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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCGCGCCTTGTTGGATCGTGGCGTCCAAGCAACGGTGGTAGCGGAGCGCGAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattcccatttcgttcatccgtcttttttctctccatcctctggggaagtttgaatctgagctttctcctgcgttcccgatcttcctcggaattg...

Basic information

species Zea mays
transcript GRMZM2G048117_T01
intron # 1
splice site 5'
intron type U2

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|32842035|gb|CD981716.1|CD981716
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|211413474|gb|FL176059.1|FL176059
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|32839933|gb|CD979614.1|CD979614
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|211416020|gb|FL176068.1|FL176068
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|211215180|gb|FL411863.1|FL411863
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|60672360|gb|DN475121.1|DN475121
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|32839755|gb|CD979436.1|CD979436
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|32839932|gb|CD979613.1|CD979613
EST:     ATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: ATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|211416024|gb|FL176072.1|FL176072
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|91052363|gb|EB162781.1|EB162781
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|211416023|gb|FL176071.1|FL176071
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|211416025|gb|FL176073.1|FL176073
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|6022585|gb|AW067397.1|AW067397
EST:     CCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: CCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|211416026|gb|FL176074.1|FL176074
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|32835798|gb|CD975476.1|CD975476
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|60672355|gb|DN475116.1|DN475116
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|109637480|gb|EC591025.1|EC591025
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGATCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|211416017|gb|FL176065.1|FL176065
EST:     GAGGCARTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTARCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|211413473|gb|FL176058.1|FL176058
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|32842107|gb|CD981788.1|CD981788
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|78023025|gb|DV491412.1|DV491412
EST:     AGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: AGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|211416016|gb|FL176064.1|FL176064
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|29945505|gb|CB815673.1|CB815673
EST:     ATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: ATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|211418562|gb|FL176078.1|FL176078
EST:     GAGGCAGTGGCCGCAKAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|32840483|gb|CD980164.1|CD980164
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|50332887|gb|CO528013.1|CO528013
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|60400222|gb|DN233029.1|DN233029
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
EST: gi|211416019|gb|FL176067.1|FL176067
EST:     GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAG                         GTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA
genomic: GAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTA

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: 46 (upstream exon), 47 (downstream exon)
Score: 72

TTCGCGCCTTGTTGGATCGTGGCGTCCAAGCAACGGTGGTAGCGGAGCGCGAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTATTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

TTCGCGCCTTGTTGGATCGTGGCGTCCAAGCAACGGTGGTAGCGGAGCGCGAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTATTCAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 70

TTCGCGCCTTGTTGGATCGTGGCGTCCAAGCAACGGTGGTAGCGGAGCGCGAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTATTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 225

TTCGCGCCTTGTTGGATCGTGGCGTCCAAGCAACGGTGGTAGCGGAGCGCGAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattc ... cattgttcagGTGGTTAGCGAGAATTATGCCAATCCCATAACATGCTTCTTCCATGTGCTATTCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCGCGCCTTGTTGGATCGTGGCGTCCAAGCAACGGTGGTAGCGGAGCGCGAGGCAGTGGCCGCAGAAGGAAGCGCGAAGCATCCATGGACCAACGCCAGgtgggtattcccatttcgttcatccgtcttttttctctccatcctctggggaagtttgaatctgagctttctcctgcgttcccgatcttcctcggaattg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcctcg