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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGGTACGCAACGCCTTCCTAGGATCATAGGGAGGTCCAGAGCAAAGGAACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctagccttgttagttgttacctgtttttacctacttattacttacagcaacaaatcgtaaatgtgtgtttgtgtttcag

Basic information

species Zea mays
transcript GRMZM2G398500_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G398500_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g43710.1 (Oryza sativa), 5'ss of exon 6
GGTGGTACGCAACGCCTTCCTAGGATCATAGGGAGGTCCAGAGCAAAGGAACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctagccttgttagttgttacctgtttttacctacttattacttacagcaacaaatcgtaaatgtgtgtttgtgtttcag
|| || || || || |||||||||||  | || ||||||||||| |||||  |||||||||| ||||| ||||||  |||| |||||||||||| |||||||||   |  ||||     ||  | |   | | | |      ||| ||| ||  ||  |    ||| ||  ||||||     |||
GGGGGCACACAGCGTCTTCCTAGGATTGTTGGAAGGTCCAGAGCGAAGGAGATGATATTCACCGGCCGTAGATGTAATGCAACTGAAGCTGTAATGATGGgtaagagttcccttacgctttccttctattatcttcacttgcatttctt-ca--aatgaggtttaattggatgtttgaaacgcag
















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|60349135|gb|DN216108.1|DN216108
EST:     ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGG                         GGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
genomic: ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctag ... tgtgtttcagGGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
EST: gi|33099185|gb|CF059145.1|CF059145
EST:     ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGG                         GGTTAGCAAACTACTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
genomic: ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctag ... tgtgtttcagGGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
EST: gi|71761660|gb|DR959597.1|DR959597
EST:     ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGG                         GGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
genomic: ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctag ... tgtgtttcagGGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
EST: gi|78024805|gb|DV493192.1|DV493192
EST:     ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGG                         GGTTAGCAAACTACTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
genomic: ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctag ... tgtgtttcagGGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
EST: gi|74244449|gb|DT652363.1|DT652363
EST:     ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGG                         GGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
genomic: ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctag ... tgtgtttcagGGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
EST: gi|33099274|gb|CF059234.1|CF059234
EST:     ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGG                         GGTTAGCAAACTACTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
genomic: ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctag ... tgtgtttcagGGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
EST: gi|60355171|gb|DN222144.1|DN222144
EST:     ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGG                         GGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
genomic: ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctag ... tgtgtttcagGGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
EST: gi|71439182|gb|DR820232.1|DR820232
EST:     ACTGATATTCACTGGCTGCAGATGTGGTGCAGCTGAAGCTGTAACGATGG                         GGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
genomic: ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctag ... tgtgtttcagGGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
EST: gi|211523276|gb|FL466418.1|FL466418
EST:     AYTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGG                         GGTTAGCAAACTATTGTGTTYCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
genomic: ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctag ... tgtgtttcagGGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
EST: gi|32850353|gb|CD990034.1|CD990034
EST:     ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGG                         GGTTAGCAAACTACTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
genomic: ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctag ... tgtgtttcagGGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
EST: gi|78110969|gb|DV529367.1|DV529367
EST:     ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGG                         GGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
genomic: ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctag ... tgtgtttcagGGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
EST: gi|101400934|gb|EB822151.1|EB822151
EST:     ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGG                         GGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAACGCTCTTG
genomic: ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctag ... tgtgtttcagGGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
EST: gi|32928287|gb|CF033099.1|CF033099
EST:     ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGG                         GGTTAGCAAACTACTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
genomic: ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctag ... tgtgtttcagGGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTG
EST: gi|78110970|gb|DV529368.1|DV529368
EST:     ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGG                         GGTTAGCAAACTATT
genomic: ACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctag ... tgtgtttcagGGTTAGCAAACTATT

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), 46 (downstream exon)
Score: 52

GGTGGTACGCAACGCCTTCCTAGGATCATAGGGAGGTCCAGAGCAAAGGAACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctag ... tgtgtttcagGGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTGACATTGCCTGTGAGATAACCCAGAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 49

GGTGGTACGCAACGCCTTCCTAGGATCATAGGGAGGTCCAGAGCAAAGGAACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctag ... tgtgtttcagGGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTGACATTGCCTGTGAGATAACCCAGAAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 33

GGTGGTACGCAACGCCTTCCTAGGATCATAGGGAGGTCCAGAGCAAAGGAACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctag ... tgtgtttcagGGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTGACATTGCCTGTGAGATAACCCAGAAG


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

GGTGGTACGCAACGCCTTCCTAGGATCATAGGGAGGTCCAGAGCAAAGGAACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctag ... tgtgtttcagGGTTAGCAAACTATTGTGTTCCAGCAGGAGAGGCTTACCAGAAGGCTCTTGACATTGCCTGTGAGATAACCCAGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGGTACGCAACGCCTTCCTAGGATCATAGGGAGGTCCAGAGCAAAGGAACTGATATTCACTGGCCGCAGATGTGGTGCAGCTGAAGCTGTAACGATGGgtaatgctagccttgttagttgttacctgtttttacctacttattacttacagcaacaaatcgtaaatgtgtgtttgtgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG