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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtccaaccgcctcctttttttcttttccgcttttgccctgctgtgctcatgcttcgggaccttgatgttgcaatgctgtatgttgggggattgagggttaatcgtggcctttttcgacgtgcgtggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCGCGCGTGCTGGTGTTCAGCGAGGACCTCTTCTTTATTTACCTGCTGCCGC

Basic information

species Zea mays
transcript GRMZM2G037342_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037342_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 3'ss of exon 1
gtgagtccaaccgcctcctttttttcttttccgcttttgccctgctgtgctcatgcttcgggaccttgatgttgcaatgctgtatgttgggggattgagggttaatcgtggcctttttcgacgtgcgtggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCGCGCGTGCTGGTGTTCAGCGAGGACCTCTTCTTTATTTACCTGCTGCCGC
||||||| |   |     | || ||   ||  ||| ||    |  | || | |   || ||||    |||| ||   || | |  ||| || | ||||  |||  | |||    | |  |  ||        ||||||||| |||| |||||||  || ||  || | | ||||||| ||||||| |||||| | ||||||||||||||||| |||||||| ||||||||||| ||||
gtgagtcgatgagt----tcttgttgagttgtgctgtt----tattatg-tgagattttggga----gatgatg--gtggttttcgtttggtgtttgattgtttgtggtgtgtgtgtctggggttt-----cttgcagGGGTTGGGTACTGGAGGAGTGATTTTGATGGTGTCGAGCTGGAAGCACTCGCGCATACTGGTGTTCAGCGAGGATCTCTTCTTCATTTACCTGCTCCCGC
















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|93016611|gb|EB642131.1|EB642131
EST:     TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATC                         GGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
genomic: TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
EST: gi|211187214|gb|FL054036.1|FL054036
EST:     TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATC                         GGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGSGGGAAGCATTCG
genomic: TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
EST: gi|148996402|gb|EE035697.2|EE035697
EST:     TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATC                         GGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
genomic: TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
EST: gi|78119306|gb|DV537690.1|DV537690
EST:     TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATC                         GGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
genomic: TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
EST: gi|71315380|gb|DR794294.1|DR794294
EST:     TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATC                         GGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
genomic: TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
EST: gi|76921052|gb|DV168433.1|DV168433
EST:     TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATC                         GGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
genomic: TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
EST: gi|20300970|gb|BQ163913.1|BQ163913
EST:     CGAGTCCATCACCGCGCTCTTCATC                         GGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
genomic: CGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
EST: gi|71426858|gb|DR807908.1|DR807908
EST:     TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATC                         GGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
genomic: TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
EST: gi|71438439|gb|DR819489.1|DR819489
EST:     TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATC                         GGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
genomic: TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
EST: gi|148956705|gb|EC902576.2|EC902576
EST:     TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATC                         GGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
genomic: TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
EST: gi|18964389|gb|BM660977.1|BM660977
EST:     CCGCGCTCTT-ATC                         GGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
genomic: CCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
EST: gi|50328971|gb|CO524097.1|CO524097
EST:     TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATC                         GGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
genomic: TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
EST: gi|148959687|gb|EC905601.2|EC905601
EST:     TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATC                         GGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
genomic: TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
EST: gi|149058822|gb|EE156843.2|EE156843
EST:     TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATC                         GGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
genomic: TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
EST: gi|76912611|gb|DV164818.1|DV164818
EST:     TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATC                         GGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
genomic: TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
EST: gi|149015463|gb|EE045330.2|EE045330
EST:     TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATC                         GGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
genomic: TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
EST: gi|148931601|gb|EC874712.2|EC874712
EST:     TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATC                         GGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
genomic: TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
EST: gi|71438478|gb|DR819528.1|DR819528
EST:     TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATC                         GGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG
genomic: TCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCG

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), 42 (downstream exon)
Score: 62

GGTGGGGCTGTTCGTGGCGCTCATGTGCGTCTGCATCGTCGTCGGGCACCTCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCGCGCGTGCTGGTGTTCAGCGAGGACCTCTTCTTTATTTACCTGCTGCCGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 17

GGTGGGGCTGTTCGTGGCGCTCATGTGCGTCTGCATCGTCGTCGGGCACCTCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCGCGCGTGCTGGTGTTCAGCGAGGACCTCTTCTTTATTTACCTGCTGCCGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 21

GGTGGGGCTGTTCGTGGCGCTCATGTGCGTCTGCATCGTCGTCGGGCACCTCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCGCGCGTGCTGGTGTTCAGCGAGGACCTCTTCTTTATTTACCTGCTGCCGC


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

GGTGGGGCTGTTCGTGGCGCTCATGTGCGTCTGCATCGTCGTCGGGCACCTCCTCGAGGAGAACCGCTGGATGAACGAGTCCATCACCGCGCTCTTCATCgtgagtccaa ... ggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCGCGCGTGCTGGTGTTCAGCGAGGACCTCTTCTTTATTTACCTGCTGCCGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttgggggattgagggttaatcgtggcctttttcgacgtgcgtggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCGCGCGTGCTGGTGTTCAGCGAGGACCTCTTCTTTATTTACCTGCTGCCGC
                ggttaat  putative branch site (score: 70)
                  ttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtccaaccgcctcctttttttcttttccgcttttgccctgctgtgctcatgcttcgggaccttgatgttgcaatgctgtatgttgggggattgagggttaatcgtggcctttttcgacgtgcgtggctttgcagGGGCTGGGAACTGGAGCGGTCATCCTGTTCGCGTCGAGCGGGAAGCATTCGCGCGTGCTGGTGTTCAGCGAGGACCTCTTCTTTATTTACCTGCTGCCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC