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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGCTGCCTTCAAGTTCCACAATGAAAGTGGAATTGATAATCTGTACAGCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAGgtgagacacacaaacccttttaatttttgtaacattgtgaactacaagaagggcaggcatggtgcaatggtgtaagttgtctccttgagtcactgggtcg...

Basic information

species Zea mays
transcript GRMZM2G081148_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081148_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g36030.1 (Oryza sativa), 5'ss of exon 3
ATATGCTGCCTTCAAGTTCCACAATGAAAGTGGAATTGATAATCTGTACAGCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAGgtgagacacacaaacccttttaatttttgtaacattgtgaactacaagaagggcaggcatggtgcaatggtgtaagttgtctccttgagtcactgggtcg---
|||||||||||||||||| ||||||||||||||||||| ||| || |||||| |||| || |||||||||||||||||||||||  | || ||| ||||||| |      |||| | |||  ||  || |||  ||||        |||     |||  |||  | ||| |  |  || |    || | | | ||  |||   
ATATGCTGCCTTCAAGTTTCACAATGAAAGTGGAATTGCTAACCTCTACAGCCTGCACTCCTGGGTTGGACTTGGAACTATCTGTTTATATGGTGTACAGgtaatttgagcaaagcattt--atcattctaatgttgtctgaattgagattta-aggtttggaactatgttagagctttttaaatttatttattgcatcggta

upper sequence: GRMZM2G081148_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G29750.1 (Glycine max), 5'ss of exon 3
ATATGCTGCCTTCAAGTTCCACAATGAAAGTGGAATTGATAATCTGTACAGCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAGgtgagacacacaaacccttttaatttttgtaacattgtgaac-tacaagaagggcaggcatggtgcaatgg--tgtaagttgtctccttgagtcactgggtcg
 ||| ||||||||||||  |||||||||||||| ||||  ||||| |||||||||||||| ||| ||||| ||||   |||   ||| || || || ||||| |  |||   |      | |   | | |    | |    |  ||||      |  | ||     ||     | | |||||  |  | | |   || |    
TTATACTGCCTTCAAGTATCACAATGAAAGTGGGATTGCCAATCTCTACAGCTTGCATTCATGGCTTGGAATTGGGGTTATTGTCCTTTATGGCATTCAGgtaaaccactgcatatgactaagcgtgtttggattcgcattcacacaactcaaacgtggatcacagaagcaacttttagttgctttttggtgcatcttga---

upper sequence: GRMZM2G081148_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G38070.1 (Glycine max), 5'ss of exon 3
ATATGCTGCCTTCAAGTTCCACAATGAAAGTGGAATTGATAATCTGTACAGCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAGgtgagacacacaaaccctt----ttaatttttgtaacattgtgaact--acaagaagggcaggcatggtgcaatggtg--taagttgtctccttgagtcactgggtcg
 ||| ||||||||||||| |||||||||||||| ||||  ||||| |||||||||||||| ||| ||||| ||||   |||   ||| || || || ||||| | ||| || |     |     |||  |     |   | | ||      |      | || |||| |   ||  ||  ||||||      || |||          
TTATACTGCCTTCAAGTTTCACAATGAAAGTGGGATTGCCAATCTCTACAGCTTGCATTCATGGCTTGGAATTGGGGTTATTGTCCTTTATGGCATTCAGgt-aaacaaaccactgtataagactaaactaaactatcctataaatgtagtataccttgaagacatgatatgattatggttaagtttataatttcagttta-------

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|71417886|gb|DR804239.1|DR804239
EST:     GCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAG                         TGGCTATTTGGCGTTGCTACCTTCTTCTTCCCTGGTGCTTCGCCAACAGTC
genomic: GCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAGgtgagacaca ... catatttcagTGGCTATTTGGCGTTGCTACCTTCTTCTTCCCTGGTGCTTCGCCAACAGTC
EST: gi|91871080|gb|EB401231.1|EB401231
EST:     GCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAG                         TGGCTATTTGGCGTTGCTACCTTCTTCTTCCCTGGTGCTTCGCCAACAGTC
genomic: GCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAGgtgagacaca ... catatttcagTGGCTATTTGGCGTTGCTACCTTCTTCTTCCCTGGTGCTTCGCCAACAGTC
EST: gi|211319649|gb|FL072381.1|FL072381
EST:     GCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAG                         TGGCTATTTGGCGTTGCTACCTTCTTCTTCCCTGGTGCTTCGCCAACA
genomic: GCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAGgtgagacaca ... catatttcagTGGCTATTTGGCGTTGCTACCTTCTTCTTCCCTGGTGCTTCGCCAACA
EST: gi|211319650|gb|FL072382.1|FL072382
EST:     GCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAG                         TGGCTATTTGGCGTTGCTACCTTCTTCTT
genomic: GCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAGgtgagacaca ... catatttcagTGGCTATTTGGCGTTGCTACCTTCTTCTT
EST: gi|28983011|gb|BQ538423.2|BQ538423
EST:     GCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAG                         TGGCTATTTGGCGTTGATACATTCTTCTTCCATGGTGCTTCGCCAACAGTC
genomic: GCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAGgtgagacaca ... catatttcagTGGCTATTTGGCGTTGCTACCTTCTTCTTCCCTGGTGCTTCGCCAACAGTC
EST: gi|76920483|gb|DV168196.1|DV168196
EST:     GCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAG                         TGGCTATTTGGCGTTGCTACCTTCTTCTTCCCTGGTGCTTCGCCAACAGTC
genomic: GCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAGgtgagacaca ... catatttcagTGGCTATTTGGCGTTGCTACCTTCTTCTTCCCTGGTGCTTCGCCAACAGTC
EST: gi|211319643|gb|FL072375.1|FL072375
EST:     GCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAG                         TGGCTATTTGGCGTTGCTACCTTCTTCTTCCCTGGTGCTTCGCCAACAGTC
genomic: GCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAGgtgagacaca ... catatttcagTGGCTATTTGGCGTTGCTACCTTCTTCTTCCCTGGTGCTTCGCCAACAGTC
EST: gi|50323966|gb|CO519092.1|CO519092
EST:     GCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAG                         TGGCTATTTGGCGTTGCTACCTTCTTCTTCCCTGGTGCTTCGCCAACAGTC
genomic: GCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAGgtgagacaca ... catatttcagTGGCTATTTGGCGTTGCTACCTTCTTCTTCCCTGGTGCTTCGCCAACAGTC

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), 39 (downstream exon)
Score: 25

ATATGCTGCCTTCAAGTTCCACAATGAAAGTGGAATTGATAATCTGTACAGCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAGgtgagacaca ... catatttcagTGGCTATTTGGCGTTGCTACCTTCTTCTTCCCTGGTGCTTCGCCAACAGTCCGGCGCAGAATGCTCCCATGGCACACTCGCGCTGGACTTGTTGTCTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 39

ATATGCTGCCTTCAAGTTCCACAATGAAAGTGGAATTGATAATCTGTACAGCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAGgtgagacaca ... catatttcagTGGCTATTTGGCGTTGCTACCTTCTTCTTCCCTGGTGCTTCGCCAACAGTCCGGCGCAGAATGCTCCCATGGCACACTCGCGCTGGACTTGTTGTCTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 88

ATATGCTGCCTTCAAGTTCCACAATGAAAGTGGAATTGATAATCTGTACAGCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAGgtgagacaca ... catatttcagTGGCTATTTGGCGTTGCTACCTTCTTCTTCCCTGGTGCTTCGCCAACAGTCCGGCGCAGAATGCTCCCATGGCACACTCGCGCTGGACTTGTTGTCTACA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 24

ATATGCTGCCTTCAAGTTCCACAATGAAAGTGGAATTGATAATCTGTACAGCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAGgtgagacaca ... catatttcagTGGCTATTTGGCGTTGCTACCTTCTTCTTCCCTGGTGCTTCGCCAACAGTCCGGCGCAGAATGCTCCCATGGCACACTCGCGCTGGACTTGTTGTCTACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGCTGCCTTCAAGTTCCACAATGAAAGTGGAATTGATAATCTGTACAGCTTGCATTCGTGGGTTGGACTTGGAACTATCTGCCTGTACGGTATACAGgtgagacacacaaacccttttaatttttgtaacattgtgaactacaagaagggcaggcatggtgcaatggtgtaagttgtctccttgagtcactgggtcg

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