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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctggaaccttttatctaatttcatttacttttttgagttgaacggttttaaatgtaatctttggttacag

Basic information

species Zea mays
transcript GRMZM2G063851_T05
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063851_T05 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 16
TGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctggaacctt-ttatctaatttcatttactttt-ttgagttgaacggttttaaatgtaatc-tttggttacag
||| ||||||||||||||||| ||||||||||| ||||||||| ||||||| |||||||||||  ||||| | |||||  ||||||||||||||||| ||||  ||||  |  ||   |   |   |   || | |     ||  |  |  || |||| ||  |    |    || |||
TGGCTTTGGTCATGGAGTTCTACGTAAGACCGATCCACGGTATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaaattctagctgcatggctctcttcagtcccactgtctcaataggatttatatcgacctatcctctttcag

upper sequence: GRMZM2G063851_T05 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 16
TGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctggaaccttttatctaatttcatttacttttttgagttgaacggttttaaatgtaatctt-tggttacag----------
||| || |||||||||||||| ||||||||||| ||||| ||| ||||||| |||||||||||  ||||| | |||||  ||||||||||||||||| ||||  ||||  ||  | |  || || | |||     | ||  |||  |||  | | |   | | |||| | | |  |           
TGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaaaatgtct-gtccaactgcatggctctcttgcagtccaactatctcattgggattcttatcgatctatatcctgtcag

upper sequence: GRMZM2G063851_T05 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA08G16770.1 (Glycine max), 5'ss of exon 16
TGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctggaaccttttatctaatttcatttacttttttgagt--tgaacggttttaaatgtaatctttggttacag---------------------------------------
||| | ||| ||||| ||| | ||  |||| || ||| | ||  ||||||| |||||||||||  ||||||||||||| || ||||||  |||||| |||||        |     | ||  ||  |  | |  | ||| ||||  |     |    | |   ||   |   ||  |                                        
TGGATATGGACATGGGGTTTTACGCCAGACAGATCCAAGATACACATGTCAGAGGGAGTTTGCTTTGAAGCATTTGCCTAATGATCCATATTTCCAGTTGgtaatcacttatttcctaattcaagattgtgttttctttggagtgctttcttgcgacacagccaaagctcacttgtaatttaatttcttcatgttctaatgcaactgaccctttcag

upper sequence: GRMZM2G063851_T05 (Zea mays), 5'ss of exon 2
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 16
TGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgt-ctggaaccttttatctaat-------ttcatttacttttttgagttgaacggttttaaatgtaatctttggttacag------
||||||||| ||||||||| ||||||| || || ||| | |||   |||||||||||||||||  ||||||| |||||  | |||||||| |||||  ||||   | ||  || |  | ||  ||        ||  |||| |||| ||          |  |  |  | | ||| | ||||        
TGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTGgttattacttaaagccctgattaaagacaatggtttgtttatttttgtgttccagttcatccttgagctga-cttggtttaccattacag

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|40335071|gb|CK369141.1|CK369141
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTG                         GTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
EST: gi|89248619|gb|DY620405.1|DY620405
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTG                         GTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
EST: gi|148929642|gb|EC876096.2|EC876096
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTG                         GTGTGCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
EST: gi|76010584|gb|DT937754.1|DT937754
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTG                         GTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
EST: gi|31363851|gb|CD448206.1|CD448206
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTG                         GTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
EST: gi|149100798|gb|EE186892.2|EE186892
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTG                         GTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
EST: gi|6973552|gb|AW438288.1|AW438288
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCTGAGGATCCACTTTTCCAATTG                         GTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
EST: gi|110202089|gb|EC883986.1|EC883986
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTG                         GTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
EST: gi|71771088|gb|DR969025.1|DR969025
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTG                         GTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
EST: gi|78021514|gb|DV489901.1|DV489901
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCTGAGGATCCACTTTTCCAATTG                         GTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
EST: gi|37380261|gb|CF626924.1|CF626924
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTG                         GTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
EST: gi|5901109|gb|AW042209.1|AW042209
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCTGAGGATCCACTTTTCCAATTG                         GTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
EST: gi|32796104|gb|CD948340.1|CD948340
EST:     GATCCACTTTTCCAATTG                         GTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
genomic: GATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
EST: gi|110954440|gb|EE174492.1|EE174492
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTG                         GTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
EST: gi|148991805|gb|EE033386.2|EE033386
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTG                         GTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
EST: gi|93284645|gb|EB676909.1|EB676909
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTG                         GTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
EST: gi|149082973|gb|EE172210.2|EE172210
EST:     GGGAGTTTG-CCTGAAAGCA-TTGCCCCAAGGATCCACTTTTCCAATTG                         GTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
genomic: GGGAGTTTGCCCTG-AAGCATTTG-CCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
EST: gi|60395299|gb|DN228168.1|DN228168
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTG                         GTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG

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: 47 (upstream exon), 47 (downstream exon)
Score: 104

TGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 506

TGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 653

TGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 294

TGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctgg ... ttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctggaaccttttatctaatttcatttacttttttgagttgaacggttttaaatgtaatctttggttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC