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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaaattttggttgtgcttgtctgcttgttagaacctcccaaatcgacatattttttcttataactttccttttgaagagaattgaataatgtt...

Basic information

species Zea mays
transcript GRMZM2G128995_T05
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128995_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 6
TATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaaattttggttgtgcttgtctgcttgttag-aacctcccaaatcgacatattttttcttataactttc-cttttgaagagaattgaataatgtt----
|||| |||| || |||||||| |||||||| |||||| ||||||| |||||||| ||||| || ||||||||||||||||||    |||||||||| ||||||||  ||   | |  || |  |    || ||  ||  |  ||  ||  || ||     | ||  ||| | ||||    ||  ||  | |||  || | |     
TATGGTCACATCAGAACATCTAGTGACACTCCTTGCAGTTGTTCCTAAGTACTCTCAAAAGGATTGGTTGTCAAGCTATGAGTCCCTTGACACATTTGTGgtaagtatatgctctt-ttatagtgacatggttagtaatagactgtcatttcaac-----tatttatatgattttcgtcctttcagcaagttgcttattttacttt

upper sequence: GRMZM2G128995_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT1G12840.1 (Arabidopsis thaliana), 5'ss of exon 6
TATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATT-CGTGgtaaggttaaattttggttgtgcttgtctg-----cttgttagaac-ctcccaaatcgacatattttttcttataactttccttttgaagagaattgaataatgtt
|||  ||   || ||||||||||| || || |||||| ||||||| ||||| ||||||||||||||| |  || | |||||||   |||||  |||  |||||||  ||      | | |  | || |        |  ||   ||| || |    | ||| ||   |   ||  | |  |   |   ||     || |        
TATTGTCGAGTCCGAACATCTCGTAACTCTCCTTGCAGTTGTTCCGAAGTATTCCCAAAAAGACTGGCTAGCATGTTATGAGACT-TTGACCGATTATGTGgtaaatttgttgacttgctaggtttattgaatagaccagtggtaacactactggtttgacgtaccgtgattttaatcaatttatcctaacttgtttcag-------

upper sequence: GRMZM2G128995_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv14s0068g01280.t01 (Vitis vinifera), 5'ss of exon 6
TATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaaatttt---ggttgtgcttgtctgcttgttagaacctcccaaatcgacatattttttcttataactttccttttgaagagaattgaataatgtt-------------------------------------------------------------------------------------
 || ||  |||| |||||| | ||||||||||||||||||||||||||||| || || || |||||||||||||  ||||| | | |    |  |  ||||||||    | ||||   || | |   |     |||    |||         |  | ||||  | |    ||  ||      ||    |  |    | ||                                                                                        
CATTATTGCCTCAGAACATTTAGTGACACTTCTTGCAATTGTTCCCAAGTATTCTCAGAAGGACTGGTTGTCAACTTATGAAACATTGACTAGCTATGTGgtaagaactattttttctggctatatattctaacttaagcgaattatggtcctgaagatatcatctgcagtaggttggtaactggctcgtgtgatgtcataccttttaaatttctggagtatttgaatacattgtttgactttttgttcattgtaatcttcctgattaattgagctaacctctttcag

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|67018576|gb|CO447325.1|CO447325
EST:     ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|40334835|gb|CK368905.1|CK368905
EST:     CCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTCCTCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: CCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|71427970|gb|DR809020.1|DR809020
EST:     ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|211452191|gb|FL398498.1|FL398498
EST:     TCCCAAAAAGACTGGGTGTCTAGCTATGAGGAAATTGGACACATTTCGGG                         GTCCCTAGGTCATCTAAAAAGCTCT
genomic: TCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTG-ACACATT-CGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCT
EST: gi|149010225|gb|EE042044.2|EE042044
EST:     ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|31348626|gb|CD432983.1|CD432983
EST:     ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTCCTCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|149000734|gb|EE037952.2|EE037952
EST:     ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|148954149|gb|EC899548.2|EC899548
EST:     ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|67013699|gb|CO442448.1|CO442448
EST:     ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|22491457|gb|BU051380.1|BU051380
EST:     ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTC
genomic: ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTC
EST: gi|87153287|gb|DY398076.1|DY398076
EST:     ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTCCTCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|148968978|gb|EE019672.2|EE019672
EST:     ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|148963815|gb|EE014912.2|EE014912
EST:     ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|149098811|gb|EE184822.2|EE184822
EST:     ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|60358961|gb|DN225934.1|DN225934
EST:     ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|78076481|gb|DV504915.1|DV504915
EST:     AAGCTATGAGAAAATTGACACATTCGTG                         GTACNTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: AAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
EST: gi|71427969|gb|DR809019.1|DR809019
EST:     AATTGACACATTCGTG                         GTCCCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC
genomic: AATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTAC

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), 47 (downstream exon)
Score: 198

TATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTACACTGTAACACTGTTTGCTAAGGTTGTTGACAATTTTAAGGTCCGTGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 214

TATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTACACTGTAACACTGTTTGCTAAGGTTGTTGACAATTTTAAGGTCCGTGCTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 190

TATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTACACTGTAACACTGTTTGCTAAGGTTGTTGACAATTTTAAGGTCCGTGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

TATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaa ... aattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTACACTGTAACACTGTTTGCTAAGGTTGTTGACAATTTTAAGGTCCGTGCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAAAAAGACTGGTTGTCAAGCTATGAGAAAATTGACACATTCGTGgtaaggttaaattttggttgtgcttgtctgcttgttagaacctcccaaatcgacatattttttcttataactttccttttgaagagaattgaataatgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagagaa