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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaccatgtcacgaaacataactagatcaattaaattaaaaaaagtgcattactgatctgcacactgatgatgagcaccaaattcttgttctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCAAGGCTTCTGTCGTCCACCAACCAGCCAAGTTTCCTGAGTCAGAAGGATA

Basic information

species Zea mays
transcript GRMZM2G004932_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 11
--------------------------------------------------------gaaccatgtcacgaaacataactagatcaattaaattaaaaaaagtgca-ttactg-atctgcacactgatgatgagcaccaa----------attcttgttctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCAAGGCTTCTGTCGTCCACCAACCAGCCAAGTTTCCTGAGTCAGAAGGATA
                                                             |   |  |  |    | |   |   | |   |  || |  ||   |||||| ||   || ||| |  || ||  ||||          | ||||    |||||||||||||||||||||||| |||||||||| ||  ||||||| ||||||||||| ||||| || || || |||||||||||||| ||||| || |||||||| |
gtgagtaacttcaagtgatcttatttgttcacatggaaaatgcagaaatgtagtgctcgttacacccgggcatcccatttttttcctgattatccaagagctgttcttactgcattctcatactaagcatcagttccaacttaacgtgaaatcttcccttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCGAGGCTGCTATCATCAACCAACCAGCCAAGCTTCCTAAGCCAGAAGGACA

upper sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT4G26270.1 (Arabidopsis thaliana), 3'ss of exon 12
gaaccatgtcacgaaacataactagatcaattaaattaaaaaaagtgcattactgatctgcacactgatgatgagcaccaaattcttgttctgatg--gcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCAAGGCTTCTGTCGTCCACCAACCAGCCAAGTTTCCTGAGTCAGAAGGATA
  | |||      |    | |  |   |  ||||| | |  |   |    |  | ||   || | | || |     |   ||   |  || | |||   |||||| | ||    | |  |||| | ||     |||| |||||||||||||||||||| || || || || |||||||| |||||| || | |  || ||| 
-catcatactgtcatcagttatcatcaccgttaaagtcatcatcctcatatcatcataatcatagt-atcacttttatgtaaacatcatttttatgttacagAGGATAACGGAGAAACAGAACCATGTGGTGATCACAGACAGGATGTGGGCAAGGCTACTCTCTTCGACAAACCAGCCGAGTTTCTTGGGCCCCAAAGATG

upper sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 12
gaaccatgtcacgaaacataactagatcaattaaattaaaaaaagtgcattactgatctg-cacactgatgatgag--caccaaattcttgt-tctgatggcagAGGGTGACATCCACAAG-----GAACAAGGTTAAAGTCACTGACAGGATGTGGGCAAGGCTTCTGTCGTCCACCAACCAGCCAAGTTTCCTGAGTCAGAAGGATA
          |  |  |||       ||  || ||| ||  |   |||  |   | | || ||||     | ||||   || ||| | |||| | |||  |  | |     |||| |  ||     ||||||||||    | || |||||||||||||||||||| || ||||| || ||||||||||| |||| ||  |  || ||| 
---------aagaattcatggtgtcctctcttgaatgaatgattttgctcttaggttttgacacagaacagttgaggttacaaaacttttgtatttgactgatgtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCAAGGCTCCTTTCGTCAACAAACCAGCCAAGCTTCCAGAACCCCAAAGATG

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|148940012|gb|EC884748.2|EC884748
EST:     CAACGGAAGACATACCTATATACCTTTCTAC                         AGGGGGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
genomic: CAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
EST: gi|6031341|gb|AW076198.1|AW076198
EST:     GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTAC                         AGGGTGACATCCACAAGGAACAAGGTTAAAGTCACGGACAGGATGTGGGCA
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
EST: gi|32936624|gb|CF041443.1|CF041443
EST:     GTTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTAC                         AGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
EST: gi|5791257|gb|AI978049.1|AI978049
EST:     GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTAC                         AGGGTGACATCCACAAGGAACAAGGTTAAAGTCACGGACAGGATGTGGGCA
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
EST: gi|211480673|gb|FK996001.1|FK996001
EST:     GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTAC                         AGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
EST: gi|71433706|gb|DR814756.1|DR814756
EST:     GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTAC                         AGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
EST: gi|71761875|gb|DR959812.1|DR959812
EST:     GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTAC                         AGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
EST: gi|60348735|gb|DN215708.1|DN215708
EST:     GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTAC                         AGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
EST: gi|94479652|gb|EB708610.1|EB708610
EST:     GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTAC                         AGGGGGACCTCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGT
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGT
EST: gi|5670940|gb|AI932203.1|AI932203
EST:     GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTAC                         AGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
EST: gi|94479651|gb|EB708609.1|EB708609
EST:     GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTTTAC                         AGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
EST: gi|4887518|gb|AI677617.1|AI677617
EST:     GTTTCACTGTTGGGATGGTCAACGGAAGACATACCTATAT-CCTTTTTAC                         AGGGTGACATCCNCAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
EST: gi|87157419|gb|DY402208.1|DY402208
EST:     GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTAC                         AGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
EST: gi|67037463|gb|CO464279.1|CO464279
EST:     GTTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTAC                         AGGGTGACATCCACAAGGAACAAGGTTAAAGTCACGGACAGGATGTGGGCA
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
EST: gi|148949704|gb|EC895179.2|EC895179
EST:     GCTTCATTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTAC                         AGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
EST: gi|60344598|gb|DN211571.1|DN211571
EST:     GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTAC                         AGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
EST: gi|26560069|gb|CA832304.1|CA832304
EST:     GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTAC                         AGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
EST: gi|89246745|gb|DY618532.1|DY618532
EST:     GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTTTAC                         AGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
EST: gi|33092222|gb|CF052216.1|CF052216
EST:     GTTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTAC                         AGGGTGACACCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
EST: gi|23199633|gb|BU582198.1|BU582198
EST:     GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTAC                         AGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
EST: gi|78026916|gb|DV495303.1|DV495303
EST:     GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTAC                         AGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA
genomic: GCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCA

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: 107

CTGTACACTTCTAGCCCACAGTGCTATCCATGGTGCAATGGCGGGGTACAGCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCAAGGCTTCTGTCGTCCACCAACCAGCCAAGTTTCCTGAGTCAGAAGGATA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 161

CTGTACACTTCTAGCCCACAGTGCTATCCATGGTGCAATGGCGGGGTACAGCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCAAGGCTTCTGTCGTCCACCAACCAGCCAAGTTTCCTGAGTCAGAAGGATA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 145

CTGTACACTTCTAGCCCACAGTGCTATCCATGGTGCAATGGCGGGGTACAGCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCAAGGCTTCTGTCGTCCACCAACCAGCCAAGTTTCCTGAGTCAGAAGGATA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 75

CTGTACACTTCTAGCCCACAGTGCTATCCATGGTGCAATGGCGGGGTACAGCTTCACTGTTGGGATGGTCAACGGAAGACATACCTATATACCTTTCTACgtgagtaata ... ctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCAAGGCTTCTGTCGTCCACCAACCAGCCAAGTTTCCTGAGTCAGAAGGATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcattactgatctgcacactgatgatgagcaccaaattcttgttctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCAAGGCTTCTGTCGTCCACCAACCAGCCAAGTTTCCTGAGTCAGAAGGATA
                                     ttcttgttct  CT-rich tract
                                  aaattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaccatgtcacgaaacataactagatcaattaaattaaaaaaagtgcattactgatctgcacactgatgatgagcaccaaattcttgttctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCAAGGCTTCTGTCGTCCACCAACCAGCCAAGTTTCCTGAGTCAGAAGGATA

- -ccatgtc
- - - - - - -aaacata
- - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - gtgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccaaa