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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAGgtttggaactgaagctgaagtgctgaactaatcctgtattttgtatttgtattttacttggttcaagtcatgcaggtatgtgaatgtatggtttctgaattctaagctttggtggtgaatcttcatctatgcag

Basic information

species Zea mays
transcript GRMZM5G835213_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835213_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 5
GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAGgtttggaactgaagctgaagtgctgaactaatcctgtattttgtatttgtattttacttggttcaagtcatgcaggtatgtgaatgtatggtttctgaattctaagctttggtggtgaatcttcatctatgcag
|| ||| ||||| || |||||||||||||||||| |||||||||  || ||||| |||||||||| |||||||||    || || | || |  ||     ||||| | || |    |  |  || |      || |   |||||||| |  | | |   ||||   ||||||| || ||  | |||||   |||||
GTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAGgttgggaactgaaa---aactgttaaa-tgttc-----ttttgcaattat----tgttctgtactgtctgtgta--catgtgaatctgagttattaaaatt--gagctttgctgatgtctgttcattcttgcag

upper sequence: GRMZM5G835213_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 5'ss of exon 5
GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAGgtttggaactgaagctgaagtgctgaactaatc-ctgtattttgtatttgtattttacttggttcaagtcatgcaggtatgtgaatgtatggtttctgaattctaagctttggtggtgaatcttcatctatgcag
|| ||||||||| || ||||| |||||||||||| | |||| || ||| ||||| ||||||||| |  |  |     |    || |  | |  |  ||| |  |||     ||| ||| | || | |   ||||       |   ||    || ||    || |  |  ||||||     |                
GTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAGgtatatatatttgtttattttggtacatttttttctgaaaattggtccagtaatttccctgttccttttcat-------tacaaac---tgattatcaaacttcat-ctttggcatgcag---------------
















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|24934275|gb|CA452493.1|CA452493
EST:     ACTCCGAGGGAGGACACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: ACTCCGAGGGAGGACACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|71436375|gb|DR817425.1|DR817425
EST:     GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|71324258|gb|DR798829.1|DR798829
EST:     GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|31361403|gb|CD445760.1|CD445760
EST:     GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|22546594|gb|BU098905.1|BU098905
EST:     GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|22545671|gb|BU098030.1|BU098030
EST:     GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|29544652|gb|CB605032.1|CB605032
EST:     GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|71317247|gb|DR795307.1|DR795307
EST:     GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|194717059|gb|FK934212.1|FK934212
EST:     GTACTCCGAGGGAGGACACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: GTACTCCGAGGGAGGACACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|5268356|gb|AI770320.1|AI770320
EST:     GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|32866442|gb|CF006124.1|CF006124
EST:     CTCCGAGGGAGGACACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: CTCCGAGGGAGGACACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA

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: 555

GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 319

GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 310

GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 580

GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAGgtttggaactgaagctgaagtgctgaactaatcctgtattttgtatttgtattttacttggttcaagtcatgcaggtatgtgaatgtatggtttctgaattctaagctttggtggtgaatcttcatctatgcag

- - - - - - - - - - - - - - - - - - - - - - - - GGAGGA