Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatcgtggttcctttttctcaagttcttatttaaccttgtattgcttgttattaattgcatttttgaattttcatatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG

Basic information

species Zea mays
transcript GRMZM2G361847_T07
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G361847_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g48820.2 (Oryza sativa), 3'ss of exon 4
gtaatatcgtggttcctttttctcaagt-tcttatttaaccttgtattgcttgttattaattgcatttttgaatttt-catatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG
|| | ||  | ||||| |||  |   || |   || | || |  | |||  ||| ||||||| ||| ||  | |||  |||    |||||||| || |||||||| ||||||||||||||||||||||||||||||||||||||||||
gtgacattttagttccgtttcttttcgtatacaatgtcacttaatcttg--tgtgattaatttcatattgtattttggcatgcaatagACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG

upper sequence: GRMZM2G361847_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G31050.3 (Glycine max), 3'ss of exon 6
gtaatatcgtggttcctttttctcaagttcttatttaaccttgtattgcttgttattaattgcatttttgaattttcatatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG
||  ||| |  ||   | | |   ||   | ||   | |||| | || ||   |  ||     |||||| | |||||||   | ||||| |  |||||||||| |||||||||||||| || || ||||| || ||||||||||||
gttgtat-gcagtaattgtgtgcaaatagcata---agccttttgttactgtgtgcta-----atttttcatttttcat---tcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG

upper sequence: GRMZM2G361847_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
gtaatatcgtggttcctttttctcaagttc--ttat----ttaacctt----gtattgcttgttattaattgc---atttttgaattttca--tatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG
  || |   || || || | | | || ||   ||||    ||||  |      | ||   || ||||  || |   ||| |||| |||| |  |||   ||||  | ||| ||||||| || ||||||||||||||||||||||||||| |||| || || 
aaaacaa-atgtttactctattttaaatttggttatgcggttaatatctaaaattttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA

upper sequence: GRMZM2G361847_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G28400.1 (Glycine max), 3'ss of exon 1
---------------gtaatatcgtggttcctttttctcaagttcttatttaaccttgtattgcttgttattaattg--catttttgaattttcatatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG
               || | ||   |      | |||  | |   | |   | |||| | || ||    |||||||   | ||||| | |||||||   | ||||| |  |||||||||| |||||||||||||| || || ||||| || |||||||||| |
ttgaccaatcaaaaggttaaatgcagtaattgtgttcaaatggcataagcaagccttttgttactatgcattaatttttctttttttatttttcat---tcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAATG

upper sequence: GRMZM2G361847_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G28320.2 (Glycine max), 3'ss of exon 6
gtaatatcgtggttcctttttctcaagttcttatttaaccttgtattgcttgttattaattg--catttttgaattttcatatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG
||  ||| |  ||   | | |   ||   | ||   | |||| | || ||    |||||||   | ||||| | |||||||   | ||||| |  |||||||||| |||||||||||||| || || ||||| || ||||||||||||
gttgtat-gcagtaattgtgttcaaatggcata---agccttttgttactatgcattaatttttctttttttatttttcat---tcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG

upper sequence: GRMZM2G361847_T04 (Zea mays), 3'ss of exon 3
lower sequence: AT3G12250.5 (Arabidopsis thaliana), 3'ss of exon 4
gtaatatcgtggttcctttttctcaa---gttcttattta-accttgtat-tgcttgttattaattgcatttttgaattttcatatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG
|| |||   |  |  || |   ||||   |    | | || |    | || ||| |  | |   |||  |  ||    |||     | |||||  | ||  ||||||| ||||||||||||||||||||||||||  |  ||||||| |||
gtgatagattcatctctgtggatcaactagcatctgtgtatattacgcatatgcataatctgttttgtttccttttcgttttgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAG

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|211145672|gb|FL260531.1|FL260531
EST:     CTAATTCTTCAGATAGGTCCGACAGGTCTGATAAACCTTTGGACCAAAAG                         ACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTG
genomic: CTAATTCTTCAGATAGGTCCGACAGGTCTGATAAACCTTTGGACCAAAAGgtaatatcgt ... catatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTG
EST: gi|211145673|gb|FL260532.1|FL260532
EST:     CTAATTCTTCAGATAGGTCCGACA-GTCTGATAAACCTTTGGACCAAAAG                         ACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTG
genomic: CTAATTCTTCAGATAGGTCCGACAGGTCTGATAAACCTTTGGACCAAAAGgtaatatcgt ... catatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTG
EST: gi|91057217|gb|EB167635.1|EB167635
EST:     CTAATTCTTCAGATAGGTCCGACAGGTCTGATAAACCTTTGGACCAAAAG                         ACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTG
genomic: CTAATTCTTCAGATAGGTCCGACAGGTCTGATAAACCTTTGGACCAAAAGgtaatatcgt ... catatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTG

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), 48 (downstream exon)
Score: 87

ATGGAGAATGGAAGTGGTGCGGTTGTACCTTCTAATTCTTCAGATAGGTCCGACAGGTCTGATAAACCTTTGGACCAAAAGgtaatatcgt ... catatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 186

ATGGAGAATGGAAGTGGTGCGGTTGTACCTTCTAATTCTTCAGATAGGTCCGACAGGTCTGATAAACCTTTGGACCAAAAGgtaatatcgt ... catatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 301

ATGGAGAATGGAAGTGGTGCGGTTGTACCTTCTAATTCTTCAGATAGGTCCGACAGGTCTGATAAACCTTTGGACCAAAAGgtaatatcgt ... catatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

ATGGAGAATGGAAGTGGTGCGGTTGTACCTTCTAATTCTTCAGATAGGTCCGACAGGTCTGATAAACCTTTGGACCAAAAGgtaatatcgt ... catatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttaaccttgtattgcttgttattaattgcatttttgaattttcatatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG
                      tattaat  putative branch site (score: 119)
                                         ttttcat  putative PPT
                     ttattaattgcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatcgtggttcctttttctcaagttcttatttaaccttgtattgcttgttattaattgcatttttgaattttcatatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA