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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGCACTGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaaggcatctgcccctcaggttcttgatgcttggcttgtgggcattatctttgaagtgaaaaagattacatgctaaaagtttatccttccctgtaacag

Basic information

species Zea mays
transcript GRMZM2G088140_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088140_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g13170.2 (Oryza sativa), 5'ss of exon 2
TTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGCACTGTTTCTGTGA---TTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaaggcatctgcccctcaggttcttgatgcttggcttgtgggcattatctttgaagtgaaa----------aagattacatgc-taaaagtttatccttccctgtaacag----------------
                           ||| |||||| || |  |||| |||| | | |||     ||||||||| |||||||| |||||  ||||| |||||  ||||||||||||||| ||||||||| | ||      || ||    ||| |||| || |   |||          || | | ||| | |||||   | |   |   |  |                    
---------------------------GGATAATGGAGTAATCACTGCTCTGTGTATCTGAGCTCACACCATGGGTAGCAGTGGCGCAGACGCACCGACTAAGACAAGCAAGGCATCTGCACCTCAGgttttggaatacatgcctgacaacataatctctgtaccaaaagatatatatgaacacttcattcctaaaaagctgtttcttttttcatttctttgttttaataatag
















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|211355419|gb|FL036287.1|FL036287
EST:     TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAG                         GAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
genomic: TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaagg ... cctgtaacagGAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
EST: gi|211353027|gb|FL036283.1|FL036283
EST:     TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAG                         GAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
genomic: TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaagg ... cctgtaacagGAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
EST: gi|211353024|gb|FL036280.1|FL036280
EST:     TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAG                         GAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
genomic: TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaagg ... cctgtaacagGAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
EST: gi|211353025|gb|FL036281.1|FL036281
EST:     TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAG                         GAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
genomic: TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaagg ... cctgtaacagGAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
EST: gi|91873165|gb|EB403122.1|EB403122
EST:     TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAG                         GAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
genomic: TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaagg ... cctgtaacagGAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
EST: gi|91056940|gb|EB167358.1|EB167358
EST:     TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAG                         GAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
genomic: TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaagg ... cctgtaacagGAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
EST: gi|211353026|gb|FL036282.1|FL036282
EST:     TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAG                         GAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
genomic: TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaagg ... cctgtaacagGAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
EST: gi|211355416|gb|FL036284.1|FL036284
EST:     TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAG                         GAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
genomic: TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaagg ... cctgtaacagGAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
EST: gi|211355418|gb|FL036286.1|FL036286
EST:     TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAG                         GAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
genomic: TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaagg ... cctgtaacagGAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
EST: gi|71767660|gb|DR965597.1|DR965597
EST:     TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAG                         GAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
genomic: TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaagg ... cctgtaacagGAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
EST: gi|211353023|gb|FL036279.1|FL036279
EST:     TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAG                         GAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
genomic: TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaagg ... cctgtaacagGAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
EST: gi|211355417|gb|FL036285.1|FL036285
EST:     TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAG                         GAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTYYNCTCC
genomic: TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaagg ... cctgtaacagGAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTA-TCC
EST: gi|211353577|gb|FL066645.1|FL066645
EST:     TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAG                         GAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA
genomic: TGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaagg ... cctgtaacagGAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCA

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: 47 (upstream exon), 48 (downstream exon)
Score: 145

TTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGCACTGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaagg ... cctgtaacagGAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 67

TTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGCACTGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaagg ... cctgtaacagGAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 91

TTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGCACTGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaagg ... cctgtaacagGAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 97

TTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGCACTGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaagg ... cctgtaacagGAGCAGCAGCCACCTGCTACCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCTTTATGCTGGTTCATTTGTCTACGGACAATGGACTAGTTGCTGCACTGTTTCTGTGATTCACCATGGGAAGCAGTGGAGCAGATACACCGTCTAAGgtaagcaaggcatctgcccctcaggttcttgatgcttggcttgtgggcattatctttgaagtgaaaaagattacatgctaaaagtttatccttccctgtaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT