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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacttgctgtgagatttactctggcattggtttgccaagttatttgggggtattggctgtgtttctgttttgaattaaactaatttcaagctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTTCTCAGAGTATACAGCCCAGCAGCTGATAGCAAAATCCGATCAGTGGGCG

Basic information

species Zea mays
transcript GRMZM2G006277_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006277_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g67730.1 (Oryza sativa), 3'ss of exon 1
--aacttgctgtg-agatttactctggcattggtttgccaagttatttgggggtattggctgtgtttctgttttgaattaaacta-atttcaagctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTTCTCAGAGTATACAGCCCAGCAGCTGATAGCAAAATCCGATCAGTGGGCG
  | |||||||   || | | |      |||| |     | |     ||      |||     | |  || |    ||| | ||| ||||   | || ||  |||| ||  | |||||| |||||||||||||||| || |||||||| |||||||| |||||| | || ||||||||||| ||||||||   ||||||    |
tgatcttgctgaacaggtgttcctccatattgctgcatgatgcctcatg----ccttgatcagggtattggtgactattgagctatatttactgttcttcacagGTGGAGGTTGAATTCACTGATGGTAGCTCATTCCATCTGTCAGCTGAATTTCTAAGAGTACATAGTCCAGCAGCTGACAGCAAAATAATATCAGTATCTG

upper sequence: GRMZM2G006277_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g10430.1 (Oryza sativa), 3'ss of exon 1
aacttgctgtgagatttactctggcattggtttgccaagttatt-tgggggtattggctgtgtttctgttttgaattaaacta---atttcaagctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTTCTCAGAGTATACAGCCCAGCAGCTGATAGCAAAATCCGATCAGTGGGCG
|     |  | |   ||  ||| | |||| |      |||  |  |  |||||| || | ||| | | ||||||  | | |||     | |  | |  |   |||| ||| | ||||| |  ||||| |||||||| || ||| | || || ||||| ||||| ||||||||||||||||||||||||||| ||||||| |  |
attaaaccatta---ttcttctcgaattgttcatatgagtgttgattagggtatgggtt-tgtgtgtcttttgacatgagctatgtgctactggtttttgtcagGTAGAAGTTGAATTTGAGGATGGCAGCTCATTCCATCTGCCTGCTGAGTTTCTTAGAGTGTACAGCCCAGCAGCTGATAGCAAAATCAGATCAGTAGCTG
















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|211392362|gb|FL377415.1|FL377415
EST:     CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
EST: gi|18172861|gb|BM348249.1|BM348249
EST:     CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
EST: gi|211443955|gb|FL410275.1|FL410275
EST:     CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
EST: gi|211108340|gb|FL388580.1|FL388580
EST:     CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
EST: gi|18167915|gb|BM337755.1|BM337755
EST:     CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
EST: gi|211301554|gb|FL430309.1|FL430309
EST:     CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
EST: gi|211321452|gb|FL399586.1|FL399586
EST:     CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
EST: gi|18176507|gb|BM351440.1|BM351440
EST:     CACCCGCCCAAATTC                         GTTGAAATCGAATTCCCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
EST: gi|67021891|gb|CO450640.1|CO450640
EST:     CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
EST: gi|211057895|gb|FL423513.1|FL423513
EST:     CGGCGCA--NCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
EST: gi|211220783|gb|FL456545.1|FL456545
EST:     CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTC                         GTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT
genomic: CGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 18

GTCTATGGCGGCTGCACTGGGCGCCGTGCTCCGGCGGCTGCATACGGCGGCGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTTCTCAGAGTATACAGCCCAGCAGCTGATAGCAAAATCCGATCAGTGGGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 44

GTCTATGGCGGCTGCACTGGGCGCCGTGCTCCGGCGGCTGCATACGGCGGCGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTTCTCAGAGTATACAGCCCAGCAGCTGATAGCAAAATCCGATCAGTGGGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 23

GTCTATGGCGGCTGCACTGGGCGCCGTGCTCCGGCGGCTGCATACGGCGGCGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTTCTCAGAGTATACAGCCCAGCAGCTGATAGCAAAATCCGATCAGTGGGCG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 13

GTCTATGGCGGCTGCACTGGGCGCCGTGCTCCGGCGGCTGCATACGGCGGCGGCGCAGCCCCCTCGCCTGACGAAATTCGCGCTGCACCCGCCCAAATTCgtgagtctcc ... ctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTTCTCAGAGTATACAGCCCAGCAGCTGATAGCAAAATCCGATCAGTGGGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggggtattggctgtgtttctgttttgaattaaactaatttcaagctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTTCTCAGAGTATACAGCCCAGCAGCTGATAGCAAAATCCGATCAGTGGGCG
                                aactaat  putative branch site (score: 13)
                                             ctcatcct  putative PPT
                      ttttgaattaaactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacttgctgtgagatttactctggcattggtttgccaagttatttgggggtattggctgtgtttctgttttgaattaaactaatttcaagctcatcctagGTTGAAATCGAATTCGCTGATGGTAGCTCATTTCACCTGTCAGCAGAATTTCTCAGAGTATACAGCCCAGCAGCTGATAGCAAAATCCGATCAGTGGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- cttgctg
- - - - - - - - - - - - - - - - tgccaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - ggctgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaactaa