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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCCACCACATCCCCGGGCCGGAGGGCGTGCGTGGGCGCAACTCAGACAACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccaccaaacctcgcacgtaccatcgctccagtccctgagctggatcacacctacatagtctgatcgttcattgcactggactcaaatttggcctgcag

Basic information

species Zea mays
transcript GRMZM2G138907_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138907_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os11g37890.3 (Oryza sativa), 5'ss of exon 5
CATCCACCACATCCCCGGGCCGGAGGGCGTGCGTGGGCGCAACTCAGACAACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactcca--ccaaacctcgcacgtaccatcgctccagtccctgagctggatcacacctacatagtctgatcgttcattgcactggactcaaatttggcc-tgcag
||||||||||||||||||||| ||||| || ||||| |||||||| ||||||||||||||||| |||||||||||||||||||| || ||||||||||||||||| |   ||     |  || | | |      ||  ||  |     |   |  |   |   | ||||||| ||||| | |    |||  | | | ||   ||||
CATCCACCACATCCCCGGGCCAGAGGGTGTCCGTGGTCGCAACTCCGACAACACGCTCATCAAAGAGAAGCTTGGCTGGGCTCCAACCATGAGGCTGAAGgtactactatccctgattttcaggcaaccatctgcctatcagttcatcgccccgaattcatgcattctgatcattcatcgga---aacttgattcttgcggcgcag

upper sequence: GRMZM2G138907_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv14s0030g02180.t01 (Vitis vinifera), 5'ss of exon 6
CATCCACCACATCCCCGGGCCGGAGGGCGTGCGTGGGCGCAACTCAGACAACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccaccaaacctcgcacgtaccatcgctccagtccctgagctggatcacacctacatagtctgatcgttcattgcactggact--caaatttggcctgcag--
|||||| ||||| || || || ||||| |||||||| || |||||||||||||| || ||||| |||||||| || |||||||| || ||||   ||||||||||  |   |||    |||   |  | ||   | | |  ||| |   |   || ||   | |  |||  | || ||     | ||  |||     |  |  |   
CATCCATCACATTCCAGGCCCAGAGGGTGTGCGTGGTCGTAACTCAGACAACACACTGATCAAAGAGAAGCTCGGTTGGGCTCCAACAATGAAATTGAAGgtactt-atataacaagacac---cgcttgccttattac--gaggtttttttaacttatg-atttggattatgcaatgggtcagtcttacaagccaagtgtatatgt

upper sequence: GRMZM2G138907_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv05s0020g04510.t01 (Vitis vinifera), 5'ss of exon 6
CATCCACCACATCCCCGGGCCGGAGGGCGTGCGTGGGCGCAACTCAGACAACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtac---tccaccaaacctcgcacgtaccatcgctccagtccctgagctgg-atcacacctacatagtctgatcgttcattgcactggactcaaatttggcctgcag
|||||| ||||| || || || ||||| || ||||| || ||||||||||| |  || ||||||||||||||||| ||||| || || |||||  |||||||||   |    | |     ||   ||  |    |  |  | || |||    |||  ||  ||  |  ||  || |  |||    | ||   || |   |       
CATCCATCACATTCCTGGCCCAGAGGGTGTACGTGGTCGAAACTCAGACAATAATCTGATCAAGGAGAAGCTTGGTTGGGCCCCTACCATGAGATTGAAGgtacaagtgggactagttaggcctttatgacaagttaatcctctcagccaatatctgactcactaatcctattcatatattttctttgat--aattacag-------

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|37374420|gb|CF623565.1|CF623565
EST:     ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAG                         GACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
genomic: ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
EST: gi|71433719|gb|DR814769.1|DR814769
EST:     ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAG                         GACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
genomic: ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
EST: gi|76282745|gb|DV022313.1|DV022313
EST:     ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAG                         GACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
genomic: ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
EST: gi|37381559|gb|CF627674.1|CF627674
EST:     ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAG                         GACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
genomic: ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
EST: gi|60395208|gb|DN228077.1|DN228077
EST:     ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAG                         GACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
genomic: ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
EST: gi|149071844|gb|EE160233.2|EE160233
EST:     ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAG                         GACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
genomic: ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
EST: gi|76287579|gb|DV027147.1|DV027147
EST:     ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAG                         GACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
genomic: ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
EST: gi|18660911|gb|BM501114.1|BM501114
EST:     ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAG                         GACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
genomic: ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
EST: gi|211437568|gb|FL434162.1|FL434162
EST:     ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAG                         GACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
genomic: ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
EST: gi|60399538|gb|DN232349.1|DN232349
EST:     ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAG                         GACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
genomic: ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
EST: gi|148949982|gb|EC895502.2|EC895502
EST:     ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAG                         GACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
genomic: ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
EST: gi|14245565|gb|BG874147.1|BG874147
EST:     ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAG                         GACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
genomic: ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
EST: gi|50337859|gb|CO532985.1|CO532985
EST:     ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAG                         GACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
genomic: ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
EST: gi|211294157|gb|FL479987.1|FL479987
EST:     ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAG                         GACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
genomic: ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
EST: gi|211294158|gb|FL479988.1|FL479988
EST:     GACTATGAGGCTGAAG                         GACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
genomic: GACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
EST: gi|71433720|gb|DR814770.1|DR814770
EST:     ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAG                         GACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG
genomic: ACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAG

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: 35

CATCCACCACATCCCCGGGCCGGAGGGCGTGCGTGGGCGCAACTCAGACAACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAGAAGGCCGAGGGCATGGATCTGTCGGTCTACGGATCATCCAAGGTCGTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 227

CATCCACCACATCCCCGGGCCGGAGGGCGTGCGTGGGCGCAACTCAGACAACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAGAAGGCCGAGGGCATGGATCTGTCGGTCTACGGATCATCCAAGGTCGTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 280

CATCCACCACATCCCCGGGCCGGAGGGCGTGCGTGGGCGCAACTCAGACAACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAGAAGGCCGAGGGCATGGATCTGTCGGTCTACGGATCATCCAAGGTCGTGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 95

CATCCACCACATCCCCGGGCCGGAGGGCGTGCGTGGGCGCAACTCAGACAACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccacc ... tggcctgcagGACGGGCTGAGGATCACGTACTCCTGGATCAAGGAGCAGCTTGAGAAGGAGAAGGCCGAGGGCATGGATCTGTCGGTCTACGGATCATCCAAGGTCGTGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATCCACCACATCCCCGGGCCGGAGGGCGTGCGTGGGCGCAACTCAGACAACACGCTCATCAAGGAGAAGCTTGGCTGGGCTCCGACTATGAGGCTGAAGgtactccaccaaacctcgcacgtaccatcgctccagtccctgagctggatcacacctacatagtctgatcgttcattgcactggactcaaatttggcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG