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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGGAGCTAGAGATGTACGGACCGCCGTCCCGAGGCGGCGGGGGAGCTGGCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctccttctctctttttctctgatccctgtttttttttgtgctcgtgaacagtgcatctggatctgggcgtacggtgattaccaagggttttgt...

Basic information

species Zea mays
transcript GRMZM5G868588_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868588_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os09g33450.2 (Oryza sativa), 5'ss of exon 1
GAGGGAGCTAGAGATGTACGGACCGCCGTCCCGAGGCGGCGGGGGAGCTGGCACTGCCGGAG---AGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctcctt--ctctctttttctctgatccctgttt---------------ttttttgtgctcgtgaacagtgcatctggatctgggcgtacggtgattaccaagggttttgt
   || |     ||||||||  || |||||||| |||||||||||||  |   ||| ||| |   |||||||||||||||||||||||||||| ||||||||||| ||| |||  |  |||||| | ||| |    |  | ||               |||| | |||  |||||| ||| |||||||||||||||  ||                    
---GGTGGGGAGGATGTACGTGCCCCCGTCCCGCGGCGGCGGGGGAGGCGCGGCTGGCGGCGGCGAGCAGCCTAGGGTTTACCAAGTTTGGCGGGGAAGCAACgtaagcgctctctagctctctgtctctttctgtctagcttcatggagcaattcgattttgtttgcctgtgaacggtggatctggatctgggcgcgcgcgc-----------------
















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|211226409|gb|FL202758.1|FL202758
EST:     GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
EST: gi|211226410|gb|FL202759.1|FL202759
EST:     GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
EST: gi|211226406|gb|FL202755.1|FL202755
EST:     GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCAAGGNCGGTTCATATTTGGACCTGATGTGAGATCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
EST: gi|211226399|gb|FL202748.1|FL202748
EST:     GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
EST: gi|94479844|gb|EB708802.1|EB708802
EST:     CACTGCCGGAGAGCAGCCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCCAGGGCGGTTCATATTTTGGACCCGATGTGAGATCATT
genomic: CACTGCCGGAGAGCAGCC-TAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTT-GGACCTGATGTGAGATCATT
EST: gi|211226404|gb|FL202753.1|FL202753
EST:     TCACTGCCGGAGAGCAGCCTAGGGTTTACMAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
EST: gi|211226401|gb|FL202750.1|FL202750
EST:     GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
EST: gi|211226408|gb|FL202757.1|FL202757
EST:     GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGGTCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
EST: gi|148970678|gb|EE021391.2|EE021391
EST:     GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
EST: gi|211226405|gb|FL202754.1|FL202754
EST:     GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGAAAGCAAC                         GNAGTTTTTCTTTTGCA-GGCCGNTTCATATTTGGGACCTGATGGTGAGAT
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagG-AGTTTTTCTT--GCAAGGCCGGTTCATATTTGG-ACCTGATG-TGAGAT
EST: gi|88747254|gb|DY531395.1|DY531395
EST:     GCACTGCCGGAGAGCACCCTAGGGTTTACCAAGTTTGGAGAGGAAGCAAC                         GAGTTTTTCTTGCAGGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
EST: gi|76013624|gb|DT940794.1|DT940794
EST:     GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG

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: 167

GAGGGAGCTAGAGATGTACGGACCGCCGTCCCGAGGCGGCGGGGGAGCTGGCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTGTTTCTCACCATATTCCTCATTCTTGCGCCAATGGTGGTCTTCTGTATAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

GAGGGAGCTAGAGATGTACGGACCGCCGTCCCGAGGCGGCGGGGGAGCTGGCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTGTTTCTCACCATATTCCTCATTCTTGCGCCAATGGTGGTCTTCTGTATAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 181

GAGGGAGCTAGAGATGTACGGACCGCCGTCCCGAGGCGGCGGGGGAGCTGGCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTGTTTCTCACCATATTCCTCATTCTTGCGCCAATGGTGGTCTTCTGTATAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 181

GAGGGAGCTAGAGATGTACGGACCGCCGTCCCGAGGCGGCGGGGGAGCTGGCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTGTTTCTCACCATATTCCTCATTCTTGCGCCAATGGTGGTCTTCTGTATAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGGAGCTAGAGATGTACGGACCGCCGTCCCGAGGCGGCGGGGGAGCTGGCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctccttctctctttttctctgatccctgtttttttttgtgctcgtgaacagtgcatctggatctgggcgtacggtgattaccaagggttttgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA