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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaactcccgctttatattagtagagatgtttgcgaatccataatctacattattggtccgttatttctttccttttaactctttatttaaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG

Basic information

species Zea mays
transcript GRMZM2G101250_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101250_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os04g09860.1 (Oryza sativa), 3'ss of exon 18
agaaactcccgctttatattagtagagatgtttgcgaatccataat-ctacattat---tggtccgttatttctttccttttaactctttatttaaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
      |||  |          | ||||    ||   | | |  || ||    ||    ||| || | ||||||||  | |||| |||    | | | ||  |||| || || || |||| ||||||||||||||| |||||||||||||| |||
---gtgtccaacgaggggccgctcgagagccatggtcaccaaagatgctgtgataaccatggcccatcatttctttgttattaa-tctcatctaatattgatagGTATTACAGTCGAGGAGTTATCCATTATTTGTCCCATGGAAAGGTGGTGTG
















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:     GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAG                         GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
genomic: GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAGgtgcgccgta ... aaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
EST: gi|60358881|gb|DN225854.1|DN225854
EST:     GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAG                         GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
genomic: GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAGgtgcgccgta ... aaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
EST: gi|148934268|gb|EC878291.2|EC878291
EST:     GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAG                         GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
genomic: GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAGgtgcgccgta ... aaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
EST: gi|78121627|gb|DV540011.1|DV540011
EST:     GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAG                         GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
genomic: GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAGgtgcgccgta ... aaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
EST: gi|40302924|gb|CK347311.1|CK347311
EST:     GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAG                         GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
genomic: GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAGgtgcgccgta ... aaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
EST: gi|60358880|gb|DN225853.1|DN225853
EST:     GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAG                         GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
genomic: GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAGgtgcgccgta ... aaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
EST: gi|9254603|gb|BE345056.1|BE345056
EST:     GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAG                         GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
genomic: GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAGgtgcgccgta ... aaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
EST: gi|211181693|gb|FL465348.1|FL465348
EST:     CAATCTATTGAGAAAGTTGAG                         GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGGAGT
genomic: CAATCTATTGAGAAAGTTGAGgtgcgccgta ... aaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGT-GGAGT
EST: gi|32834623|gb|CD974301.1|CD974301
EST:     GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAG                         GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
genomic: GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAGgtgcgccgta ... aaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
EST: gi|60353136|gb|DN220109.1|DN220109
EST:     TAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAG                         GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
genomic: TAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAGgtgcgccgta ... aaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
EST: gi|32930313|gb|CF035125.1|CF035125
EST:     GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAG                         GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
genomic: GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAGgtgcgccgta ... aaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
EST: gi|32833197|gb|CD972875.1|CD972875
EST:     GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAG                         GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
genomic: GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAGgtgcgccgta ... aaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
EST: gi|78121626|gb|DV540010.1|DV540010
EST:     GGTTCGCCCTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAG                         GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
genomic: GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAGgtgcgccgta ... aaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
EST: gi|91056340|gb|EB166758.1|EB166758
EST:     GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAG                         GTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
genomic: GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAGgtgcgccgta ... aaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG

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: 280

GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAGgtgcgccgta ... aaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 171

GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAGgtgcgccgta ... aaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAGgtgcgccgta ... aaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 143

GGTTCGCACTAAAATTTCAGCAAACCAATCTATTGAGAAAGTTGAGgtgcgccgta ... aaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctacattattggtccgttatttctttccttttaactctttatttaaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG
                             ttttaac  putative branch site (score: 143)
                             ttttaactctttattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaactcccgctttatattagtagagatgtttgcgaatccataatctacattattggtccgttatttctttccttttaactctttatttaaaatggcagGTGTTGCAATCTAGGACTTATCCATTATTTGTTCCATGGAAAGGTGGAGTG

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