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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtatcagtcactactactgtcgtctgtatgactgtatcgatggtgacggcaacaatataatccaattaattattcagcgaacttaaaaacgacgttgatttccttgcagGGTCTTTGTCAAGTCAGTGAAGCGGCTCAAGATACTTGCGTAGCCGACGGTCGGCGCCTCAGAGACGTCGTGTGGTCCGTCTCACCAGGATCGGAGCAGT

Basic information

species Zea mays
transcript GRMZM2G000158_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000158_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g07040.1 (Oryza sativa), 3'ss of exon 3
gtacgtatcagtcactactactgtcgtctgtatgactgtatcgatggtgacggcaacaatataatccaattaattattcagcgaacttaaaaacgacgttgatttc---cttgcagGGTCTTTGTCAAGTCAGTGAAGCGGCTCAAGATACTTGCGTAGCCGACGGTCGGCGCCTCAGAGACGTCGTGTGGTCCGTCTCACCAGGATCGGAGCAGT---
||| ||     ||| | || |       ||| |  |  |  | |   |      |||||| | ||| || |  | | |   ||| | |||   |||   ||| ||     |||||||| ||||| |||||| ||||| |||||||||||||| | ||| | ||| |        | ||  ||      | |||  |   ||   ||    |   ||   
gtaagt-----tcatttcttcccggcattgtgtcgccatcacaaaattatt--taacaatttcatcaaact--tgact--acgagcctaacggcgagtctgaattttcatttgcagGGCCTTTGCCAAGTCGGTGAAACGGCTCAAGATACTGGTGTAACTGACTGCAAAT---TAAGCTACTAGTACTAGTCTTTACTACTTCGAATAAAATTGTACG
















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|22490343|gb|BU050266.1|BU050266
EST:     GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGA                         GGTCTTTGTCAAGTCAGTGAAGCGGC
genomic: GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGAgtacgtatca ... ttccttgcagGGTCTTTGTCAAGTCAGTGAAGCGGC
EST: gi|18964862|gb|BM661253.1|BM661253
EST:     GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGA                         GGTCTTTGTCA-GTCAGTGAAGCGGC
genomic: GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGAgtacgtatca ... ttccttgcagGGTCTTTGTCAAGTCAGTGAAGCGGC
EST: gi|87151978|gb|DY396767.1|DY396767
EST:     GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGA                         GGTCTTTGTCAAGTCAGTGAAGCGGC
genomic: GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGAgtacgtatca ... ttccttgcagGGTCTTTGTCAAGTCAGTGAAGCGGC
EST: gi|211020776|gb|FL433464.1|FL433464
EST:     GTTGCTCGTCGGAGATGATGTGCCGTGGGA                         GGTCTTTGTCAAGTCAGTGAAGCGGCTCAAGATACTTGCGTAGCCGACGGT
genomic: GTTGCTCGTCGGAGATGATGTGCCGTGGGAgtacgtatca ... ttccttgcagGGTCTTTGTCAAGTCAGTGAAGCGGCTCAAGATACTTGCGTAGCCGACGGT
EST: gi|74234745|gb|DT642659.1|DT642659
EST:     GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGA                         GGTCTTTGTCAAGTCAGTGAAGCGGCTCAAGATACTTGCGTAGCCGACGGT
genomic: GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGAgtacgtatca ... ttccttgcagGGTCTTTGTCAAGTCAGTGAAGCGGCTCAAGATACTTGCGTAGCCGACGGT
EST: gi|94475942|gb|EB704900.1|EB704900
EST:     GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGA                         GGTCTTTGTCAAGTCAGTGAAGCGGCTCAAGATACTTGCGTAGCCGACGGT
genomic: GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGAgtacgtatca ... ttccttgcagGGTCTTTGTCAAGTCAGTGAAGCGGCTCAAGATACTTGCGTAGCCGACGGT
EST: gi|71762442|gb|DR960379.1|DR960379
EST:     GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGA                         GGTCTTTGTCAAGTCAGTGAAGCGGCTCAAGATACTTGCGTAGCCGACGGT
genomic: GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGAgtacgtatca ... ttccttgcagGGTCTTTGTCAAGTCAGTGAAGCGGCTCAAGATACTTGCGTAGCCGACGGT
EST: gi|14243352|gb|BG841066.2|BG841066
EST:     GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGA                         GGTCTTTGTCAAGTCAGTGAAGCGGCTCAAGATACTTGCGTAGCCGACGGT
genomic: GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGAgtacgtatca ... ttccttgcagGGTCTTTGTCAAGTCAGTGAAGCGGCTCAAGATACTTGCGTAGCCGACGGT
EST: gi|60350945|gb|DN217918.1|DN217918
EST:     GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGA                         GGTCTTTGTCAAGTCAGTGAAGCGGCTCAAGATACTTGCGTAGCCGACGGT
genomic: GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGAgtacgtatca ... ttccttgcagGGTCTTTGTCAAGTCAGTGAAGCGGCTCAAGATACTTGCGTAGCCGACGGT
EST: gi|87151801|gb|DY396590.1|DY396590
EST:     GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGA                         GGTCTTTGTCAAGTCAGTGAAGCGGC
genomic: GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGAgtacgtatca ... ttccttgcagGGTCTTTGTCAAGTCAGTGAAGCGGC
EST: gi|78081855|gb|DV510267.1|DV510267
EST:     GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGA                         GGTCTTTGTCAAGT
genomic: GAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGAgtacgtatca ... ttccttgcagGGTCTTTGTCAAGT

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 2 RNA-Seq libraries.


Block sizes: 20 (upstream exon), 34 (downstream exon)
Score: 3

TGGTGGTCTCGCACGAGCGCCGCCGTCGCCATCCTTATGTAGTCACCTACGAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGAgtacgtatca ... ttccttgcagGGTCTTTGTCAAGTCAGTGAAGCGGCTCAAGATACTTGCGTAGCCGACGGTCGGCGCCTCAGAGACGTCGTGTGGTCCGTCTCACCAGGATCGGAGCAGT


Block sizes: 15 (upstream exon), 46 (downstream exon)
Score: 9

TGGTGGTCTCGCACGAGCGCCGCCGTCGCCATCCTTATGTAGTCACCTACGAGGACGGCGAAGGGGACTGGTTGCTCGTCGGAGATGATGTGCCGTGGGAgtacgtatca ... ttccttgcagGGTCTTTGTCAAGTCAGTGAAGCGGCTCAAGATACTTGCGTAGCCGACGGTCGGCGCCTCAGAGACGTCGTGTGGTCCGTCTCACCAGGATCGGAGCAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atataatccaattaattattcagcgaacttaaaaacgacgttgatttccttgcagGGTCTTTGTCAAGTCAGTGAAGCGGCTCAAGATACTTGCGTAGCCGACGGTCGGCGCCTCAGAGACGTCGTGTGGTCCGTCTCACCAGGATCGGAGCAGT
                                            tttccttgc  CT-rich tract
     atccaattaattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtatcagtcactactactgtcgtctgtatgactgtatcgatggtgacggcaacaatataatccaattaattattcagcgaacttaaaaacgacgttgatttccttgcagGGTCTTTGTCAAGTCAGTGAAGCGGCTCAAGATACTTGCGTAGCCGACGGTCGGCGCCTCAGAGACGTCGTGTGGTCCGTCTCACCAGGATCGGAGCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG