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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttacatctcttctcacttgaagtatttcatccatttttcctacatagcttgggtgaatttctgctgcagcaaactcaatatggcatcgaagctaa...

Basic information

species Zea mays
transcript GRMZM2G101250_T01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101250_T02 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os04g09860.2 (Oryza sativa), 5'ss of exon 19
GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttacatctcttctcacttgaagtatttcatccatttttcctacatagcttgggtgaatttctgc-tgcagcaaactcaat-atggcatcgaagctaa
|| || || || |||| ||||||||||||||| |||||||||||||| |||||||||||||||| |  ||| |    || ||       || ||   | | |   |     |||   | | |    ||   | | | ||    ||    |   
GTATTACAGTCGAGGAGTTATCCATTATTTGTCCCATGGAAAGGTGGTGTGgtaagttacatctatcttcagtctg-gtgttctcctatttcttgtaagacaaactaatgaaatcattacatattacatgataatttatattttcagtacat-
















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|60399530|gb|DN232341.1|DN232341
EST:     TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG                         ATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
genomic: TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
EST: gi|60358881|gb|DN225854.1|DN225854
EST:     TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG                         ATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
genomic: TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
EST: gi|148934268|gb|EC878291.2|EC878291
EST:     TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG                         ATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
genomic: TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
EST: gi|78121627|gb|DV540011.1|DV540011
EST:     TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG                         ATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
genomic: TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
EST: gi|16916971|gb|BM073068.1|BM073068
EST:     TGTTGCAATTTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG                         ATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
genomic: TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
EST: gi|40302924|gb|CK347311.1|CK347311
EST:     TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG                         ATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
genomic: TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
EST: gi|60358880|gb|DN225853.1|DN225853
EST:     TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG                         ATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
genomic: TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
EST: gi|211220507|gb|FL445398.1|FL445398
EST:     GCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG                         ATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
genomic: GCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
EST: gi|9254742|gb|BE345210.1|BE345210
EST:     AATCTAGGACTTATCCCTTATTTGTTCCATGGAAAGGTGGAGTG                         ATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
genomic: AATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
EST: gi|9254603|gb|BE345056.1|BE345056
EST:     TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG                         ATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
genomic: TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
EST: gi|211181693|gb|FL465348.1|FL465348
EST:     GTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGGAGTG                         ATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAG-TAAGA
genomic: GTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGT-GGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGA
EST: gi|32834623|gb|CD974301.1|CD974301
EST:     TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG                         ATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
genomic: TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
EST: gi|60353136|gb|DN220109.1|DN220109
EST:     TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG                         ATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
genomic: TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
EST: gi|32930313|gb|CF035125.1|CF035125
EST:     TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG                         ATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
genomic: TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
EST: gi|32833197|gb|CD972875.1|CD972875
EST:     TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG                         ATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
genomic: TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
EST: gi|78121626|gb|DV540010.1|DV540010
EST:     TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG                         ATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
genomic: TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
EST: gi|91056340|gb|EB166758.1|EB166758
EST:     TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG                         ATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT
genomic: TGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGAT

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: 125

GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGATTGGATTAAAAATGGTGTCCACATCGGGAGTGGCAGAAAATATAAGGATT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 68

GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGATTGGATTAAAAATGGTGTCCACATCGGGAGTGGCAGAAAATATAAGGATT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 37

GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGATTGGATTAAAAATGGTGTCCACATCGGGAGTGGCAGAAAATATAAGGATT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 112

GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttaca ... attagtgcagATTTTGGGCGTCCTTGATATTGGTAAGGATGCGTGGATTCATAGAGAAGATTGGATTAAAAATGGTGTCCACATCGGGAGTGGCAGAAAATATAAGGATT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTGgtaagttacatctcttctcacttgaagtatttcatccatttttcctacatagcttgggtgaatttctgctgcagcaaactcaatatggcatcgaagctaa

- - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - -  GTGGAG