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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tataggtccatcatgaatatgagattggatgttcttccttaatataccttttgttttgtcccccctcccacctgaaagatacttttgaacctttatgcagGACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTG

Basic information

species Zea mays
transcript GRMZM2G164743_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164743_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 12
tataggtccatcatgaatatgagattggatgttcttccttaata--taccttttgttttgtcccccctcccacctgaaagat--act-tttgaaccttt---atgcagGACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTG
           ||   | |||           || |   | | |  ||  ||  || ||   |    ||  | || |  | |  |||  |||||| | |   ||||||||||||||| ||||||||||   |||||||||||  |||||||| ||||| |||  ||||| | | || ||||| ||||
--------tgacactgaaatgcatccaatacctcctaaatgacagttaatttgggtattcatcgtgttcaaagctcatggttttactgcttgaacttgttgaatgcagGACAAAATCCATAACTGGAGATCGACAGCTCTTACCTTGACATCTATCCTCTTCATTGCAGCTATATTTTGGTTTATTG
















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|211351534|gb|FL310930.1|FL310930
EST:     TCCATATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAG                         GACAAAATCAATAACTGGAGGGAGA
genomic: TCCATATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAGgtgcttattc ... ctttatgcagGACAAAATCAATAACTGGAGGGAGA
EST: gi|5325067|gb|AI783258.1|AI783258
EST:     TCCATATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAG                         GACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTT
genomic: TCCATATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAGgtgcttattc ... ctttatgcagGACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTT
EST: gi|211002558|gb|FL365524.1|FL365524
EST:     TCCATATATT-GGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAG                         GACAAAATCAAT
genomic: TCCATATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAGgtgcttattc ... ctttatgcagGACAAAATCAAT
EST: gi|71429290|gb|DR810340.1|DR810340
EST:     TCCATATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAG                         GACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTT
genomic: TCCATATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAGgtgcttattc ... ctttatgcagGACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTT
EST: gi|6056590|gb|AW090995.1|AW090995
EST:     TCCATATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAG                         GACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATNCATCCTT
genomic: TCCATATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAGgtgcttattc ... ctttatgcagGACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTT
EST: gi|32907645|gb|CF012458.1|CF012458
EST:     TCCATATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAG                         GACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTT
genomic: TCCATATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAGgtgcttattc ... ctttatgcagGACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTT
EST: gi|78110258|gb|DV528673.1|DV528673
EST:     TCCATATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAG                         GACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTT
genomic: TCCATATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAGgtgcttattc ... ctttatgcagGACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTT
EST: gi|5846879|gb|AI999962.1|AI999962
EST:     TCCATATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAG                         GACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTT
genomic: TCCATATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAGgtgcttattc ... ctttatgcagGACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTT
EST: gi|211532277|gb|FL465631.1|FL465631
EST:     ATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAG                         GACAAAATCAATAAYTGGAGGGAGACAGCTCTTATATTGACATCCATCCTT
genomic: ATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAGgtgcttattc ... ctttatgcagGACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTT

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), 47 (downstream exon)
Score: 72

CGTGAAGCCACATTTGCGGCCATTGGCAATGGCCGTATCCACTGTTTCGATCCATATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAGgtgcttattc ... ctttatgcagGACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

CGTGAAGCCACATTTGCGGCCATTGGCAATGGCCGTATCCACTGTTTCGATCCATATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAGgtgcttattc ... ctttatgcagGACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

CGTGAAGCCACATTTGCGGCCATTGGCAATGGCCGTATCCACTGTTTCGATCCATATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAGgtgcttattc ... ctttatgcagGACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 116

CGTGAAGCCACATTTGCGGCCATTGGCAATGGCCGTATCCACTGTTTCGATCCATATATTTGGTGATGTCCCTTCTTCACCTCTTGTTGGGCTGCTTCAGgtgcttattc ... ctttatgcagGACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttttgttttgtcccccctcccacctgaaagatacttttgaacctttatgcagGACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTG
                                            cctttat  CT-rich tract
                                 atactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tataggtccatcatgaatatgagattggatgttcttccttaatataccttttgttttgtcccccctcccacctgaaagatacttttgaacctttatgcagGACAAAATCAATAACTGGAGGGAGACAGCTCTTATATTGACATCCATCCTTTTCGCTGCAGTTGTGTTCTGGTTCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - -catgaat
- - - - - - - - - - - - ttggatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaagata