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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACATAGTACGAATCAAGATACTGCGTAACAAACCAGATCATGCACTTGTTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAGgtacattcatattcacaagtcactgatatatgtgttctcagttgcattcctattgtttgttgcagttgacgatacatattctttgcag

Basic information

species Zea mays
transcript GRMZM2G052926_T02
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052926_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os05g36120.1 (Oryza sativa), 5'ss of exon 14
AAACATAGTACGAATCAAGATACTGCGTAACAAACCAGATCATGCACTTGTTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAGgtacattcatattcacaagtcactgatatatgtgttctcagttgcattcctattgtttgttgcagttgacgatacatattct-ttgcag------------------------
 |||||||| |||||||| |||||||| |||||||||||||| || |||||||| |||||||||||||| ||||| |||||||||||||||||| |||||||||  |||||||| ||| |  ||| |  || ||   | |||   | |  | || | | ||    |  | |||   | || |   |||                         
GAACATAGTCCGAATCAAAATACTGCGCAACAAACCAGATCACGCCCTTGTTGAAATGGCTGATGGGTTTCAGGCTGAGCTAGCTGTGCATTATCTGAAGgtactctcatattcgcaattatctgcttcat-tgcattgagtaaaactaattttctattttcatatgtatgattactgttttgccgcattttggatgccaatgtttttcacag
















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|31361372|gb|CD445729.1|CD445729
EST:     TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAG                         GGGTCTATACTATTTGGTAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
genomic: TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAGgtacattcat ... ttctttgcagGGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
EST: gi|67014377|gb|CO443126.1|CO443126
EST:     TTGAGATGGCTGATGGGTTGCAGGCANAGCTAGCTGTGCATTATTTGAAG                         GGGTCTATACTATNTTGG-AAGAAGCTGGAAGT-AACTACTCAAA-TATCC
genomic: TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAGgtacattcat ... ttctttgcagGGGTCTATACTAT-TTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCC
EST: gi|60342999|gb|DN209972.1|DN209972
EST:     TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAG                         GGGTCTATACTATTTGGTAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
genomic: TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAGgtacattcat ... ttctttgcagGGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
EST: gi|24769512|gb|CA404641.1|CA404641
EST:     TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAG                         GGGTCTATACTATTTGGTAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
genomic: TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAGgtacattcat ... ttctttgcagGGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
EST: gi|32945206|gb|CF050025.1|CF050025
EST:     TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAG                         GGGTCTATACTATTTGGTAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
genomic: TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAGgtacattcat ... ttctttgcagGGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
EST: gi|61118024|gb|DN558985.1|DN558985
EST:     TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAG                         GGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
genomic: TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAGgtacattcat ... ttctttgcagGGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
EST: gi|32930271|gb|CF035083.1|CF035083
EST:     TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAG                         GGGTCTATACTATTTGGTAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
genomic: TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAGgtacattcat ... ttctttgcagGGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
EST: gi|32837372|gb|CD977050.1|CD977050
EST:     GAGCTAGCTGTGCATTATTTGAAG                         GGGTCTATACTATTTGGTAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
genomic: GAGCTAGCTGTGCATTATTTGAAGgtacattcat ... ttctttgcagGGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
EST: gi|78080904|gb|DV509316.1|DV509316
EST:     TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAG                         GGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
genomic: TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAGgtacattcat ... ttctttgcagGGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
EST: gi|78087000|gb|DV515393.1|DV515393
EST:     TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAG                         GGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
genomic: TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAGgtacattcat ... ttctttgcagGGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
EST: gi|61118023|gb|DN558984.1|DN558984
EST:     TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAG                         GGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
genomic: TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAGgtacattcat ... ttctttgcagGGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
EST: gi|32932167|gb|CF036979.1|CF036979
EST:     TGAGATGGCTGATGGG-TGCAGGCAGAAGCTAGCTGTGCATTATTTGAAG                         GGGTCTATACTATTTGGTAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
genomic: TGAGATGGCTGATGGGTTGCAGGCAG-AGCTAGCTGTGCATTATTTGAAGgtacattcat ... ttctttgcagGGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCT
EST: gi|111433433|gb|EE297750.1|EE297750
EST:     TTGAGATGGCTGATGGGTTGTAGGCAGAGCTAGCTGTGCATTATTTGAAG                         GGGTCTATACTATTTGGGAAGAAGCTGGAAGTTAACTACTCAAAGTATCCT
genomic: TTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAGgtacattcat ... ttctttgcagGGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCT

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: 47 (upstream exon), 49 (downstream exon)
Score: 171

AAACATAGTACGAATCAAGATACTGCGTAACAAACCAGATCATGCACTTGTTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAGgtacattcat ... ttctttgcagGGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCTAACATCACACCTGCTCCTGACGCCCACGACTACTTAAACTCAAGCATAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 65

AAACATAGTACGAATCAAGATACTGCGTAACAAACCAGATCATGCACTTGTTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAGgtacattcat ... ttctttgcagGGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCTAACATCACACCTGCTCCTGACGCCCACGACTACTTAAACTCAAGCATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 91

AAACATAGTACGAATCAAGATACTGCGTAACAAACCAGATCATGCACTTGTTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAGgtacattcat ... ttctttgcagGGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCTAACATCACACCTGCTCCTGACGCCCACGACTACTTAAACTCAAGCATAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 87

AAACATAGTACGAATCAAGATACTGCGTAACAAACCAGATCATGCACTTGTTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAGgtacattcat ... ttctttgcagGGGTCTATACTATTTGGGAAGAAACTGGAAGTTAACTACTCAAAGTATCCTAACATCACACCTGCTCCTGACGCCCACGACTACTTAAACTCAAGCATAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACATAGTACGAATCAAGATACTGCGTAACAAACCAGATCATGCACTTGTTGAGATGGCTGATGGGTTGCAGGCAGAGCTAGCTGTGCATTATTTGAAGgtacattcatattcacaagtcactgatatatgtgttctcagttgcattcctattgtttgttgcagttgacgatacatattctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG