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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgcacttgtaaatggatgaactgatataatctaccgttcatttcgattcaaaggaccttgtctgcttgaataactgtttgtacttttttacatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT

Basic information

species Zea mays
transcript GRMZM2G081622_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g10370.1 (Oryza sativa), 3'ss of exon 1
---gtgcacttgtaaatggatgaactgatataatctaccgttcatttcgattcaaaggaccttgtctgcttgaataactgtttgtacttttttacatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT
||| | ||| | | | | | | | | || | | | ||| || | | | || | |||| || |||| || || ||||||||||||||||||||||||||||||||||| ||||||||||||||||| || |||||||| ||||||
catgtgggccaacttctggtttatattagcgagtaaaatggatatgctttgttacta-atattgcttgatgaggattcaacatatattcctttatat--gcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGCTGGGAAAACATCGCTTGTGAATGTCATTGCT

upper sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT5G67560.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgcacttgtaaatggatgaactgatataatctaccgttcatttcgattcaaaggaccttg-------tctgcttga-ataactgtttgtacttttttacatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT
||| ||| | ||| | | || | | | |||| |||| | ||| || || | | || | || ||||||||||||||||||||||| ||||||||||| |||||||| || |||||||| || || || |||||||| ||| | ||||
-------agtagatgaagattgtgagagcaagaacttagtttcccaaaaaaaagttgcttgcttcgcatttgcccgatatgcatagtctcacaatgccttat-tgcagCCTCTTCTTCAAGCAAGAAATGGAGCTTTCATTGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTTAACGTTGTTGCA

upper sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G49870.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgcacttgtaaatggatgaactgatataatctaccgttcatttcgattcaaaggaccttgtctgcttgaataactgtttgtacttttttacat----ctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT
|| || | | | | || || | |||| ||| | | | | | | || || |||| ||| | || ||||||||||||||||||||||| ||||||||||| |||||||| || |||||||| || || || |||||||| || | ||||
---ttctaacaatcgtaaaatttcatgaaagat-tggttctttttggtatctaatttatgtttcgattcggtattcaattgtttgtttccatatgattttgcagCCTCTTCTTCAAGCAAGAAATGGAGCTTTCTTTGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTAAATGTTGTTGCA

upper sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv00s0601g00030.t01 (Vitis vinifera), 3'ss of exon 1
gtgcacttgtaaatggatgaactgatataatctac-cgttcatttcgattcaaaggaccttgtctgcttgaataactgtttgtacttttt-tacatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT
||| | | | | | || | | || || ||| || | |||| ||| | || || || || | || || |||||||||| |||||||| || ||||||||||| |||||||| || || |||||||||||||| |||||||| || | ||||
--tcacatattatgacaatgttttattttctttatgtctttattcattctcttattcccttttcttaatatgtagctcattctattgcttatatgatcgcagCCTCTTTTTCAAGCAGGAAATGGAGCTTTCTTTGATAGGACTTCAGAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCA

upper sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv03s0091g00970.t01 (Vitis vinifera), 3'ss of exon 1
gtgcacttgtaaatggatgaactgatataatctaccgttcatttcgattcaaagga-ccttgtctgcttgaataactgtttgtacttt--tttacatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT
| || || | | | | | ||| || || | |||| || ||| || | | | || |||||| ||| ||||||||||||| ||||| ||||| |||||||| || |||||||| || || ||||| || ||||| |||||||| || ||||||
-cttgcctgaaattacttctgataaaaaaatttat--ttaaacagagctcaactgagcctcagttgtcttgacttttccttttactttatttttattctgcagCCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGCAGGAAAAACATCACTTGTAAATGTTATTGCA

upper sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S6_409V6.2 (Physcomitrella patens), 3'ss of exon 2
gtgcact-tgtaaatggatgaactgatataatct--accgttcatttcgattcaaaggaccttgtctgcttgaataactgtttgtacttttttacatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT
| || | | ||| || || | | | || | | | | | ||| |||| ||| | | | | ||| | | | ||||||| ||||||||||||||||||||||| || ||||||| || || || ||||||||||| || ||||| || ||||||
ataaacgatttcaatttat-aattactgtgatgttgatggattgggttgatctcctaattcttga--gctagtgtgattaattggagagagattgtgcggcagCCTGTTCTTCAAGCAAGAGATGGAGCTGTCGCTGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCG

upper sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S103_13V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------------------------------------------gtgcacttgtaaatggatga---act--gatataatctaccgt-tcatttcgattcaaaggaccttgtctgcttgaataactgtttgtacttttttacatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT
|| ||||| | || || ||| | || | || | ||||| | || | | | |||| || || | || | | | | || ||||| || |||||||||||||||||| | || ||||||||| | ||||||||||| ||||| || || ||||| |||||
gtagatgtcaaccttggcctgtatgtattgctaagtctcgatttcgctgaattctcttgtggtgttttttcattttgtggctcatgtacttgcttacagaagatatacttggggattgttagtggtataatttctgtgtaatgctgactctgtgctgacatggatgga-atggttctct-cgtgtgtagCCTATTTTTCAAGCAAGAGATGGAGTTGTCTTTGATAGGGTTGCAAAATGCTGGCAAAACTTCTCTCGTGAATGTCATTGCG

upper sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S263_59V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------------------------------------------------gtgcacttgtaaat---ggatgaactgatataatctaccgttcatttcgattcaaaggaccttgtctgcttgaataactgtttgtac--ttttttacatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT
||| ||| | || | || || | | || | ||| || | | ||| | | | || ||| || | | | ||||| ||||| ||||| |||||||||||||| || ||||||||||| || || || || ||||| || || || || |||||
gtagttactgaatttctgtctgtccatgcgattaagattcaattacacaattttataatttttcttgttatgttgttttgtgctgtgagtttgacgccttcgaatcagaggacatg--cgggcattggtatcggtttggttgctcgaagatgca-ggctctgtacttatacggttctcatcctgtgcagTCTCTTTTTCAAACAAGAGATGGAGCTGTCTTTGATAGGGCTGCATAACGCCGGAAAAACCTCTCTCGTCAATGTCATTGCG

upper sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ23242 (Selaginella moellendorffii), 3'ss of exon 1
gtgcacttgtaaatggatgaactgatataatctaccgttcatttcgattcaaaggaccttgtctgc-ttgaataactgtttgtacttttttacatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT
| | || || || || | | || | | | || || | |||| ||||||||||||||||||||||||||| | || | ||||| || ||||| ||||| || ||||| ||||| ||||| || |||
----------------------------------------gtatggagcgtcgaatccatgcttgggtctcacaattctcttggattgattgc-tctgtagCCTCTTCTTCAAGCAAGAGATGGAGTTATCAGTAATAGGACTACAAAAGGCTGGCAAGACGTCCCTTGTCAACTCCATCGCT

upper sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ25249 (Selaginella moellendorffii), 3'ss of exon 1
gtgcacttgtaaatggatgaactgatataatctaccgttcatttcgattcaaaggaccttgtctgc-ttgaataactgtttgtacttttttacatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT
| | || || || || | | || | | | || || | |||| |||||||||||||||||||||||||| | || | ||||| || ||||| ||||| || ||||| ||||| ||||| || |||
----------------------------------------gtatggagcgtcgaatccatgcttgggtctcacaattctcttggattgattgc-tctgtagCCTCTTCTTCAAGCAAGAGATGGAATTATCAGTAATAGGACTACAAAAGGCTGGCAAGACGTCCCTTGTCAACTCCATCGCT

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|211286502|gb|FL423661.1|FL423661
EST:     GGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTTCGCAG                         CCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
genomic: GGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTCCGCAGgtacgatgct ... acatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
EST: gi|9566366|gb|BE475875.1|BE475875
EST:     GGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTCCGCAG                         CCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
genomic: GGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTCCGCAGgtacgatgct ... acatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
EST: gi|32800459|gb|CD952695.1|CD952695
EST:     TAACTGGCTCCGCAG                         CCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
genomic: TAACTGGCTCCGCAGgtacgatgct ... acatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
EST: gi|211212173|gb|FL397456.1|FL397456
EST:     GGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTTCGCAG                         CCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
genomic: GGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTCCGCAGgtacgatgct ... acatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
EST: gi|211536538|gb|FL409971.1|FL409971
EST:     GGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTTCGCAG                         CCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
genomic: GGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTCCGCAGgtacgatgct ... acatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
EST: gi|149086640|gb|EE176182.2|EE176182
EST:     GGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTCCGCAG                         CCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
genomic: GGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTCCGCAGgtacgatgct ... acatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
EST: gi|148949509|gb|EC894973.2|EC894973
EST:     GGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTCCGCAG                         CCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
genomic: GGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTCCGCAGgtacgatgct ... acatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
EST: gi|78105314|gb|DV523732.1|DV523732
EST:     GGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTCCGCAG                         CCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
genomic: GGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTCCGCAGgtacgatgct ... acatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
EST: gi|211135638|gb|FL266964.1|FL266964
EST:     GGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTTCGCAG                         CCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
genomic: GGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTCCGCAGgtacgatgct ... acatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
EST: gi|211184547|gb|FL382110.1|FL382110
EST:     GGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTTCGCAG                         CCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
genomic: GGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTCCGCAGgtacgatgct ... acatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
EST: gi|76283087|gb|DV022655.1|DV022655
EST:     TTTCTTAACTGGCTCGGCAG                         CCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC
genomic: TTTCTTAACTGGCTCCGCAGgtacgatgct ... acatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGC

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), 49 (downstream exon)
Score: 58

GCCTTCTTCGCCGCCGGCCTCCGGACCGCGCAGCTCCCCGGAGCCGACAAGGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTCCGCAGgtacgatgct ... acatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 58

GCCTTCTTCGCCGCCGGCCTCCGGACCGCGCAGCTCCCCGGAGCCGACAAGGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTCCGCAGgtacgatgct ... acatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 51

GCCTTCTTCGCCGCCGGCCTCCGGACCGCGCAGCTCCCCGGAGCCGACAAGGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTCCGCAGgtacgatgct ... acatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 79

GCCTTCTTCGCCGCCGGCCTCCGGACCGCGCAGCTCCCCGGAGCCGACAAGGACCCGGCGCCATGGGGTTCTGGGAGGCTTTTCTTAACTGGCTCCGCAGgtacgatgct ... acatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattcaaaggaccttgtctgcttgaataactgtttgtacttttttacatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT
                       gaataac  putative branch site (score: 79)
 cttttttac  putative PPT
 tttgtactttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcacttgtaaatggatgaactgatataatctaccgttcatttcgattcaaaggaccttgtctgcttgaataactgtttgtacttttttacatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
-tgcactt
- - - - - - atggatg
- - - - - - - - - - - - - - - - - - -ttcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgttt