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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtatttgcatagctgtggatactaggatacaaatttgagttcattccaatctgatgttcagtttgtccctactggtctcacttcttttccattctcagCATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAATAATGAATATGGTGAACAATGTGAAGAAGAACTTCTCCCTGGTGGGAGGG

Basic information

species Zea mays
transcript GRMZM2G101098_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101098_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g06690.3 (Oryza sativa), 3'ss of exon 20
ttgtatttgcatagc--tgtggatactaggatacaaatttgagttcattccaatctgatgtt-cagtttgtccctactggtctcacttcttttccattctcagCATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAATAATGAATATGGTGAACAATGTGAAGAAGAACTTCTCCCTGGTGGGAGGG
    |   |||| |     | |   ||   ||||  |  | | |||||   |   | || || || |||     |  |   ||| || ||||| ||| ||||||||||  |||||||||||||  | |||||  | || ||||||||||||||||| |||||||||||||||| |||||||||||| ||||| |||||||| |
---gaagcgcattgtatcttagcagctttaatacttacattacttcatcagatgttcattttgcacttttatgattttttactctctccttttacatcctcagCATTATGATGGTGATATCTCGCAATTGGAGTTATACTTTGTTATTGTGAATAACGAATATGGTGAACAATCTGAAGAAGAACTGCTCCCAGGTGGGAGAG

upper sequence: GRMZM2G101098_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G36390.1 (Glycine max), 3'ss of exon 19
-ttgtatttgcatagctgtggatactaggatacaaatttgagttcattccaatctgatgttcagtttgtccctactggtctcacttcttttccattctcagCATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAATAATGAATATGGTGAACAATGTGAAGAAGAACTTCTCCCTGGTGGGAGGG
   |    |   ||| |    |   |   |||      || | |  | |   | |  | || | |   |   |        || |   |||  | |  |||||||| || ||||| || || ||||||||||| || |||||||| || |||||||||||||| ||||||   || || ||||| || ||||| || ||| 
ggaggtgatatgtagtttgtaaagatgatatatttcagtgggattctgctgttttcttattgactcaatttttggcc-caccaatctgttttgactaacagCATTATAAGGGTGACATTTCGGAGTTGGAACTATACTTTGTTATAGTAAATAATGAATATGGAGAACAAACAGAGGAGGAACTGCTTCCTGGAGGAAGGA

upper sequence: GRMZM2G101098_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G04180.1 (Glycine max), 3'ss of exon 19
--------ttgta-tttgcatagctgtggatactaggatacaaatttgagttcattccaatctgatgttcagtttgtccctactggtctcacttcttttccattctcagCATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAATAATGAATATGGTGAACAATGTGAAGAAGAACTTCTCCCTGGTGGGAGGG
         |||| |||| | || ||   ||| |    |   |  |    |   |||  || |||   ||||||| | |||     |  || |   |||    |  |||||||| || ||||| || || ||||||||||| || |||||||| || |||||||||||||| ||||||   || || ||||| || || || || ||| 
ggggtgatgtgtagtttgtaaagatg-atatatttcagtgggacatctgctgttttcttat-tgac--tcagttttttcct-----taccaatatgttttggctaacagCATTATAAGGGTGACATTTCGGAGTTGGAACTATACTTTGTTATAGTAAATAATGAATATGGAGAACAAACAGAGGAGGAACTGCTTCCCGGAGGAAGGA

upper sequence: GRMZM2G101098_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G17205.1 (Arabidopsis thaliana), 3'ss of exon 19
ttgtatttgcatagctgtggatactaggatacaaatttgagttcattccaatctgatgttcagttt---gtccctactggtctcacttcttttccattctcagCATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAATAATGAATATGGTGAACAATGTGAAGAAGAACTTCTCCCTGGTGGGAGGG
 | | ||| | || ||  |   | |  |   |   |||   ||  ||    | || |  | || ||      |||  |  | |      | |   |||  |||| ||| || |||||||||||||| ||||| || || ||||||||| |||||||||||||||| ||       || ||||| || || || || ||    |
-tttgtttacctacctacgataattttggctc--ttttttttttttttttttttgcttcttagctttatacacctttttatgtattcattatgatatttgcagCGTTATAAGGGTGATATCTCAGACTTGGAGCTTTACTTTGTTATTTTGAATAATGAATATGGAGAGAGGACAGAGGAAGAGCTACTTCCAGGGGGCCAAG

upper sequence: GRMZM2G101098_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv05s0077g00470.t01 (Vitis vinifera), 3'ss of exon 20
ttgtatttgcatagctgtggatactaggatacaaatttgagttcattccaatctgatgttcagtttgtccctactggtctcacttcttttccat---tctcagCATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAATAATGAATATGGTGAACAATGTGAAGAAGAACTTCTCCCTGGTGGGAGGG
    |  || |   || |   ||| |    |||   |   |     ||   ||| || | |  ||| | |  |||  | |  | | |||    |      |||||||   | |||||  | ||||| |||||||| |||||||||||||| ||||||||||| || ||||||   || || || || || ||||| || |   
--caaaatggaactcttttattaccatttgacaccctattgcgtcctcagttcttat-tactatttttgcacactcattttgcctatttattgtgacctgcagCATTTTGAAGGTGACTTATCAGAATTGGAACTTTATTTTGTTATTGTAAATAATGAATACGGGGAACAAACAGAGGAGGAGCTGCTTCCTGGAGGAAAAA

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|20811283|gb|BQ295761.1|BQ295761
EST:     TGGATCCAGAATTGTATCGACATCTTCTATTTTTAAAG                         CATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAAT
genomic: TGGATCCAGAATTGTATCGACATCTTCTATTTTTAAAGgtttgtccct ... ccattctcagCATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAAT
EST: gi|6020745|gb|AW065553.1|AW065553
EST:     ATCTTCCTTCATTGGATCCAGAATTGTATCGACATCTTCTATTTTTAAAG                         CATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAAT
genomic: ATCTTCCTTCATTGGATCCAGAATTGTATCGACATCTTCTATTTTTAAAGgtttgtccct ... ccattctcagCATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAAT
EST: gi|26456975|gb|CA828558.1|CA828558
EST:     ATCTTCCTTCATTGGATCCAGAATTGTATCGACATCTTCTATTTTTAAAG                         CATTACAATGG-GATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAAT
genomic: ATCTTCCTTCATTGGATCCAGAATTGTATCGACATCTTCTATTTTTAAAGgtttgtccct ... ccattctcagCATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAAT
EST: gi|37419105|gb|CF647228.1|CF647228
EST:     ATCTTCCTTCATTGGATCCAGAATTGTATCGACATCTTCTATTTTTAAAG                         CATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAAT
genomic: ATCTTCCTTCATTGGATCCAGAATTGTATCGACATCTTCTATTTTTAAAGgtttgtccct ... ccattctcagCATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAAT

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: 61

ATACAATTTTTTAAATGATCTTCCTTCATTGGATCCAGAATTGTATCGACATCTTCTATTTTTAAAGgtttgtccct ... ccattctcagCATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAATAATGAATATGGTGAACAATGTGAAGAAGAACTTCTCCCTGGTGGGAGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 50

ATACAATTTTTTAAATGATCTTCCTTCATTGGATCCAGAATTGTATCGACATCTTCTATTTTTAAAGgtttgtccct ... ccattctcagCATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAATAATGAATATGGTGAACAATGTGAAGAAGAACTTCTCCCTGGTGGGAGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 84

ATACAATTTTTTAAATGATCTTCCTTCATTGGATCCAGAATTGTATCGACATCTTCTATTTTTAAAGgtttgtccct ... ccattctcagCATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAATAATGAATATGGTGAACAATGTGAAGAAGAACTTCTCCCTGGTGGGAGGG


Block sizes: 45 (upstream exon), 42 (downstream exon)
Score: 29

ATACAATTTTTTAAATGATCTTCCTTCATTGGATCCAGAATTGTATCGACATCTTCTATTTTTAAAGgtttgtccct ... ccattctcagCATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAATAATGAATATGGTGAACAATGTGAAGAAGAACTTCTCCCTGGTGGGAGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccaatctgatgttcagtttgtccctactggtctcacttcttttccattctcagCATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAATAATGAATATGGTGAACAATGTGAAGAAGAACTTCTCCCTGGTGGGAGGG
                               gtctcac  putative branch site (score: 29)
                                tctcacttcttttcca  CT-rich tract
                                      ttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtatttgcatagctgtggatactaggatacaaatttgagttcattccaatctgatgttcagtttgtccctactggtctcacttcttttccattctcagCATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAATAATGAATATGGTGAACAATGTGAAGAAGAACTTCTCCCTGGTGGGAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - -tttgcat
- - - - - - agctgtg
- - - - - - - - - - - - - - atacaaa
- - - - - - - - - - - - - - - - - - - - - -cattcca
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctactg