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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTTATTTACATGTGGTTACACCTTCATCACAGCGATGGCAAAGCTTTTGTCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCTgtacagtcctttattatcccttttcatttgttgtatttacctactatcaaatgattaactggtattttgatcttttttccatcttttccatcattccattttgttgagtgtcctaatttactatatatttggtaatactttgcag

Basic information

species Zea mays
transcript GRMZM2G149224_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149224_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g29170.2 (Oryza sativa), 5'ss of exon 8
ACTTATTTACATGTGGTTACACCTTCATCACAGCGATGGCAAAGCTTTTGTCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCTgtacagtcctttattatcccttttcatttgttgtatttacctactatcaaatgattaactggtattttgatcttttttccatcttttccatcattccattttgttgagtgtcctaatttactatatatttggtaatactttgcag
| |||||||||||||||||||||||||| ||||| |||||||||||||| |||||||| || ||||| |||||||||||||| || |||||  ||||| ||||  ||||| | | ||   ||  | ||   || || | |||| |||||  || | ||     || | |  ||||| |||||||| |      |||||  | || || |||   |   || ||  |||   |             
ATTTATTTACATGTGGTTACACCTTCATTACAGCAATGGCAAAGCTTTTCTCACTAACCGCACTGTTTTTATTCATTCATGGGATTCTGCCTGCAAATGTgtatggtcctctgtcatt--ttccctttaactgaatatgcctattatcagctggtgaaacaccatctagg-cttttatccatcttctgt----ttccagatagt-gattgttgaa---taatacttatgcag-------------
















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|87151705|gb|DY396494.1|DY396494
EST:     TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCT                         GTTCGGTCACAAAGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
genomic: TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCTgtacagtcct ... tactttgcagGTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
EST: gi|32863056|gb|CF002738.1|CF002738
EST:     TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCT                         GTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
genomic: TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCTgtacagtcct ... tactttgcagGTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
EST: gi|149072463|gb|EE160739.2|EE160739
EST:     TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCT                         GTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
genomic: TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCTgtacagtcct ... tactttgcagGTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
EST: gi|211480846|gb|FL457134.1|FL457134
EST:     TCACTAACTGCTCTGTTCTTATTCATTCAT-GCATGCTGCCATCAAATCT                         GTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
genomic: TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCTgtacagtcct ... tactttgcagGTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
EST: gi|18450804|gb|BM429082.1|BM429082
EST:     TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCT                         GTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
genomic: TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCTgtacagtcct ... tactttgcagGTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
EST: gi|32836792|gb|CD976470.1|CD976470
EST:     TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCT                         GTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
genomic: TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCTgtacagtcct ... tactttgcagGTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
EST: gi|32837008|gb|CD976686.1|CD976686
EST:     TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCT                         GTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
genomic: TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCTgtacagtcct ... tactttgcagGTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
EST: gi|18650185|gb|BM499004.1|BM499004
EST:     GCATGCTGCCATCAAATCT                         GTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
genomic: GCATGCTGCCATCAAATCTgtacagtcct ... tactttgcagGTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
EST: gi|37381967|gb|CF627894.1|CF627894
EST:     TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCT                         GTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCAA
genomic: TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCTgtacagtcct ... tactttgcagGTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
EST: gi|60337162|gb|DN204135.1|DN204135
EST:     TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCT                         GTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
genomic: TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCTgtacagtcct ... tactttgcagGTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
EST: gi|32846686|gb|CD986367.1|CD986367
EST:     TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCT                         GTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
genomic: TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCTgtacagtcct ... tactttgcagGTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
EST: gi|31364078|gb|CD448433.1|CD448433
EST:     TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCT                         GTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA
genomic: TCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCTgtacagtcct ... tactttgcagGTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCA

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: 97

ACTTATTTACATGTGGTTACACCTTCATCACAGCGATGGCAAAGCTTTTGTCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCTgtacagtcct ... tactttgcagGTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCAGGCACAGGCTCATCATATTGCTAATTCCATTAGTTCGAATTGGAACTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 75

ACTTATTTACATGTGGTTACACCTTCATCACAGCGATGGCAAAGCTTTTGTCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCTgtacagtcct ... tactttgcagGTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCAGGCACAGGCTCATCATATTGCTAATTCCATTAGTTCGAATTGGAACTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 90

ACTTATTTACATGTGGTTACACCTTCATCACAGCGATGGCAAAGCTTTTGTCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCTgtacagtcct ... tactttgcagGTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCAGGCACAGGCTCATCATATTGCTAATTCCATTAGTTCGAATTGGAACTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 87

ACTTATTTACATGTGGTTACACCTTCATCACAGCGATGGCAAAGCTTTTGTCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCTgtacagtcct ... tactttgcagGTTCGGTCACAAGGTTGAGAAACTCGAGGCCTCTAATTTTCACATCACCCAGGCACAGGCTCATCATATTGCTAATTCCATTAGTTCGAATTGGAACTCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTATTTACATGTGGTTACACCTTCATCACAGCGATGGCAAAGCTTTTGTCACTAACTGCTCTGTTCTTATTCATTCATGGCATGCTGCCATCAAATCTgtacagtcctttattatcccttttcatttgttgtatttacctactatcaaatgattaactggtattttgatcttttttccatcttttccatcattccattttgttgagtgtcctaatttactatatatttggtaatactttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC