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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCAGAGCAAGGTATGGTGTCATGTTGGAAAAGGGTGCATTTGATAAGCGGACTGCAGATTTCTTATGGATGATGATATTTGGTGCCATCTCACTATTGgtcagttatttttactttttgcatttacaatttcaaatttgaccaaaccaagggacattctagaacttttactaaacttgtatacaactctgtattgcttgaatcag

Basic information

species Zea mays
transcript GRMZM2G117388_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117388_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g09550.3 (Oryza sativa), 5'ss of exon 3
ATGCAGAGCAAGGTATGGTGTCATGTTGGAAAAGGGTGCATTTGATAAGCGGACTGCAGATTTCTTATGGATGATGATATTTGGTGCCATCTCACTATTGgtcagttatttttactttttgcatttacaatttcaaatttgaccaaaccaagggacattctagaacttttactaaact--tgtatacaactctgtattgcttgaatcag
|||||| || || || ||| ||||||||||||||||| ||||| || || |||||||| ||||||||||||||||||||||| ||||| |||||||| | | | || |||| | | || | || ||| | |||| | || ||| | | | ||| || ||| | ||||||| |||||
------AGCAAGATACGGCGTGCAGTTAGAAAAGGGTGCATTTGAAAAGCGCACAGCTGATTTCTTGTGGATGATGATATTTGGTGCCATATCACTGCTGgtcagtgctagct-tgtactgtatttttagc----agcttaatcagaccttaaaa-attcaattcattggactcacatactacatataaatctttcttgcttggatcag

upper sequence: GRMZM2G117388_T04 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA05G35990.1 (Glycine max), 5'ss of exon 4
ATGCAGAGCAAGGTATGGTGTCATGTTGGAAAAGGGTGCATTTGATAAGCGGACTGCAGATTTCTTATGGATGATGATATTTGGTGCCATCTCACTATTGgtcagttatttttactttttgcatttacaatttcaaatttgaccaaaccaagggacattctagaacttttactaaacttgtatacaactctgtattgcttgaatcag----
|| ||||||||||||| | || || || ||||||| |||||||| |||||||| ||||||||||||||||||||| | |||||||||| || | || | | ||| || | | || | | | |||| | | || ||| | || || || | | || | |||||
------AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGACCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgtatgtgtgatcatctatatatcttttgcatcttatgatt-----atttatgtgacaattt----tttccttcaaaatggtg-gcagctttattctg-tagaatctattct

upper sequence: GRMZM2G117388_T04 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G03630.1 (Glycine max), 5'ss of exon 4
ATGCAGAGCAAGGTATGGTGTCATGTTGGAAAAGGGTGCATTTGATAAGCGGACTGCAGATTTCTTATGGATGATGATATTTGGTGCCATCTCACTATTGgtcagttatttttactttttgcatttacaatttcaaatttgaccaaaccaagggacattctagaacttttactaaacttgtatacaactctgtattgcttgaatcag------
|| ||||||||||||| | || || || |||||||| |||||||| |||||||| ||||||||||||||||||||| | |||||||||| || | | | ||| |||| || ||| | | | | || | || ||| | || || || || | | ||| | |||||
------AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTGgt-----atgtgtgat-----catctacatttctt--tttcatcttatgattatttatataacaattttccttcaaaatggtggcagctttattttg-tagaatctattctag

upper sequence: GRMZM2G117388_T04 (Zea mays), 5'ss of exon 4
lower sequence: Vv04s0008g00510.t01 (Vitis vinifera), 5'ss of exon 4
ATGCAGAGCAAGGTATGGTGTCATGTTGGAAAAGGGTGCATTTGATAAGCGGACTGCAGATTTCTTATGGATGATGATATTTGGTGCCATCTCACTATTGgtcagttatttttactttttgcatttacaatttcaaatttgaccaaaccaagg-gacattctagaacttttactaaacttgtatacaactctgt---attgct---tgaatcag-----------------------------------------------------
||| || ||||| ||| | |||| ||||| | |||||| | ||| || ||||||||||| ||||||||||||||||| || | || | |||| || | || | || | ||| | || || || | | |||| || || | | | ||||| |||| || || |
------AGCCAGATATGGGGTCCAGCTGGAGAAGGGAGTATTTGAAAGGCGCACGGCAGATTTCTTGTGGATGATGATATTTGGAGCTCTGACATTGCTGgtatgtc--tgaaacctatttttctcttaatattttatctggtcattttagactgtcattttaagttggctaatgcatcagagagttcttctgttagattgtcatgtgcattaaaatacattagaatactatctttattcttgtcttgttggactttggatgcttag

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|32919438|gb|CF024250.1|CF024250
EST:     GGACTGCAGATTTCTTATGGATGATGATATTTGGTGCCATCTCACTATTG                         GTGTTGTCTATTATTCCCCTATTCAATTCTTTTTTCTTAGGAATACCTATG
genomic: GGACTGCAGATTTCTTATGGATGATGATATTTGGTGCCATCTCACTATTGgtcagttatt ... cttgaatcagGTGTTGTCTATTATTCCCCTATTCAATTCTTTTTTCTTAGGAATACCTATG
EST: gi|211211598|gb|FL477381.1|FL477381
EST:     TATGGATGATGATATTTGGTGCCATCTCACTATTG                         GTGTTGTCTATTATCCCCCTATTCAA-TCTTTTTTCTTAGGAATACNTATG
genomic: TATGGATGATGATATTTGGTGCCATCTCACTATTGgtcagttatt ... cttgaatcagGTGTTGTCTATTATTCCCCTATTCAATTCTTTTTTCTTAGGAATACCTATG
EST: gi|40336279|gb|CK370349.1|CK370349
EST:     TATTTGGTGCCATCTCACTATTG                         GTGTTGTCTATTATTCCCCTATTCAATTCTTTTTTCTTAGGAATACCTATG
genomic: TATTTGGTGCCATCTCACTATTGgtcagttatt ... cttgaatcagGTGTTGTCTATTATTCCCCTATTCAATTCTTTTTTCTTAGGAATACCTATG
EST: gi|60349033|gb|DN216006.1|DN216006
EST:     GGATGATGATATTTGGTGCCATCTCACTATTG                         GTGTTGTCTATTATTCCCCTATTCAATTCTTTTTTCTTAGGAATACCTATG
genomic: GGATGATGATATTTGGTGCCATCTCACTATTGgtcagttatt ... cttgaatcagGTGTTGTCTATTATTCCCCTATTCAATTCTTTTTTCTTAGGAATACCTATG
EST: gi|71767311|gb|DR965248.1|DR965248
EST:     AGACTGCAGATTTCTTATGGATGATGATATTTGGTGCCATCTCACTATTG                         GTGTTGTCTATTATTCCCCTATTCAATTCTTTTTTCTTAGGAATACCTATG
genomic: GGACTGCAGATTTCTTATGGATGATGATATTTGGTGCCATCTCACTATTGgtcagttatt ... cttgaatcagGTGTTGTCTATTATTCCCCTATTCAATTCTTTTTTCTTAGGAATACCTATG
EST: gi|16927150|gb|BM080219.1|BM080219
EST:     TGGATGATGATATTTGGTGCCATCTCACTATTG                         GTGTTGTCTATTATTCCCCTATTCAATTCTTTTTTCTTAGGAATACCTATG
genomic: TGGATGATGATATTTGGTGCCATCTCACTATTGgtcagttatt ... cttgaatcagGTGTTGTCTATTATTCCCCTATTCAATTCTTTTTTCTTAGGAATACCTATG
EST: gi|37392930|gb|CF633718.1|CF633718
EST:     GATGATATTTGGTGCCATCTCACTATTG                         GTGTTGTCTATTATTCCCCTATTCAATTCTTTTTTCTTAGGAATACCTATG
genomic: GATGATATTTGGTGCCATCTCACTATTGgtcagttatt ... cttgaatcagGTGTTGTCTATTATTCCCCTATTCAATTCTTTTTTCTTAGGAATACCTATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCAGAGCAAGGTATGGTGTCATGTTGGAAAAGGGTGCATTTGATAAGCGGACTGCAGATTTCTTATGGATGATGATATTTGGTGCCATCTCACTATTGgtcagttatttttactttttgcatttacaatttcaaatttgaccaaaccaagggacattctagaacttttactaaacttgtatacaactctgtattgcttgaatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT