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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgacacatccctgtgctgaactgccagtgccagattgaaacaaaacaaaaatgtgatttcatcgtagctgtgctttaattcccaattgttcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAGCACACGTCATTTGCCCGGTGACACGGCAACGCTGGCAGTTGGAGGCATT

Basic information

species Zea mays
transcript GRMZM2G087105_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087105_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g07970.1 (Oryza sativa), 3'ss of exon 8
gcgacacatccct-gtgctgaactgccagtgccagattgaaacaaaacaaaaatgtgatttc-atcgtagctgtgctttaattcccaattgttcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAGCACACGTCATTTGCCCGGTGACACGGCAACGCTGGCAGTTGGAGGCATT
  | ||||    | || || |||||| | ||    |    |  ||  || |  |||||| || ||   |||  | |||  |||| |  || ||| | ||||||||  ||||||||||||||||||| ||||| ||||||||||||||||||||| ||| ||| ||||| |||||||| ||||| |||||||| || || |||
--ggcacacttatagtactaaactgctaatggtgtaccacagtaagtcatagctgtgatctccattagagccatacttatattctctgttattcgtgctcagGACCCTGAGGCCTCTCTGGGAAAAGAGAGTTAGCCCAAATGTCATCTACAGCGCACATCACTTGCCAGGTGACACAGCAACACTGGCAGTCGGCGGTATT
















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|211348371|gb|FL045511.1|FL045511
EST:     ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
EST: gi|76011997|gb|DT939167.1|DT939167
EST:     ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
EST: gi|211348374|gb|FL045514.1|FL045514
EST:     ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGGGAAAAAAGARTCAGCCCAAATGTCATCTACA
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACA
EST: gi|37377364|gb|CF625279.1|CF625279
EST:     ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
EST: gi|78544333|gb|DV621831.1|DV621831
EST:     ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
EST: gi|76011998|gb|DT939168.1|DT939168
EST:     ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
EST: gi|71441000|gb|DR822050.1|DR822050
EST:     ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
EST: gi|78107837|gb|DV526255.1|DV526255
EST:     ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATTTACAG
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
EST: gi|211348369|gb|FL045509.1|FL045509
EST:     ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
EST: gi|76021369|gb|DT948539.1|DT948539
EST:     ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
EST: gi|7216529|gb|AW562651.1|AW562651
EST:     ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
EST: gi|6465589|gb|AW191184.1|AW191184
EST:     ATGATATTTGCTGGTTCGTCAGCTGGTTATGCCCATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
EST: gi|74238279|gb|DT646193.1|DT646193
EST:     ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
EST: gi|211348368|gb|FL045508.1|FL045508
EST:     ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGAGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
EST: gi|211348375|gb|FL045515.1|FL045515
EST:     ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
EST: gi|148986028|gb|EE029875.2|EE029875
EST:     ATGATATTTGGTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATTTACAG
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
EST: gi|211348373|gb|FL045513.1|FL045513
EST:     MTGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
EST: gi|101383656|gb|EB813883.1|EB813883
EST:     ATGATATTTGCTGGTTCGTCAGCGGGTTATGCACATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATTTACAG
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
EST: gi|50337803|gb|CO532929.1|CO532929
EST:     ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
EST: gi|12972665|gb|BG268095.1|BG268095
EST:     ATGATATTTGCTGGTTCGTCAGCTGGTTATGCGCATTGCTGGGACTTAAG                         GACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG
genomic: ATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAG

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: 145

CAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAGCACACGTCATTTGCCCGGTGACACGGCAACGCTGGCAGTTGGAGGCATT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 80

CAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAGCACACGTCATTTGCCCGGTGACACGGCAACGCTGGCAGTTGGAGGCATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

CAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAGCACACGTCATTTGCCCGGTGACACGGCAACGCTGGCAGTTGGAGGCATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

CAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAGgttagtatca ... tcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAGCACACGTCATTTGCCCGGTGACACGGCAACGCTGGCAGTTGGAGGCATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaaaatgtgatttcatcgtagctgtgctttaattcccaattgttcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAGCACACGTCATTTGCCCGGTGACACGGCAACGCTGGCAGTTGGAGGCATT
                                            ttcttac  putative branch site (score: 73)
                                            ttcttactc  CT-rich tract
                             tttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgacacatccctgtgctgaactgccagtgccagattgaaacaaaacaaaaatgtgatttcatcgtagctgtgctttaattcccaattgttcttactcagGACTTTGAGGCCTCTCTGGGAAAAAAGAGTCAGCCCAAATGTCATCTACAGCACACGTCATTTGCCCGGTGACACGGCAACGCTGGCAGTTGGAGGCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - cacatcc
- - - - - - - tgctgaa
- - - - - - - - - - - - ccagtgc
- - - - - - - - - - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtagctg