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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcatgtatattatgttggttcagagttcaggggactcaattgaactcttgtgcatatgcaatgcgaaaacatgtataaataacaatttctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCACCTTCATTCGAGGATATTTCTCAAGCCATAGATTTCATCCATC

Basic information

species Zea mays
transcript GRMZM2G051288_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051288_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g53710.1 (Oryza sativa), 3'ss of exon 2
ttgcatgtatattatgttggttcagag---ttcaggggactcaattgaactcttgtgcatatgcaatgcgaaaacatgt--ataaataacaatttct--cttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCACCTTCATTCGAGGATATTTCTCAAGCCATAGATTTCATCCATC
| ||| || ||||| | || ||| ||| ||| || |||||| | | | | | | |||||| | || || ||||| ||| |||||| ||||| | ||||| |||||||| ||||| |||||||| | || ||||||||| ||||||||||||||| ||||| |
------attcatttgattcattcaggggattttcaatcactttattttgtgtttgca-atcaacaatgcaagatcctcctgacgagtaacaagtcctacttttgcagGCCCATGGGATTGACCACCTTATTATTCCCACAAGAGACTACCTGTTTGCACCAGCCCTCCAGGATATTTGTCAAGCCATAGATTTTATCCACC

upper sequence: GRMZM2G051288_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv11s0016g02890.t01 (Vitis vinifera), 3'ss of exon 3
ttgcatgtatattatgttggttcagagttcaggggactcaattgaactcttgtgcatatgcaatgcgaaaacatgtataaataacaatttctc--ttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCACCTTCATTCGAGGATATTTCTCAAGCCATAGATTTCATCCATC
| | | |||||| || || || | | |||||| | | | || || | | | | ||| || |||||| ||||||| || |||||||||||||| |||||||||||||| ||||| |||||||| | ||||||| | || |||||||||| |||
-tcctttgctattattccctttaagtatttaaaattttggcttgaacattcttttttgtg-gatttatgacctctcccattccattgtttgatggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA
















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|50332926|gb|CO528052.1|CO528052
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
EST: gi|149104022|gb|EE289453.2|EE289453
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
EST: gi|148932664|gb|EC876596.2|EC876596
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
EST: gi|93014040|gb|EB639560.1|EB639560
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCCACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
EST: gi|67018199|gb|CO446948.1|CO446948
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCTACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
EST: gi|76928986|gb|DV171845.1|DV171845
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
EST: gi|149009261|gb|EE041354.2|EE041354
EST:     AACCGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTC
genomic: AAC-GTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTC
EST: gi|50327588|gb|CO522714.1|CO522714
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
EST: gi|71444037|gb|DR825087.1|DR825087
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
EST: gi|149080697|gb|EE169757.2|EE169757
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGAATACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
EST: gi|148985353|gb|EE029663.2|EE029663
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
EST: gi|71310365|gb|DR791488.1|DR791488
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACA-GAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
EST: gi|101385912|gb|EB815004.1|EB815004
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
EST: gi|50338986|gb|CO534112.1|CO534112
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
EST: gi|71766290|gb|DR964227.1|DR964227
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
EST: gi|91055876|gb|EB166294.1|EB166294
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
EST: gi|78119952|gb|DV538336.1|DV538336
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
EST: gi|148952076|gb|EC897867.2|EC897867
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAGCAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
EST: gi|88756074|gb|DY540215.1|DY540215
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACA-GAGATTACCTCTTTG
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTG
EST: gi|89250671|gb|DY622457.1|DY622457
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
EST: gi|50328153|gb|CO523279.1|CO523279
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
EST: gi|71331076|gb|DR802368.1|DR802368
EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

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), 49 (downstream exon)
Score: 73

TTTCCCAAGTGATGTTCCACGGTTGAAGCAGCTTGGAGTTCAAGGGGTTGTAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCACCTTCATTCGAGGATATTTCTCAAGCCATAGATTTCATCCATC


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 85

TTTCCCAAGTGATGTTCCACGGTTGAAGCAGCTTGGAGTTCAAGGGGTTGTAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCACCTTCATTCGAGGATATTTCTCAAGCCATAGATTTCATCCATC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 99

TTTCCCAAGTGATGTTCCACGGTTGAAGCAGCTTGGAGTTCAAGGGGTTGTAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCACCTTCATTCGAGGATATTTCTCAAGCCATAGATTTCATCCATC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 78

TTTCCCAAGTGATGTTCCACGGTTGAAGCAGCTTGGAGTTCAAGGGGTTGTAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCACCTTCATTCGAGGATATTTCTCAAGCCATAGATTTCATCCATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcttgtgcatatgcaatgcgaaaacatgtataaataacaatttctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCACCTTCATTCGAGGATATTTCTCAAGCCATAGATTTCATCCATC
                                 aaataac  putative branch site (score: 78)
 tttctcttacc  putative PPT
 aaaacatgtataaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcatgtatattatgttggttcagagttcaggggactcaattgaactcttgtgcatatgcaatgcgaaaacatgtataaataacaatttctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCACCTTCATTCGAGGATATTTCTCAAGCCATAGATTTCATCCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
-tgcatgt
- -catgtat
- - - - - - - tgttggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaca