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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTAGATGTGATTCTTTTGCTACAGAATATGATCTTGAAGCTGAAGAGTATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAGgtatcattctgattcaatcttaaccttaacatttcaatattttctgcagtgatttttttcacatggtacctttgttagtgaatgttatcaacttatcatg...

Basic information

species Zea mays
transcript GRMZM2G032267_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 5'ss of exon 5
TGGTAGATGTGATTCTTTTGCTACAGAATATGATCTTGAAGCTGAAGAGTATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAGgtatcattctgattca--atcttaacc-ttaacatttcaatattttctgcagtga--tttttttcacatggtacc-tttgttagtgaatgttatcaacttatcatg
|||||||||||||||||||||||||||||| |||||||||||||| ||||||||||| || |||||||| || |||||||||||||||||||||||||||||| | ||| || |||||| || | ||||| |||| | | || || ||| || | | ||| | |||||| | |
TGGTAGATGTGATTCTTTTGCTACAGAATACGATCTTGAAGCTGAGGAGTATGTTCCGATTCCCAAAGGAGAGGTCCATAAGAAAAAGGAAATAGTGCAGgtaatttgatgaatctttgtcttaaggatttttgcccatacattttgcacagtcaactcttctttgcattgtgctatccattaattaatgttgttgataa------

upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 5'ss of exon 5
TGGTAGATGTGATTCTTTTGCTACAGAATATGATCTTGAAGCTGAAGAGTATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAGgtatcattctgattcaatcttaaccttaacatttcaatattttctgcagtgatttttttcacatggtacc-tttgttagtgaatgttatcaacttatcatg-------
||||||||||||| |||||||||||||||| |||||||||||||| ||||||||||| ||||||||||| || ||||||||||| |||||||||||||||||| ||| | | ||| ||| ||| || || || | ||||| ||| |||| | | | | | ||||| | | | |
TGGTAGATGTGATGCTTTTGCTACAGAATACGATCTTGAAGCTGAGGAGTATGTTCCAATCCCCAAAGGGGAGGTCCATAAGAAGAAGGAAATAGTGCAGgta--atttgg--tgaattttagcctaaaagattt----ttgcacaggcaagtcttttttgcattgtactatctatgaatttatgttggtgataattaaagaaatgaa

upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G21830.1 (Glycine max), 5'ss of exon 5
TGGTAGATGTGATTCTTTTGCTACAGAATATGATCTTGAAGCTGAAGAGTATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAGgtatc--attctgattcaatcttaaccttaacattt---caatattttctgcagtgatttttttcacatggtacctttgttagtgaatgttatcaacttatcatg
||| || ||||| |||| |||||||| | ||| ||||||||||||||||||||||| | || || || || || || || |||||||| || || ||||||| ||| ||| | | || | ||| ||||| | | | ||| || | | || ||||| | || | ||
GGGTCGAAGTGATGCTTTCGCTACAGAGTTTGACCTTGAAGCTGAAGAGTATGTTCCACTGCCTAAGGGAGAGGTTCACAAAAAAAAGGAGATTGTTCAGgtatttaatttgaatttgaagaccaattttatgtttatgcaatacccctaagatttgctaatttagtataattatcatatt--tgaatcct-ctaattgatgg--

upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 5
TGGTAGATGTGATTCTTTTGCTACAGAATATGATCTTGAAGCTGAAGAGTATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAGgt--atcattctgattcaatcttaaccttaacatttcaatattttctgcagtgatttttttcacatggtacctttgttagtgaatgttatcaactta--tcatg-----------------------------------------------------
|||||| ||||| ||||||| || |||| |||||| ||||| ||||| |||||||| | |||||||| || ||||| || || || || ||||||||||| | | | | | || | | | | |||||||| |||||| || | | || ||| || ||| | | |||| || |
AGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAGAAGAATATGTTCCACTTCCCAAAGGAGAGGTCCACAAAAAGAAAGAGATAGTGCAGgtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatag

upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 5'ss of exon 5
TGGTAGATGTGATTCTTTTGCTACAGAATATGATCTTGAAGCTGAAGAGTATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAGgtatcattctgattcaatctta-accttaacatttcaatattttctgcagtgatttttttcacatggtacctttgttagtgaatgttatcaacttatcatg
|| ||| ||||| ||||||||||||||| ||| ||||| || |||||||||||||| | || ||||| || || || || || ||||| ||||| ||||| | || |||| | ||| | ||| | || | || | | | || ||| | ||| | | || || ||| | |
GGGCAGAAGTGATGCTTTTGCTACAGAATTTGACCTTGAGGCGGAAGAGTATGTTCCACTTCCTAAAGGAGAGGTTCACAAAAAGAAGGAGATAGTTCAGgtttgtttttgataaattctgggatcttcatgaacca-tgcttggaacttgattctattgttcatttctcagttgcaatggtatcttgggtgctttgcctt

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|60342617|gb|DN209590.1|DN209590
EST:     ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAG                         GATGTCACACTCCATGACCTTGATGCAGCAAATGCCCAGCCACAAGGTGGC
genomic: ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAGgtatcattct ... ttttttgcagGATGTCACACTCCATGACCTTGATGCAGCAAATGCCCAGCCACAAGGTGGC
EST: gi|32933015|gb|CF037827.1|CF037827
EST:     ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAG                         GATGTCACACTCCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGC
genomic: ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAGgtatcattct ... ttttttgcagGATGTCACACTCCATGACCTTGATGCAGCAAATGCCCAGCCACAAGGTGGC
EST: gi|32933753|gb|CF038565.1|CF038565
EST:     ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAG                         GATGTCACACTCCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGC
genomic: ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAGgtatcattct ... ttttttgcagGATGTCACACTCCATGACCTTGATGCAGCAAATGCCCAGCCACAAGGTGGC
EST: gi|74241474|gb|DT649388.1|DT649388
EST:     ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAG                         GATGTCACACTCCATGACCTTGATGCAGCAAATGCCCAGCCACAAGGTGGC
genomic: ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAGgtatcattct ... ttttttgcagGATGTCACACTCCATGACCTTGATGCAGCAAATGCCCAGCCACAAGGTGGC
EST: gi|60356915|gb|DN223888.1|DN223888
EST:     ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAG                         GATGTCACACTCCATGACCTTGATGCAGCAAATGCCCAGCCACAAGGTGGC
genomic: ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAGgtatcattct ... ttttttgcagGATGTCACACTCCATGACCTTGATGCAGCAAATGCCCAGCCACAAGGTGGC
EST: gi|78103432|gb|DV521860.1|DV521860
EST:     ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAG                         GATGTCACACTCCATGACCTTGATGCAGCAAATGCCCAGCCACAAGGTGGC
genomic: ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAGgtatcattct ... ttttttgcagGATGTCACACTCCATGACCTTGATGCAGCAAATGCCCAGCCACAAGGTGGC

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), 49 (downstream exon)
Score: 225

TGGTAGATGTGATTCTTTTGCTACAGAATATGATCTTGAAGCTGAAGAGTATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAGgtatcattct ... ttttttgcagGATGTCACACTCCATGACCTTGATGCAGCAAATGCCCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 58

TGGTAGATGTGATTCTTTTGCTACAGAATATGATCTTGAAGCTGAAGAGTATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAGgtatcattct ... ttttttgcagGATGTCACACTCCATGACCTTGATGCAGCAAATGCCCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 77

TGGTAGATGTGATTCTTTTGCTACAGAATATGATCTTGAAGCTGAAGAGTATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAGgtatcattct ... ttttttgcagGATGTCACACTCCATGACCTTGATGCAGCAAATGCCCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 60

TGGTAGATGTGATTCTTTTGCTACAGAATATGATCTTGAAGCTGAAGAGTATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAGgtatcattct ... ttttttgcagGATGTCACACTCCATGACCTTGATGCAGCAAATGCCCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTAGATGTGATTCTTTTGCTACAGAATATGATCTTGAAGCTGAAGAGTATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAGGAAATAGTGCAGgtatcattctgattcaatcttaaccttaacatttcaatattttctgcagtgatttttttcacatggtacctttgttagtgaatgttatcaacttatcatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA