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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcaaaatatcttgtggtgttgtttatatatatcgttgcttcatgcttccctttggattaaaatactacactggttatttatcggtttatggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACT

Basic information

species Zea mays
transcript GRMZM2G118731_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118731_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g43930.1 (Oryza sativa), 3'ss of exon 3
gtaatcaaaatatcttgtggtgttgtttatatatatcgttgcttcatgcttccctttggattaaaatactacactggttatttatcggtttatggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACT------
||||| ||| |||   |     |  ||||  |  ||| ||  | | | ||    ||| || | ||||| | |||    ||||||  | ||| ||||| | ||  |||||      ||||| ||||||||||||||| ||||||||||| ||||||||||||||||| ||||| || ||||| ||||| || ||||| |||||      
gtaataaaattat---gaaaaatgctttactttgatcctttatcctt-ctatattttagaatgaaata-tgcacc---tatttactgttttgtggttgaaagTAGGTAG------AGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGGTTTCTTTAGAAGACCTGTATAATGGTACTACCAAAAAACTGTCTTT

upper sequence: GRMZM2G118731_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g43930.3 (Oryza sativa), 3'ss of exon 3
gtaatcaaaatatcttgtggtgttgtttatatatatcgttgcttcatgcttccctttggattaaaatactacactggttatttatcggtttatggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACT---------
||||| ||| |||   |     |  ||||  |  ||| ||  | | | ||    ||| || | ||||| | |||    ||||||  | ||| ||||| | ||  |||||      ||||| ||||||||||||||| ||||||||||| ||||||||||||||||| ||||| || ||||| ||||| || ||||| |||||         
gtaataaaattat---gaaaaatgctttactttgatcctttatcctt-ctatattttagaatgaaata-tgcacc---tatttactgttttgtggttgaaagtagGTAG------AGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGGTTTCTTTAGAAGACCTGTATAATGGTACTACCAAAAAACTGTCTTTGTC

upper sequence: GRMZM2G118731_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G14540.2 (Glycine max), 3'ss of exon 3
gtaatcaaaatatcttgtggtgtt-gtttatatatatcgttgcttcatgcttccctttggattaaaatactacactggttatttatcggtt--tatggt----taatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACT
          |     | | ||||   || || || | |||  |||||  |    | || ||     | ||  | || | |  |  |  ||  ||| ||    ||   |||||||| ||  ||||  | ||||| |||| ||||||||||||||||||| || | ||||||||||| || ||  | || || || ||||| |||||   
---------gtggtgagagatgttcacttttacat-ttgttatttcattttcatttatgaatcttcttgct-tattgatcaactcactattactattgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGCATTCTTTAAAGGTTTCCTTGGAGGACGTCTATAACGGCACAACAAAGAA---

upper sequence: GRMZM2G118731_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G27030.1 (Glycine max), 3'ss of exon 3
gtaatcaaaatatcttgtggtgttgtttatatatatcgttgcttcatgcttccctttggat--taaaatactacactggttatttat-cggtttatggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACT
            |    || |    |||| || ||| ||| ||||||       | || ||  |  |||| |   |   | | |  |    |      |||   |||||||| ||  ||||  | ||||| |||| ||||||||||||||||||| || | ||||||||||| || ||  | || ||||| ||||| |||||   
-----------gtgagatgttcacttttacatttat-gttacttcatttaaatttgtgaatcttgcaatattgatcaactcactattattatcgcctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGCATTCTTTAAAGGTTTCCTTGGAGGACGTTTATAATGGCACAACAAAGAA---

upper sequence: GRMZM2G118731_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G14540.1 (Glycine max), 3'ss of exon 3
gtaatcaaaatatcttgtggtgttgtttatatatatcgttgcttcatgcttccctttggattaaaatactacactggttatttatcggtttatggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACT
|| |   | || |    |  |    ||  ||| |    ||  || |||  ||   |||  |   | |  |  |||   ||||   |  ||     |||   |||||||| ||  ||||  | ||||| |||| ||||||||||||||||||| || | ||||||||||| || ||  | || || || ||||| |||||   
gtga--gagatgttcacttttacatttgttatttcattttcatttatgaatcttcttgctt---attgatcaactcactatt--actattgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGCATTCTTTAAAGGTTTCCTTGGAGGACGTCTATAACGGCACAACAAAGAA---

upper sequence: GRMZM2G118731_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv15s0021g02090.t01 (Vitis vinifera), 3'ss of exon 3
------------gtaatcaaaat-----atcttgtggtgttgttt-atatatatcgttgcttcatgcttccctttggattaaaatactacactggttatttatcggttt----atggttaata--------gGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACT
             || | ||| |     |||||    | || ||| | || | |  ||  ||| ||  | |||||  |   ||||  |  | |   ||||||  | ||      |   ||||         |||||||||||||||||| | || || || || ||||||||||| ||||||||| |||||||||| || || ||  |||| ||||| ||| | |||||   
gtaagaggatgcttacttaaatttcttgatctttatttattttttcaaatgtgtacttatttcctgtctacctttaaa--gaaattttcaattatatatttactgattcccaagtatctaattttgtagGTGGTGGTAGCTCAAGAGGAAGAAGGCAGAAACGAGGTGAAGATGTTGTGCATACTTTGAAGGTTTCTTTGGAGGACTTGTATAATGGCACATCAAAGAA---

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|76909048|gb|DV163196.1|DV163196
EST:     CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGG                         GTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
genomic: CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
EST: gi|76293182|gb|DV032750.1|DV032750
EST:     CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGG                         GTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
genomic: CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
EST: gi|211439726|gb|FL188864.1|FL188864
EST:     CCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTTGGGG                         GTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCAT
genomic: CCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTT-GGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCAT
EST: gi|18964087|gb|BM660802.1|BM660802
EST:     CCCTTTTGACATTTTTGAGCACCTTTTTCCGGGTTCTAGCACCTTTGGGG                         GTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
genomic: CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
EST: gi|33094456|gb|CF054450.1|CF054450
EST:     CCCTTTTGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGG                         GTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
genomic: CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
EST: gi|18963673|gb|BM660567.1|BM660567
EST:     GGTTCTAGCACCTTTGGGG                         GTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
genomic: GGTTCTAGCACCTTTGGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
EST: gi|148964320|gb|EC905716.2|EC905716
EST:     CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGG                         GTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
genomic: CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
EST: gi|31348685|gb|CD433042.1|CD433042
EST:     CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGG                         GTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
genomic: CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
EST: gi|32932432|gb|CF037244.1|CF037244
EST:     CCCTTTTGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGG                         GTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
genomic: CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
EST: gi|91877653|gb|EB407610.1|EB407610
EST:     CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGG                         GTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
genomic: CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
EST: gi|148931484|gb|EC874496.2|EC874496
EST:     CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGG                         GTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
genomic: CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
EST: gi|149037356|gb|EE155375.2|EE155375
EST:     CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGG                         GTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
genomic: CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
EST: gi|148955629|gb|EC901294.2|EC901294
EST:     CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGG                         GTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
genomic: CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATA
EST: gi|18963675|gb|BM660568.1|BM660568
EST:     CCCTTTTGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGG                         GTGGTAGCTCAAG
genomic: CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAG
EST: gi|18964089|gb|BM660803.1|BM660803
EST:     CCCTTTTGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTCTGGGG                         GTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGAT
genomic: CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGAT
EST: gi|13150523|gb|BG320845.1|BG320845
EST:     BBCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGG                         GTGGTAGCTCAAGVAGGACGCAGACAAAAGCGTGGTGAAGATGTKGTGCAT
genomic: CCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAG-AGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 212

GATGCCCTTAAGGAAGGAATGGGAGGAGGCAGCAGCAGTGATTTCCATAGCCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 195

GATGCCCTTAAGGAAGGAATGGGAGGAGGCAGCAGCAGTGATTTCCATAGCCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 180

GATGCCCTTAAGGAAGGAATGGGAGGAGGCAGCAGCAGTGATTTCCATAGCCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 288

GATGCCCTTAAGGAAGGAATGGGAGGAGGCAGCAGCAGTGATTTCCATAGCCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGGgtaatcaaaa ... tggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttccctttggattaaaatactacactggttatttatcggtttatggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACT
       tttggattaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcaaaatatcttgtggtgttgtttatatatatcgttgcttcatgcttccctttggattaaaatactacactggttatttatcggtttatggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA