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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcatgcttttaatgatactgcacatatattaacttgtcatatgcccgttatgtctcttagagtacggatctttctcatctcagGTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTTAGTGACCGTTGTTTTAGAATATATGGCCCTGCTGTTCCAGTGCTGGAAA

Basic information

species Zea mays
transcript GRMZM5G899168_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G899168_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g56560.1 (Oryza sativa), 3'ss of exon 3
gtaaa-tcatgcttttaatgatactgcacatatattaacttgtcatatgcccgttatgtctc---ttagagtacggatctttctcatctcagGTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTTAGTGACCGTTGTTTTAGAATATATGGCCCTGCTGTTCCAGTGCTGGAAA
||||| |||| | ||  | |||  |||||||  |     ||  ||| |  | || || | ||       |||  | | |||| |||| ||||||||| || ||||||||||||||||||||||| ||  ||||||||||| ||||||| ||||||| |||||| ||||| ||| |  |||| ||||||||||
gtaaaatcatccgtt--acgatcgtgcacatgaagcgcatt--catttaactgtgatttatcagtccttagtctgaagcttt-tcatttcagGTTGCTTCCATGTTCTTCAAGGAAGTTGTTTCCCGGTTAGTGAGCTCACTTAGTGATCGTTGTTATAGAATTTATGGGCCTCCCATTCCTGTGCTGGAAA
















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|113703127|gb|EE680631.1|EE680631
EST:     ACATCTATTTCTTAGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAG                         GTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
genomic: ACATCTATTTCTTAGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAGgtaaatcatg ... ctcatctcagGTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
EST: gi|211244285|gb|FL461030.1|FL461030
EST:     ACATCTATTTCTTAGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAG                         GTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
genomic: ACATCTATTTCTTAGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAGgtaaatcatg ... ctcatctcagGTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
EST: gi|211468600|gb|FL255660.1|FL255660
EST:     AGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAG                         GTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
genomic: AGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAGgtaaatcatg ... ctcatctcagGTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
EST: gi|211064849|gb|FL464106.1|FL464106
EST:     ACATCTATTTCTTAGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAG                         GTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
genomic: ACATCTATTTCTTAGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAGgtaaatcatg ... ctcatctcagGTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
EST: gi|88754655|gb|DY538796.1|DY538796
EST:     ACATCTATTTCTTAGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAG                         GTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
genomic: ACATCTATTTCTTAGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAGgtaaatcatg ... ctcatctcagGTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
EST: gi|14244480|gb|BG842515.2|BG842515
EST:     ACATCTATTTCTTAGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAG                         GTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
genomic: ACATCTATTTCTTAGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAGgtaaatcatg ... ctcatctcagGTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
EST: gi|32789154|gb|CD941390.1|CD941390
EST:     TAAGTTTCAATCACCACTGTATCGTCAG                         GTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
genomic: TAAGTTTCAATCACCACTGTATCGTCAGgtaaatcatg ... ctcatctcagGTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
EST: gi|37373856|gb|CF623251.1|CF623251
EST:     ACATCTATTTCTTAGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAG                         GTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
genomic: ACATCTATTTCTTAGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAGgtaaatcatg ... ctcatctcagGTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
EST: gi|32804361|gb|CD956597.1|CD956597
EST:     TAAGTTACAATCACCACTGTATCGTCAG                         GTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
genomic: TAAGTTTCAATCACCACTGTATCGTCAGgtaaatcatg ... ctcatctcagGTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
EST: gi|213167710|gb|FM180716.1|FM180716
EST:     CACTGTATCGTCAG                         GTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
genomic: CACTGTATCGTCAGgtaaatcatg ... ctcatctcagGTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
EST: gi|74232387|gb|DT640301.1|DT640301
EST:     ACATCTATTTCTTAGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAG                         GTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT
genomic: ACATCTATTTCTTAGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAGgtaaatcatg ... ctcatctcagGTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTT

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: 47 (upstream exon), 48 (downstream exon)
Score: 20

TTTGGTAAACGTTTGGGAGTTTAAGCCTGGTCCTGTTCCAGGGACATGTGACATCTATTTCTTAGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAGgtaaatcatg ... ctcatctcagGTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTTAGTGACCGTTGTTTTAGAATATATGGCCCTGCTGTTCCAGTGCTGGAAA


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 15

TTTGGTAAACGTTTGGGAGTTTAAGCCTGGTCCTGTTCCAGGGACATGTGACATCTATTTCTTAGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAGgtaaatcatg ... ctcatctcagGTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTTAGTGACCGTTGTTTTAGAATATATGGCCCTGCTGTTCCAGTGCTGGAAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 22

TTTGGTAAACGTTTGGGAGTTTAAGCCTGGTCCTGTTCCAGGGACATGTGACATCTATTTCTTAGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAGgtaaatcatg ... ctcatctcagGTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTTAGTGACCGTTGTTTTAGAATATATGGCCCTGCTGTTCCAGTGCTGGAAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 18

TTTGGTAAACGTTTGGGAGTTTAAGCCTGGTCCTGTTCCAGGGACATGTGACATCTATTTCTTAGTCAATTTTAAGTTTCAATCACCACTGTATCGTCAGgtaaatcatg ... ctcatctcagGTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTTAGTGACCGTTGTTTTAGAATATATGGCCCTGCTGTTCCAGTGCTGGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaacttgtcatatgcccgttatgtctcttagagtacggatctttctcatctcagGTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTTAGTGACCGTTGTTTTAGAATATATGGCCCTGCTGTTCCAGTGCTGGAAA
 tattaac  putative branch site (score: 18)
                                        tctttctcatctc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatcatgcttttaatgatactgcacatatattaacttgtcatatgcccgttatgtctcttagagtacggatctttctcatctcagGTTGCATCAATGTTCTTCAAGGAAGTTGTTTCTCGACTAGTGAGCTCATTTAGTGACCGTTGTTTTAGAATATATGGCCCTGCTGTTCCAGTGCTGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA