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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcattcctgatcttttaagatagtttgcatgcttttagtcattatctctcttttatttgtgctttcattttgttgatttacttatatgagtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACCGGTGACATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT

Basic information

species Zea mays
transcript GRMZM2G125556_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G125556_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g40890.2 (Oryza sativa), 3'ss of exon 5
ttcattcctgatcttttaagatagtttgcatgcttttagtcat-tatctctcttttatttgtgctt--tcattttgttgatttacttatatgagtgatcg-cagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACCGGTGACATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT
        ||   || |  || |  ||   |  |||  ||||| | |   || ||||||||   ||  ||  |||||     | || |||||||  || | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| || || ||||| |||||||| ||||||||||| |
---ggctttgcctttctgtgagaagttctttaattt-ggtcatgtttgcttcctttatttgcttttcctccgtttgtatgagtgctcatatgagaaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACGGGTGACATAAAAGCTGATATCGAGAAATTCTGCACGACCTTTT
















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|76285485|gb|DV025053.1|DV025053
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|93282355|gb|EB674619.1|EB674619
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTTTAGTTTTACG                         GTGGCAATGAAGCTTGCTCTTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211041272|gb|FL124819.1|FL124819
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCCTA-TAGAGAGAAATTTATGGA
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCC-TAATAGAGAGAAATTTATGGA
EST: gi|211464236|gb|FL298400.1|FL298400
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATT
EST: gi|211377924|gb|FL095474.1|FL095474
EST:     CCAAGACTTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211041270|gb|FL124817.1|FL124817
EST:     CCAAGACTTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211041278|gb|FL124825.1|FL124825
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         -TGGGCA-TGAAGCTTGCTCCTAATAG-GAGAAATTTATGGAG
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGG-CAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAG
EST: gi|71771167|gb|DR969104.1|DR969104
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211249240|gb|FL481701.1|FL481701
EST:     CCAAGACTTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211041276|gb|FL124823.1|FL124823
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|60400894|gb|DN233701.1|DN233701
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211475759|gb|FL124816.1|FL124816
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211484414|gb|FL480094.1|FL480094
EST:     CCAAGACTTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211475757|gb|FL124814.1|FL124814
EST:     CCAAGACTTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|93282356|gb|EB674620.1|EB674620
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211466760|gb|FL298405.1|FL298405
EST:     CAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT

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: 68

GCTTGAGCATCCAGACTGGACCATGGGTCAATCTTGCACTGATTCATACACCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACCGGTGACATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

GCTTGAGCATCCAGACTGGACCATGGGTCAATCTTGCACTGATTCATACACCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACCGGTGACATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 221

GCTTGAGCATCCAGACTGGACCATGGGTCAATCTTGCACTGATTCATACACCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACCGGTGACATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 84

GCTTGAGCATCCAGACTGGACCATGGGTCAATCTTGCACTGATTCATACACCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACCGGTGACATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctcttttatttgtgctttcattttgttgatttacttatatgagtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACCGGTGACATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT
                          tgttgat  putative branch site (score: 84)
                      attttgttgatttact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcattcctgatcttttaagatagtttgcatgcttttagtcattatctctcttttatttgtgctttcattttgttgatttacttatatgagtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACCGGTGACATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- cattcct
- - - - - - - - - - - - - tgcatgc