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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgacataattcacgattaatgtttgcacatatgttatttttctttgtaagtggggaacttcaagggaatctttaattggttggtagttttatagtttgtaatgttacttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG

Basic information

species Zea mays
transcript GRMZM2G410515_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 3'ss of exon 3
gtctgacataattcacgattaatgtttgcacatatgttatttttctttgtaagtggggaacttcaagggaatctttaattggttggtagttttatagtttgtaatgtta----cttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG
|| ||| |||||||  |  |    ||  || ||   | ||||   | | ||  |    |||||  |  | |     |    | |  |||  || |||||| ||   ||      |||| ||||||| |||||| ||||||| || || ||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||
gtatgatataattctaggat----ttgacagatgaataatttacatatatatct----aactttgatagcagtcacatcgtggtcttagcattgtagtttttagctttgatttttttttcagGATTAGCTGGTTTATCAACGGCAAAATATCTGGCAGATGCTGGTCATAAACCCATATTGCTTGAGGCAAGGGATGTTTTGGGTGGAAAG

upper sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G00720.1 (Glycine max), 3'ss of exon 2
gtctgacataat-tcacgattaatgtttgcacatatgttatttttctttgtaagtggggaacttcaagggaatctttaattggttggtagttttatagtttgtaatgttacttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG
      | | || ||| | |  || |||  | | |   || |   ||||| |  |  |    ||    ||  ||| |   |  | | | | |  || ||||  |||     | | ||||||||||||||| ||||||| || || ||| |||| |||||||| |||||||| |||||||| || |||||||| ||| | |||||||||
----accctgatatcatgttggatatttaaagacaaactaat---ctttgcacattag---tttt---ggcctctctgtctattggattgatgcat-gtttcaaat-----tatcgcagGATTGGCTGGTTTATCAACTGCAAAATATTTGGCTGATGCTGGGCATAAACCTATATTGCTGGAAGCAAGAGACGTTCTAGGTGGAAAG

upper sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G36810.1 (Glycine max), 3'ss of exon 2
gtctgacataattcacgattaatgtttgcacatatgttatttttctttgtaagtggggaacttcaagggaatctttaattggttggtagttttatagtttgtaatgttacttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG
             || | |  || |||  | | |    |      |||||||         | ||    | | ||    |   ||    ||  || | |     | | | | ||||||||||||||||| ||||||| || || ||| |||| |||||||| |||||||| |||||||| || |||||||| ||| | |||||||||
-------------catgttggatatttaaagacaaaaaa-----atttgtaaactaatctttgcacattagttttggcctctctgcctattggattgatgcatgtttcattattgcagGATTGGCTGGTTTATCAACTGCAAAATATTTGGCTGATGCTGGGCATAAACCTATATTGCTGGAAGCAAGAGACGTTCTAGGTGGAAAG

upper sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 3
gtctgacataattcacgattaatgtttgcacatatgttatttttctttgtaagtggggaacttcaagggaatctttaattggttggt--agttttatagtttgtaatgttacttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG
                     |||| | ||  |   ||  ||     | |   ||||    |   | |||||   |  |    || |  |||| | | |  | | |  | |   ||||||||||||||||  | ||||| || ||||| ||||| ||||| || || |||||  | |||||||| |||||||||||| | |||||||||
-------------------gtatgtctacaacttcatttcttactgctttgtttggga---tctgatggaattaatgttcatgtgatgaagttcttttggctctcaaataa---ttgcagGATTGGCTGGATTGTCAACTGCAAAGTACCTGGCTGATGCAGGCCACAAACCTCTGTTGCTTGAAGCAAGAGATGTTCTTGGTGGAAAG

upper sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 3
gtctgacataattcacgattaatgtttgcacatatgttatttttctttgta-agtggg--gaacttcaagggaatctttaattg-gttggtagttttatagtttgtaatgttacttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG
                    |||| ||    | |||  | ||   |||| | |||||   |  |||  |     |||||  ||| |     |  ||   | ||| |||    ||  ||||||| ||||||||| | || || || || ||| |||||||||| || || || || |||||| | || |||||||||||||| |||||||||
-----------------taaaatgattatgta-atgcaaattgcttttgaagagtggtttgccctttgataccttctttggttgtgacatcaaattgccaatttttaa----acacttgcagGTTTGGCTGGTTTGTCTACTGCAAAATATTTGGCAGATGCAGGTCACAAGCCTATATTGTTGGAAGCAAGAGATGTTTTAGGTGGAAAG

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|211005246|gb|FL018196.1|FL018196
EST:     AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAG                         GATTGGCTGGTCTATCAACAGC
genomic: AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGC
EST: gi|211002473|gb|FL018192.1|FL018192
EST:     AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAG                         GAATGGCTGGTCTATCAACAGCGAAGTAT
genomic: AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGCGAAGTAT
EST: gi|211417844|gb|FL018174.1|FL018174
EST:     AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAG                         GATTGGCTGGTCTATCAACAGCGAAGTATCTTGCAGATGCTGGACATAAAC
genomic: AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC
EST: gi|211417848|gb|FL018178.1|FL018178
EST:     AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAG                         GATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC
genomic: AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC
EST: gi|211417840|gb|FL018170.1|FL018170
EST:     AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAG                         GATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC
genomic: AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC
EST: gi|211417841|gb|FL018171.1|FL018171
EST:     AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAG                         GATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC
genomic: AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC
EST: gi|74236167|gb|DT644081.1|DT644081
EST:     AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAG                         GATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC
genomic: AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC
EST: gi|211002466|gb|FL018185.1|FL018185
EST:     AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAG                         GATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC
genomic: AAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAAC

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: 43 (upstream exon), 43 (downstream exon)
Score: 27

GAAAGCACAATAAACTATTTGGAAGCTGGACAGCTCTCTTCATTTTTTAGAAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 139

GAAAGCACAATAAACTATTTGGAAGCTGGACAGCTCTCTTCATTTTTTAGAAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 80

GAAAGCACAATAAACTATTTGGAAGCTGGACAGCTCTCTTCATTTTTTAGAAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 93

GAAAGCACAATAAACTATTTGGAAGCTGGACAGCTCTCTTCATTTTTTAGAAACAGCGAACGCCCCAGTAAGCCGTTGCAGGTCGTGGTTGCTGGTGCAGgtctgacata ... acttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagggaatctttaattggttggtagttttatagtttgtaatgttacttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG
         ctttaat  putative branch site (score: 93)
                                           ttactttt  putative PPT
                          ttttatagtttgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgacataattcacgattaatgtttgcacatatgttatttttctttgtaagtggggaacttcaagggaatctttaattggttggtagttttatagtttgtaatgttacttttgcagGATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA