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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatagagcacatttgtcttttagaatccttagattcctgcttaaacttgatggattgtaagacatcaaacaccttacaagatttcttatgtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGCCTGTATGTCTTTGGGTTCTGCTGGGTGTTCATTATTAAGATCAGAAATG

Basic information

species Zea mays
transcript GRMZM2G433942_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G433942_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g70100.1 (Oryza sativa), 3'ss of exon 3
atatagagcacatttgtcttttagaatccttagattcctgcttaaacttgatggattgtaagacatcaaacaccttacaagatttcttatgtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGCCTGTATGTCTTTGGGTTCTGCTGGGTGTTCATTATTAAGATCAGAAATG
|| |              || | |  | || ||  ||||| ||  |||  |    ||| ||  | ||||    |||| ||  || | ||||  |||||||||||||||||||||||| ||||||||||| |||||||||||| |||||||||| || |||||||||||||||||||| | |||| |||||||||||||  
atctctgcagttccaaaattctcgctttctaagtctcctgtttttactatagattttgaaatgcttcaacatgcttataaatttgcatatgactgtgcagAGGAATTACAGGTTCTTTTATATGTTTGTCTTCTCAACAACTCTGCTCTGCCTCTACGTCTTTGGGTTCTGCTGGGTATACATTGTTAAGATCAGAAACT

upper sequence: GRMZM2G433942_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv17s0000g00800.t01 (Vitis vinifera), 3'ss of exon 3
atatagagcacatttgtcttttagaatccttagattcctgcttaaacttgatggat---tgtaagacatcaaacaccttacaagatttcttatgtttg-tgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGCCTGTATGTCTTTGGGTTCTGCTGGGTGTTCATTATTAAGATCAGAAATG
    | |  ||   |   |||   |   |||      || | | || || ||  ||   |||    ||||   |||  |  |  ||   | ||  ||| ||||| | ||||||||||||||||  |||||||| ||||| |||||| | || ||| ||||||| ||||| || |||||||| | ||| || | |||||   |||
----aaattactggtaaatttagaagggcttgctagactacctcaagtttatccatatatgtttctcatctctcacaatgaattatcattaattcttggtgcagCGAAATTACAGGTTCTTCTTCATGTTTGTCTTCTCCACAACTCTTCTGTGCGTGTATGTATTTGGATTTTGCTGGGTCTACATCATGAGGATCATGGATG
















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|71330995|gb|DR802320.1|DR802320
EST:     TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTT                         AGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAAACA-CTTTGCTCTG
genomic: TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTTgtaagtttat ... gtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAA-CAACTTTGCTCTG
EST: gi|26558272|gb|CA830507.1|CA830507
EST:     TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTT                         AGGAATTACAGGTTCTTCTATAT
genomic: TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTTgtaagtttat ... gtttgtgcagAGGAATTACAGGTTCTTCTATAT
EST: gi|149046484|gb|EE048006.2|EE048006
EST:     TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTT                         ANGAATTACAGGTTCTTCTATATGTTTGTATT
genomic: TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTTgtaagtttat ... gtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATT
EST: gi|91868690|gb|EB400117.1|EB400117
EST:     TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTT                         AGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGC
genomic: TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTTgtaagtttat ... gtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGC
EST: gi|148953730|gb|EC899096.2|EC899096
EST:     TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTT                         AGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGC
genomic: TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTTgtaagtttat ... gtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGC
EST: gi|50332834|gb|CO527960.1|CO527960
EST:     TGGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTT                         ANGAATTACAGGTTCTTCTATATGTTTGTATTCTCGACAACTTTGCTCTGC
genomic: TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTTgtaagtttat ... gtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGC
EST: gi|148990678|gb|EE032074.2|EE032074
EST:     TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTT                         AGGAATTACAGGTTCCTCTATA
genomic: TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTTgtaagtttat ... gtttgtgcagAGGAATTACAGGTTCTTCTATA
EST: gi|4753375|gb|AI657280.1|AI657280
EST:     TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTT                         AGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGC
genomic: TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTTgtaagtttat ... gtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGC
EST: gi|76921843|gb|DV168729.1|DV168729
EST:     TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTT                         AGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGC
genomic: TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTTgtaagtttat ... gtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGC
EST: gi|148944134|gb|EC889222.2|EC889222
EST:     TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTT                         AGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGC
genomic: TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTTgtaagtttat ... gtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGC
EST: gi|149106439|gb|EE188329.2|EE188329
EST:     TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTT                         AGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGC
genomic: TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTTgtaagtttat ... gtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGC
EST: gi|148973614|gb|EE024722.2|EE024722
EST:     TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTT                         AGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGC
genomic: TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTTgtaagtttat ... gtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGC
EST: gi|21987320|gb|BQ778848.1|BQ778848
EST:     TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTT                         AGGAATTACAGGTTCTTCTATATGTTTGTATTCTC
genomic: TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTTgtaagtttat ... gtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTC
EST: gi|76017769|gb|DT944939.1|DT944939
EST:     TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTT                         AGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGC
genomic: TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTTgtaagtttat ... gtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGC
EST: gi|148943919|gb|EC888999.2|EC888999
EST:     TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTT                         AGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGC
genomic: TAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTTgtaagtttat ... gtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGC

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: 284

GTTGTACAGGCCTCCTCGTTGCTCCCATTGCTCTATCTGCAACAACTGCGTAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTTgtaagtttat ... gtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGCCTGTATGTCTTTGGGTTCTGCTGGGTGTTCATTATTAAGATCAGAAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 37

GTTGTACAGGCCTCCTCGTTGCTCCCATTGCTCTATCTGCAACAACTGCGTAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTTgtaagtttat ... gtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGCCTGTATGTCTTTGGGTTCTGCTGGGTGTTCATTATTAAGATCAGAAATG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 41

GTTGTACAGGCCTCCTCGTTGCTCCCATTGCTCTATCTGCAACAACTGCGTAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTTgtaagtttat ... gtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGCCTGTATGTCTTTGGGTTCTGCTGGGTGTTCATTATTAAGATCAGAAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 217

GTTGTACAGGCCTCCTCGTTGCTCCCATTGCTCTATCTGCAACAACTGCGTAGAACGTTTTGACCATCACTGCCCCTGGGTTGGACAATGCATAGGACTTgtaagtttat ... gtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGCCTGTATGTCTTTGGGTTCTGCTGGGTGTTCATTATTAAGATCAGAAATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgatggattgtaagacatcaaacaccttacaagatttcttatgtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGCCTGTATGTCTTTGGGTTCTGCTGGGTGTTCATTATTAAGATCAGAAATG
                          accttac  putative branch site (score: 217)
                                    atttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatagagcacatttgtcttttagaatccttagattcctgcttaaacttgatggattgtaagacatcaaacaccttacaagatttcttatgtttgtgcagAGGAATTACAGGTTCTTCTATATGTTTGTATTCTCAACAACTTTGCTCTGCCTGTATGTCTTTGGGTTCTGCTGGGTGTTCATTATTAAGATCAGAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - -gcacatt
- - - - - - - - - - - - - - - - - - cctgctt
- - - - - - - - - - - - - - - - - - - - - - - cttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcaaa