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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatacgttgtctatcatttttcccataatggatatgatgtatctgcaaaagttgaaacaaaattgtatgcattttgtagAAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTGAGAGCTGAATAAACCTTGGAGGACATCATAAGTCATTTTGGCTATGTTC

Basic information

species Zea mays
transcript GRMZM2G088653_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088653_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g25370.1 (Oryza sativa), 3'ss of exon 8
-------------------------------gtaatacgttgtctatcatttttcccataatgga---tatgatgtatctgcaaa----agttgaaa-----caaaattgtatgcattttgtagAAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTGAGAGCTGAATAAACCTTGGAGGACATCATAAGTCATTTTGGCTATGTTC
                                | ||| | | |   |          | ||||||   |||||| | | |   ||    | || |         ||||||  ||  |||  ||||| || ||||||||||| || | |||||| || ||||||||  ||| ||||||||||||||||||  || |||||||   | | || || |  | |   |
gtaccaaattggatcttgcgcttcctgccaatttatatgctctacttggaagaagttaaaatggaatttatgatttttttttcaagtgaaattaactggttttgaaattggttgtctttcatagAAACATATGCATTACTTTCGGAAGAGGACTGCCAAGGAAATTTTGAATTTGAGAGCTGAATAAACTGTGAAGGACATATAAGGCCACTTAGAATGTTCAC
















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|37388193|gb|CF631303.1|CF631303
EST:     TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAG                         AAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTG
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAGgtaatacgtt ... cattttgtagAAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTG
EST: gi|12971305|gb|BG267416.1|BG267416
EST:     TCAAATCCATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAG                         AAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTG
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAGgtaatacgtt ... cattttgtagAAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTG
EST: gi|71305240|gb|DR788757.1|DR788757
EST:     TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAG                         AAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTG
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAGgtaatacgtt ... cattttgtagAAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTG
EST: gi|78084564|gb|DV512957.1|DV512957
EST:     TCAAATACATTGACTTTTACAGCAGAGATATGGACCTCATTTTCGGACAG                         AAGCAAATGCATTACTTCCGCAGGAGGACAGGGAAGGAAATACTGAGTTTG
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAGgtaatacgtt ... cattttgtagAAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTG
EST: gi|78118658|gb|DV537042.1|DV537042
EST:     TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAG                         AAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTG
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAGgtaatacgtt ... cattttgtagAAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTG
EST: gi|86471498|gb|DY237868.1|DY237868
EST:     AATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAG                         AAGCAAATGCATTATTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTG
genomic: AATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAGgtaatacgtt ... cattttgtagAAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTG
EST: gi|5439429|gb|AI820350.1|AI820350
EST:     TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAG                         AAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTG
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAGgtaatacgtt ... cattttgtagAAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTG
EST: gi|78025320|gb|DV493707.1|DV493707
EST:     TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAG                         AAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTG
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAGgtaatacgtt ... cattttgtagAAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTG
EST: gi|5455863|gb|AI833553.1|AI833553
EST:     TTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAG                         AAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTG
genomic: TTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAGgtaatacgtt ... cattttgtagAAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTG
EST: gi|22542666|gb|BU093104.1|BU093104
EST:     TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAG                         AAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTG
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAGgtaatacgtt ... cattttgtagAAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTG

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), 49 (downstream exon)
Score: 69

ATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAGgtaatacgtt ... cattttgtagAAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTGAGAGCTGAATAAACCTTGGAGGACATCATAAGTCATTTTGGCTATGTTC


Block sizes: 49 (upstream exon), 35 (downstream exon)
Score: 16

ATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAGgtaatacgtt ... cattttgtagAAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTGAGAGCTGAATAAACCTTGGAGGACATCATAAGTCATTTTGGCTATGTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 46

ATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAGgtaatacgtt ... cattttgtagAAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTGAGAGCTGAATAAACCTTGGAGGACATCATAAGTCATTTTGGCTATGTTC


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 25

ATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAGgtaatacgtt ... cattttgtagAAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTGAGAGCTGAATAAACCTTGGAGGACATCATAAGTCATTTTGGCTATGTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatggatatgatgtatctgcaaaagttgaaacaaaattgtatgcattttgtagAAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTGAGAGCTGAATAAACCTTGGAGGACATCATAAGTCATTTTGGCTATGTTC
                              aaacaaaattgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatacgttgtctatcatttttcccataatggatatgatgtatctgcaaaagttgaaacaaaattgtatgcattttgtagAAGCAAATGCATTACTTCCGCAGGAGGACAGCGAAGGAAATACTGAGTTTGAGAGCTGAATAAACCTTGGAGGACATCATAAGTCATTTTGGCTATGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA