaatttctggtatgagttctcttcttttgtgctga--------tagGTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTG---

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|60342860|gb|DN209833.1|DN209833
EST:     TTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCA                         GTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATA
genomic: TTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCAgtaagtgtat ... aattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATA
EST: gi|91053792|gb|EB164210.1|EB164210
EST:     TTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCA                         GTTGCTCGTGGTGATAACACTGGGGAATCAATTCTTATGCTCTTAAGGATA
genomic: TTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCAgtaagtgtat ... aattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATA
EST: gi|211115391|gb|FK954864.1|FK954864
EST:     TTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCA                         GTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATA
genomic: TTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCAgtaagtgtat ... aattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATA
EST: gi|78086708|gb|DV515101.1|DV515101
EST:     GTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCA                         GTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATA
genomic: GTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCAgtaagtgtat ... aattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATA
EST: gi|211094546|gb|FL478908.1|FL478908
EST:     CATGAAAGCGTCATGATTGCA                         G-TGCTCGTGGTGATAACACTGGGGAATCAATTTCCTATGCTCCTAAGGAT
genomic: CATGAAAGCGTCATGATTGCAgtaagtgtat ... aattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAA-TTCCTATGCTCCTAAGGAT
EST: gi|76932551|gb|DV173063.1|DV173063
EST:     TTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCA                         GTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATA
genomic: TTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCAgtaagtgtat ... aattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATA
EST: gi|211116170|gb|FK954868.1|FK954868
EST:     TTGGGTGTTCATTTCACCTCTTATATTCSCATGAAAGCGTCATGATTGCA                         GTTGCAAMGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGAT
genomic: TTGGGTGTTCATTTCACCTCTTATATTC-CATGAAAGCGTCATGATTGCAgtaagtgtat ... aattactcagGTTGC-TCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGAT
EST: gi|74246173|gb|DT654087.1|DT654087
EST:     TTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCA                         GTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATA
genomic: TTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCAgtaagtgtat ... aattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATA
EST: gi|71313933|gb|DR793572.1|DR793572
EST:     TTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCA                         GTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATA
genomic: TTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCAgtaagtgtat ... aattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATA
EST: gi|78086709|gb|DV515102.1|DV515102
EST:     GTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCA                         GTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATA
genomic: GTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCAgtaagtgtat ... aattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATA
EST: gi|211115393|gb|FK954866.1|FK954866
EST:     TTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCA                         GTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATA
genomic: TTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCAgtaagtgtat ... aattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATA
EST: gi|91049743|gb|EB160161.1|EB160161
EST:     TTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCA                         GTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATA
genomic: TTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCAgtaagtgtat ... aattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATA
EST: gi|71771233|gb|DR969170.1|DR969170
EST:     TCATGATTGCA                         GTTGCTCGTGGTGATAACACTGGGGAATCAATTTCCTATGCTCCTAAGGAT
genomic: TCATGATTGCAgtaagtgtat ... aattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAA-TTCCTATGCTCCTAAGGAT

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: 212

GTTGCATCGGCACTTCTTAGTGCTGCATTTGTGTATGACATCTTTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCAgtaagtgtat ... aattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

GTTGCATCGGCACTTCTTAGTGCTGCATTTGTGTATGACATCTTTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCAgtaagtgtat ... aattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 155

GTTGCATCGGCACTTCTTAGTGCTGCATTTGTGTATGACATCTTTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCAgtaagtgtat ... aattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 328

GTTGCATCGGCACTTCTTAGTGCTGCATTTGTGTATGACATCTTTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCAgtaagtgtat ... aattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacccattgagtcctgattattcttgctgtattcatgctttggaaattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTG
            tcctgat  putative branch site (score: 328)
                 attattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attacatatacagggaacttgaccagccaacatttgctttaccttctacccattgagtcctgattattcttgctgtattcatgctttggaaattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTG

- - - - - - - - - - - - -gccaaca
- - - - - - - - - - - - - - - - tttgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcatgc