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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGACCCCGTGCTTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttcgtatcagggaccaaaaccaaacattgccgaataaactgcggatctgtttagtttcctgaaattttaattttacttgattcatttgtagga...

Basic information

species Zea mays
transcript GRMZM2G578572_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G578572_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g34330.1 (Oryza sativa), 5'ss of exon 2
GAGGACCCCGTGCTTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttcgtatcagggaccaaaaccaaacattgccgaataaactgcggatctgtttagtttcctgaaattttaattttacttgattcatttgtagga-----
|||||||| ||||| |||||||||||||| |||||  |||| || ||||||||||||||||||||||||| | | ||||    |     || | |  ||   |||  |    |||  |||||       | ||||| |    ||   |    |||    | ||     
GAGGACCCGGTGCTGCTCACGCCTGAGGATAGCAAGGAGAAACCTTATGTCGCCATCCTCAAGgtctgtgat-gaatcactc-ctgttgccgatc--tggacaatgtatcaaggaattgttttaggcattcaaattatgtcattttgtcgc-catcaccaagatctgt
















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|18384174|gb|BM417374.1|BM417374
EST:     AGCAATCAGAAGCCCTATGTCGCCATCCTCAAG                         GATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
genomic: AGCAATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttc ... ctttgaacagGATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
EST: gi|211046004|gb|FL422505.1|FL422505
EST:     TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAG                         GATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
genomic: TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttc ... ctttgaacagGATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
EST: gi|211214550|gb|FL384291.1|FL384291
EST:     TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAG                         GATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
genomic: TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttc ... ctttgaacagGATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
EST: gi|211198908|gb|FL376287.1|FL376287
EST:     TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAG                         GATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
genomic: TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttc ... ctttgaacagGATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
EST: gi|18649943|gb|BM498762.1|BM498762
EST:     AATCAGAAGCCCTATGTCGCCATCCTCAAG                         GATATACCAGAANCTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
genomic: AATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttc ... ctttgaacagGATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
EST: gi|22489451|gb|BU049374.1|BU049374
EST:     TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAG                         GATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
genomic: TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttc ... ctttgaacagGATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
EST: gi|18650017|gb|BM498836.1|BM498836
EST:     TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAG                         GATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
genomic: TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttc ... ctttgaacagGATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
EST: gi|22489672|gb|BU049595.1|BU049595
EST:     TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAG                         GATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
genomic: TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttc ... ctttgaacagGATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
EST: gi|87152388|gb|DY397177.1|DY397177
EST:     TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAG                         GATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
genomic: TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttc ... ctttgaacagGATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
EST: gi|211389853|gb|FL384028.1|FL384028
EST:     TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAG                         GATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
genomic: TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttc ... ctttgaacagGATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
EST: gi|74242363|gb|DT650277.1|DT650277
EST:     TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAG                         GATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
genomic: TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttc ... ctttgaacagGATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
EST: gi|211487814|gb|FL394401.1|FL394401
EST:     TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAG                         GATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
genomic: TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttc ... ctttgaacagGATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
EST: gi|211168239|gb|FL423106.1|FL423106
EST:     TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAG                         GATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
genomic: TTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttc ... ctttgaacagGATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
EST: gi|19822469|gb|BQ048493.1|BQ048493
EST:     CAGAAGCCCTATGTCGCCATCCTCAAG                         GATATAACAGAANCTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT
genomic: CAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttc ... ctttgaacagGATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTAT

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), 48 (downstream exon)
Score: 158

GAGGACCCCGTGCTTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttc ... ctttgaacagGATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTATAGACCAGAAGAGGCTGACAAAAAGGAGGGTGGATTCTGGGTAGCACGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 108

GAGGACCCCGTGCTTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttc ... ctttgaacagGATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTATAGACCAGAAGAGGCTGACAAAAAGGAGGGTGGATTCTGGGTAGCACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

GAGGACCCCGTGCTTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttc ... ctttgaacagGATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTATAGACCAGAAGAGGCTGACAAAAAGGAGGGTGGATTCTGGGTAGCACGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 85

GAGGACCCCGTGCTTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttc ... ctttgaacagGATATAACAGAAACTGATGGGAGCCTATATGTAACTGGCCAATGGTTTTATAGACCAGAAGAGGCTGACAAAAAGGAGGGTGGATTCTGGGTAGCACGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGACCCCGTGCTTCTCACGCCTGAGGACAGCAATCAGAAGCCCTATGTCGCCATCCTCAAGgtctgtgttcgtatcagggaccaaaaccaaacattgccgaataaactgcggatctgtttagtttcctgaaattttaattttacttgattcatttgtagga

- - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaccaa