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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCATCTGAATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatggatataccttgcatatctattactacctctgtttgtttatatgtcgttggtcagttcaattttgaactaagcggtgtcatatattgaactaa...

Basic information

species Zea mays
transcript GRMZM2G054247_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054247_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g50360.1 (Oryza sativa), 5'ss of exon 5
CATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCATCTGAATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatggatataccttgcatatctattactacctctgtttgtttata-tgtcgttggtcagttcaattttgaactaagcggtgtcatatattgaactaa-
|||||||||| |||||||||||||||||| | || || ||||||||  |||||||||||||||||||| | |||||||||||||| || |||||||||||||||| ||    ||         |||| |  |   |    | ||  | | |||  |        | | ||||| |   | | |  |||   |||  | |   
CATTCATTCATACATTTATGCTCCAAATTTCGGTGTTGTCCAATCACTTGAATGGGAGGGATACTCATATTCGACAGATCAAGATATATGGGCCAAGACCgtaagttgatattatacaaagcctctagttgtgttttaagtagtacagaatgtgataatctcaattagttttgcatccatcag-atcagg-attttattggc

upper sequence: GRMZM2G054247_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv04s0023g01940.t01 (Vitis vinifera), 5'ss of exon 5
CATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCATCTGAATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatggatataccttgcatatctattactacctctgtttgtttatatgtcgttggtcagttcaattttgaactaagcggtgtcatatattgaactaa
| ||  |  |||| |||||| | ||||||||| | || || ||||| || |||||||| ||||||||||| || ||||||||  | || |||||   |||||| |   ||   | | |   |||   |    |||  |    | |      |  ||   |    | || ||||  || ||  |||   |           
CTTTTGTGAACACTTTTATGTTGCAAATTGCTATATTGTCAAATCACCTTAATGGGAGAGATACTCATGTGCGCCAGATCAAAGTTTATGGGCCTCCACCgtatgtcaga---atcct---tattcttgttcaccagtcacagatatgggattcttaaactaacccatcttgatgtatgctatgttgcag----------
















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|32914925|gb|CF019737.1|CF019737
EST:     AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACC                         GAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
genomic: AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
EST: gi|32791611|gb|CD943847.1|CD943847
EST:     GATCTACGGGCCAAGACC                         GAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
genomic: GATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
EST: gi|32857021|gb|CD996702.1|CD996702
EST:     AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACC                         GAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
genomic: AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
EST: gi|8273087|gb|BE012181.1|BE012181
EST:     AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACC                         GAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
genomic: AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
EST: gi|76915292|gb|DV165923.1|DV165923
EST:     AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACC                         GAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCCGGGAG
genomic: AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAG
EST: gi|22490544|gb|BU050467.1|BU050467
EST:     AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTATGGGCCAAGACC                         GAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
genomic: AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
EST: gi|71297609|gb|DR784753.1|DR784753
EST:     AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACC                         GAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
genomic: AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
EST: gi|6952537|gb|AW424605.1|AW424605
EST:     AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACC                         GAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
genomic: AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
EST: gi|16379595|gb|BI993037.1|BI993037
EST:     AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACC                         GAATCCTGTTCCCCACCAACCGTTTCATTTTACTTCCAGGGAGTTCATCAC
genomic: AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
EST: gi|91873253|gb|EB403210.1|EB403210
EST:     AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACC                         GAATCCTGTTNNNNNNNAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
genomic: AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
EST: gi|87153735|gb|DY398524.1|DY398524
EST:     AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTATGGGCCAAGACC                         GAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
genomic: AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
EST: gi|110941176|gb|EE161333.1|EE161333
EST:     AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACC                         GAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
genomic: AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
EST: gi|71427965|gb|DR809015.1|DR809015
EST:     AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAATACC                         GAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
genomic: AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
EST: gi|32808899|gb|CD961133.1|CD961133
EST:     GATCTACGGGCCAAGACC                         GAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
genomic: GATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
EST: gi|32806361|gb|CD958595.1|CD958595
EST:     GATCTACGGGCCAAGACC                         GAATCCTGGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCA
genomic: GATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCT-GTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCA
EST: gi|211368075|gb|FL362342.1|FL362342
EST:     AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACC                         GAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
genomic: AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC
EST: gi|94476642|gb|EB705600.1|EB705600
EST:     AATGGGAGGGATATTCATGTCCGACAGATCAAGATTTACGGGCCAAGACC                         GAATCCTGTTNNNNNNNAGCCGTTTCATTTTATTTCCAGGGAGTTCATCAC
genomic: AATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCAC

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: 48 (upstream exon), 49 (downstream exon)
Score: 138

CATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCATCTGAATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCACATACTCTACTATTAGATGACAGTGGATGAGCAATCAAGATAGGATCGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 162

CATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCATCTGAATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCACATACTCTACTATTAGATGACAGTGGATGAGCAATCAAGATAGGATCGGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 162

CATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCATCTGAATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCACATACTCTACTATTAGATGACAGTGGATGAGCAATCAAGATAGGATCGGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 183

CATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCATCTGAATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatgga ... cttgtttcagGAATCCTGTTCCCCACCAGCCGTTTCATTTTACTTCCAGGGAGTTCATCACATACTCTACTATTAGATGACAGTGGATGAGCAATCAAGATAGGATCGGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCATCTGAATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCAAGACCgtaagatggatataccttgcatatctattactacctctgtttgtttatatgtcgttggtcagttcaattttgaactaagcggtgtcatatattgaactaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA