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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaatgtgaatcatcatcaaatagtgtaatgctagaaagccaagagaatacatttttatttgaacagtacctgcaaattgggaggatgttctaca...

Basic information

species Zea mays
transcript GRMZM2G114126_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114126_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 5'ss of exon 2
GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaatgtgaatcatcatcaaa-tagtg----taatgctagaaagccaagagaatacatttttatttgaacagtacctgcaaattgggaggatgttctaca
| || | || |||||||| ||||||||||||||||| |||||||||||||| ||||| ||||  || ||||| || || |||||||| |||||||| || |    ||||   ||| |||| ||||     || | || ||||  ||||     |  || |||     ||  |      |  ||  | | ||||      
GTTGGTCGGCTATGAAGGACTTGAAGTTATTAACCCAGATGGAGGCACAGAAGATGCGGAAGCTGAGGCTTTGAGAGGGCGATGGAAACAAGAGgtgagaatcactgaaatgtcaacaaaatagtaattttatttcttgaaatacaag----catgttattagactgaccattgtactagtttatgtgtatgtcaatt-

upper sequence: GRMZM2G114126_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 5'ss of exon 2
GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaatgtg--aatcatca-----tcaaatagtgtaatgctagaaagccaagagaatacatttttatttgaacagtacctgcaaattgggaggatgttctaca
| ||||||||||||||||  | |||||||| ||||| || ||||||| ||| ||||| ||||||||||||  ||| ||  |||||||| | |||| | |    | ||  | || | |     |    || |  | |  ||        |  |  |  |||  || ||      |     |  | ||||   |||       
GTTGCTTGGTTATGAAGGTGTGGAAGTTATAAACCCAGAGGGAGGCAAAGAAGATGCGGAAGAAGAAGCTCAAAGAGGAAGATGGAAGGAGGAGgcatgttgctttgccattctttaatcccttttgtattagatttttattttttttaatggttgaattcatacttattttattgacacttagtgggcctatg-------
















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|23357490|gb|BU645139.1|BU645139
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAG                         GATCGTGATAGCTATTGGAAGATGATGCATAAGTACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
EST: gi|211354689|gb|FL118768.1|FL118768
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAG                         GATCGTGATAGCTATTGGAAGATGATGCATAAGTACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
EST: gi|211354687|gb|FL118766.1|FL118766
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAG                         GATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
EST: gi|211354688|gb|FL118767.1|FL118767
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAG                         GATCGTGATAGCTATTGGAAGATGATGCATAAGTACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
EST: gi|91055718|gb|EB166136.1|EB166136
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAG                         GATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
EST: gi|67040089|gb|CO466344.1|CO466344
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAG                         GATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
EST: gi|74236529|gb|DT644443.1|DT644443
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAG                         GATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
EST: gi|26558339|gb|CA830574.1|CA830574
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAG                         GATCGTGATAGCTATTGGAAGATGATGCATAAGTACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
EST: gi|211354691|gb|FL118770.1|FL118770
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTANGGGGCCGATGGAAGCAAGAG                         GATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
EST: gi|211354684|gb|FL118763.1|FL118763
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAG                         GATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCA
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCA
EST: gi|211354686|gb|FL118765.1|FL118765
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAG                         GATCGTGATAGCTATTGGAAGATGATGCATAAGTACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
EST: gi|149105113|gb|EE290596.2|EE290596
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAG                         GATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
EST: gi|148961873|gb|EE012659.2|EE012659
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAG                         GATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
EST: gi|78120437|gb|DV538821.1|DV538821
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAG                         GATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
EST: gi|32801394|gb|CD953630.1|CD953630
EST:     TAAGAGGCCGATGGAAGCAAGAG                         GATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
genomic: TAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT
EST: gi|87155561|gb|DY400350.1|DY400350
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAG                         GATCGTGATAGCTATTGGAAGATGATGCATAAGTACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTT

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), 48 (downstream exon)
Score: 186

GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 325

GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 364

GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 222

GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaat ... taatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTAAGGGGCCGATGGAAGCAAGAGgtaaggaaatgtgaatcatcatcaaatagtgtaatgctagaaagccaagagaatacatttttatttgaacagtacctgcaaattgggaggatgttctaca

- - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA