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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcgatattatattattatcttcggcgggtacgatgatgaacaccaccagcagcagcagcatactgattgtttgatgggtggaatggattggaattcaattgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGCCCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGA

Basic information

species Zea mays
transcript GRMZM2G071154_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071154_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g36950.3 (Oryza sativa), 3'ss of exon 1
-----------------gtgagcgatattatattattatcttcgg-cgggtac--gatgatgaacaccaccagcagcagcagcata---ctgattgtttgatgggtggaatggattggaattcaattgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGCCCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGA
                  | |     || |||  |  |||   |    |||||  ||     ||     |  | | ||  |   ||   |  ||    | | |  |   ||| |    |      ||||||||||||| || || || |||||||| || ||| | || ||| | || || ||||||||||||||||||||||||||||| |||||||||||||||||||||||
gtaagcataaccaacctataaattcgatgataaaaccatccaagaattggtacttgaaccctaattattcttgaaccaagaaattatgtcccataaaattaagtttctcatgaac-aaatcgtgcttgatgcagGGCTTCCATCGAGATACAGGGATTCAGTGAGGGCGATCAGGCCAGGGCTGCCCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGA
















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|149002886|gb|EE038882.2|EE038882
EST:     TGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCG                         GGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
genomic: CGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCGgtgagcgata ... attgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
EST: gi|8367109|gb|BE050054.1|BE050054
EST:     CGTCTGCAACAACGACACCATGGACGAGAACCTCAGGAGGGAGCTGTTCG                         GGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
genomic: CGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCGgtgagcgata ... attgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
EST: gi|50336543|gb|CO531669.1|CO531669
EST:     CGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCG                         GGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
genomic: CGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCGgtgagcgata ... attgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
EST: gi|149082668|gb|EE171878.2|EE171878
EST:     CGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCG                         GGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
genomic: CGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCGgtgagcgata ... attgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
EST: gi|60338891|gb|DN205864.1|DN205864
EST:     CGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCG                         GGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
genomic: CGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCGgtgagcgata ... attgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
EST: gi|93015747|gb|EB641267.1|EB641267
EST:     CGTTTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCG                         GGGTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
genomic: CGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCGgtgagcgata ... attgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
EST: gi|211386348|gb|FL456698.1|FL456698
EST:     CGTCTGCAACAACGACACCATGGACGAGAACCTCAGGAGGGAGCTGTTCG                         GGCTGCCGTCCAGGTACAGGGACTCGGTGCGGGCTATCCGCCCGGGACTGC
genomic: CGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCGgtgagcgata ... attgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
EST: gi|78022808|gb|DV491195.1|DV491195
EST:     GGTCTGCAACAACGACATTATGGACGAGAACCTCAGGAGGGAGCTGTTCG                         GGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
genomic: CGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCGgtgagcgata ... attgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
EST: gi|149088944|gb|EE178087.2|EE178087
EST:     CGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCG                         GGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
genomic: CGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCGgtgagcgata ... attgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
EST: gi|149090354|gb|EE179660.2|EE179660
EST:     AACCTCAGGAGGGAGCTGTTCG                         GGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
genomic: AACCTCAGGAGGGAGCTGTTCGgtgagcgata ... attgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
EST: gi|71444740|gb|DR825790.1|DR825790
EST:     CGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCG                         GGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
genomic: CGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCGgtgagcgata ... attgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
EST: gi|211171601|gb|FL423137.1|FL423137
EST:     CGTCTGCAACAACGACACCATGGACGAGAACCTCAGGAGGGAGCTGTTCG                         GGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC
genomic: CGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCGgtgagcgata ... attgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGC

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: 48 (upstream exon), 46 (downstream exon)
Score: 129

CCGGCGTCGGAGGCGCTGCCGCGGGGCCAGGCCATCGGCGGGTACATCTTCGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCGgtgagcgata ... attgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGCCCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 778

CCGGCGTCGGAGGCGCTGCCGCGGGGCCAGGCCATCGGCGGGTACATCTTCGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCGgtgagcgata ... attgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGCCCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1184

CCGGCGTCGGAGGCGCTGCCGCGGGGCCAGGCCATCGGCGGGTACATCTTCGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCGgtgagcgata ... attgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGCCCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 768

CCGGCGTCGGAGGCGCTGCCGCGGGGCCAGGCCATCGGCGGGTACATCTTCGTCTGCAACAACGACACTATGGACGAGAACCTCAGGAGGGAGCTGTTCGgtgagcgata ... attgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGCCCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcagcatactgattgtttgatgggtggaatggattggaattcaattgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGCCCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGA
                                       aattcaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcgatattatattattatcttcggcgggtacgatgatgaacaccaccagcagcagcagcatactgattgtttgatgggtggaatggattggaattcaattgatgcagGGCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGCCCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC