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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcacttccaacacaagtagaatctgaattcactgtgtatgccatttgttcatacaatgatgcacatttccttcctcatcgatttctgttggaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGAT

Basic information

species Zea mays
transcript GRMZM5G825902_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825902_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g05650.1 (Oryza sativa), 3'ss of exon 7
tcacttccaacacaagtagaatctgaattcactgtgtatgccatttgttcatacaatgatgcacattt-ccttcctcatcgatttctgttgga-attcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGAT
||| |  ||   |   || ||  ||         | | ||   ||  | ||||  ||| |   |||    ||||||||| ||| |  |||  | ||   |||||| || ||||||||||| || || |||||||| |||||||| || ||| | ||||||||| | |||   ||  |||||||||||||||||||||| |||
tcaatatcacatctgatataacatgtgccttacttctctgt--ttgctccatatgatgttcatcatccgtcttcctcattgatattagttaaacatgtgcagCATGCTGTACATAGAGACAGCTGATCGGCCTGGTCTACTTCTGGAAATAGTGAAGATCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGAT
















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|32859294|gb|CD998975.1|CD998975
EST:     AGTTGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: AGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|211056798|gb|FL037810.1|FL037810
EST:     GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|60394392|gb|DN227262.1|DN227262
EST:     GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|116828950|gb|EC862572.1|EC862572
EST:     GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG                         CGTACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATACA
genomic: GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATA-A
EST: gi|60354178|gb|DN221151.1|DN221151
EST:     GATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCGTGGCATACTTCTTGAGATAAT
genomic: GATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|60394317|gb|DN227187.1|DN227187
EST:     GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|16922165|gb|BM075455.1|BM075455
EST:     GCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: GCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|71762075|gb|DR960012.1|DR960012
EST:     GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|24934311|gb|CA452529.1|CA452529
EST:     GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|31356321|gb|CD440678.1|CD440678
EST:     GTTGATATTGCAACACATATAGGTGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGGCTGGCCTACTTCTTGAGATAAT
genomic: GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|6827302|gb|AW330945.1|AW330945
EST:     TATTGC-ACACATATAGGTGTTGAAGATGACGG-CCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: TATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|24767769|gb|CA402905.1|CA402905
EST:     GTTGATATTGCAACACATATAGTTG-TGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|31353042|gb|CD437399.1|CD437399
EST:     GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|148950230|gb|EC895780.2|EC895780
EST:     GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|6194493|gb|AW146597.1|AW146597
EST:     GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|194716957|gb|FK934116.1|FK934116
EST:     GTTGATATTGCAACACATATAGTCGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|32859295|gb|CD998976.1|CD998976
EST:     AGTTGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: AGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|31360452|gb|CD444809.1|CD444809
EST:     GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|16927075|gb|BM080144.1|BM080144
EST:     TATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: TATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|149074677|gb|EE163095.2|EE163095
EST:     GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|32828950|gb|CD968628.1|CD968628
EST:     GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|32828741|gb|CD968419.1|CD968419
EST:     GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: GTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|8929966|gb|BE224730.1|BE224730
EST:     ATATAGTTGTTGAAGATGACGGACCAAAAAGAAG                         CATACTTTACATAGAGACCCCCGACCGGCCTGGCCTACTTCTTGAGATAAT
genomic: ATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAAT

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 3 RNA-Seq libraries.


Block sizes: 33 (upstream exon), 17 (downstream exon)
Score: 1

GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGAT


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 10

GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGAT


Block sizes: 49 (upstream exon), 8 (downstream exon)
Score: 4

GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAGgtttgattct ... gaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcatacaatgatgcacatttccttcctcatcgatttctgttggaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGAT
                                                ttccc  CT-rich tract
     atacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcacttccaacacaagtagaatctgaattcactgtgtatgccatttgttcatacaatgatgcacatttccttcctcatcgatttctgttggaattcccagCATACTTTACATAGAGACCGCCGACCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA