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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtatgctatgtttactttcgtcaatgcctctgggctctggcatctggttttggcagtagtctgtgtctgtcaactcacttcagttttctgacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGTCTGCACTTTTCTTACACAGTAACTACGTCTCTGTTGGTGCCTCTGGGGC

Basic information

species Zea mays
transcript GRMZM2G157384_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157384_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g43320.1 (Oryza sativa), 3'ss of exon 2
agtatgctatgtttactttcgtcaatgcctctgggctctggcatctggttttggcagtagtc-tgtgtctgtcaactcacttcagttttctgacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGTCTGCACTTTTCTTACACAGTAACTACGTCTCTGTTGGTGCCTCTGGGGC
 | |  |     || | |  |||||||  |      |      | ||  ||||    | ||  |||  |||   ||| ||  |||||| || |||| | |||||| |||||  ||||||||||| ||||||||||||| || || ||| ||||||  || || ||||  | ||||||| |||| |||||||||||||| ||
-ggacccataactttcatatgtcaatgtgtacccatttctcattttgagtttgaatctggtaatgttcctgcacactgacaacagtttccttacttactagTGCGTATTGGAATCATCTACTTGCTATCTGGCTTTGGCGGTAGCGTGCTGTCTGTGCTGTTTTTACGTAATAACTACATCTCCGTTGGTGCCTCTGGAGC
















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|60342822|gb|DN209795.1|DN209795
EST:     AGCAACAATTTGGGTTTG                         TGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
genomic: AGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
EST: gi|86468307|gb|DY234677.1|DY234677
EST:     GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTG                         TGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
genomic: GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
EST: gi|148933642|gb|EC877531.2|EC877531
EST:     GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTG                         TGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
genomic: GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
EST: gi|74241938|gb|DT649852.1|DT649852
EST:     GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTG                         TGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
genomic: GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
EST: gi|149080701|gb|EE169761.2|EE169761
EST:     GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTG                         TGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
genomic: GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
EST: gi|76289252|gb|DV028820.1|DV028820
EST:     GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTG                         TGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
genomic: GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
EST: gi|71446277|gb|DR827327.1|DR827327
EST:     GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTG                         TGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
genomic: GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
EST: gi|148941580|gb|EC886517.2|EC886517
EST:     CGCCTGGAGCAACAATTTGGGTTTG                         GGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
genomic: CGCCTTGAGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
EST: gi|87156908|gb|DY401697.1|DY401697
EST:     CGCCTTGAGCAACAATTTGGGTTTG                         TGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
genomic: CGCCTTGAGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
EST: gi|86468306|gb|DY234676.1|DY234676
EST:     GCAACAATTTGGGTTTG                         TGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
genomic: GCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
EST: gi|78088539|gb|DV516932.1|DV516932
EST:     GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTG                         TGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
genomic: GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
EST: gi|149055187|gb|EE156106.2|EE156106
EST:     GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTG                         TGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
genomic: GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
EST: gi|148941581|gb|EC886518.2|EC886518
EST:     GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTG                         TGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
genomic: GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
EST: gi|71448535|gb|DR829585.1|DR829585
EST:     GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTG                         TGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
genomic: GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
EST: gi|74236232|gb|DT644146.1|DT644146
EST:     GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTG                         TGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
genomic: GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
EST: gi|211213835|gb|FL012224.1|FL012224
EST:     GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTG                         TGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTT
genomic: GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTT
EST: gi|71447543|gb|DR828593.1|DR828593
EST:     GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTG                         TGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT
genomic: GCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGT

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), 47 (downstream exon)
Score: 154

ATTAGCTGTATCTGGCTCCATGCTGGCCTAGTTCACTTGGTTGTCAACATGCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGTCTGCACTTTTCTTACACAGTAACTACGTCTCTGTTGGTGCCTCTGGGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

ATTAGCTGTATCTGGCTCCATGCTGGCCTAGTTCACTTGGTTGTCAACATGCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGTCTGCACTTTTCTTACACAGTAACTACGTCTCTGTTGGTGCCTCTGGGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 117

ATTAGCTGTATCTGGCTCCATGCTGGCCTAGTTCACTTGGTTGTCAACATGCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGTCTGCACTTTTCTTACACAGTAACTACGTCTCTGTTGGTGCCTCTGGGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

ATTAGCTGTATCTGGCTCCATGCTGGCCTAGTTCACTTGGTTGTCAACATGCTAAGCTTGCTCTTCATTGGAATCCGCCTTGAGCAACAATTTGGGTTTGgtaagcttct ... gacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGTCTGCACTTTTCTTACACAGTAACTACGTCTCTGTTGGTGCCTCTGGGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttttggcagtagtctgtgtctgtcaactcacttcagttttctgacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGTCTGCACTTTTCTTACACAGTAACTACGTCTCTGTTGGTGCCTCTGGGGC
                                         ttctgac  putative branch site (score: 164)
                                       ttttctg  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtatgctatgtttactttcgtcaatgcctctgggctctggcatctggttttggcagtagtctgtgtctgtcaactcacttcagttttctgacttgcaagTGCGCATTGGTGTCATCTACTTGATATCTGGCTTTGGGGGCAGTGTGTTGTCTGCACTTTTCTTACACAGTAACTACGTCTCTGTTGGTGCCTCTGGGGC

-gtatgct
- - - - - - - - - - - - - gcctctg
- - - - - - - - - - - - - - - - - - - - gcatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gcagtag