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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCTCGAAAATTGATACCTCAAAAGATTCTGCTGGAGCTGTCCCACTACTGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatctgttatgagttttctttatctgaaaaagggttctctcctggagaaaagttttcagccatttccccttgtaaggctagtttgggaactcca...

Basic information

species Zea mays
transcript GRMZM2G030312_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030312_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os09g11250.1 (Oryza sativa), 5'ss of exon 4
CTTCTCGAAAATTGATACCTCAAAAGATTCTGCTGGAGCTGTCCCACTACTGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc-----tgttatgagtttt--ctttatctgaaaa-------agggttctctcctggagaaaagttttcagccatttccccttgtaaggctagtttgggaactcca----------------------------------------
|||||| ||||| ||||| || ||||||||| |||||||||| |||||||| ||||| ||| ||||||||||||||||||| || || |||||||  |||||  | | |      | |||| | || |   || || |  |||       |   | |  |   | || |    | ||| ||| |   ||   ||| | ||   ||  |    ||                                        
CTTCTCAAAAATAGATACATCTAAAGATTCTACTGGAGCTGTTCCACTACTAAAAACACTGTTGGAGGGTGTGGACATGACAGATAAACAACTTGGTGAGgtaatctgttgcggatattataatttatgctttgattttgaaacttgtgtacaatgccttttagtagcatttctctcaaccaatattcccactaatg-tatgatgaaactgacagtgtaccctgtattcaatctatgccttcaaaattgaacag

upper sequence: GRMZM2G030312_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv19s0090g01190.t01 (Vitis vinifera), 5'ss of exon 3
CTTCTCGAAAATTGATACCTCAAAAGATTCTGCTGGAGCTGTCCCACTACTGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtg----ctttatctgttatgagttttctttatctgaaaaagggttctctcctggagaaaagttttcagccatttccccttgtaaggctagtttgggaactcca
 || || || ||||||   || |||||| ||||||||||||| |||||  | ||||| || ||||||||||| || |||||||| || || |||| ||||||     | |||| | | ||  ||  ||| ||  ||   |    |  |  |      | ||||  |     | |          ||| |  | |    ||    
TTTTTCAAAGATTGATGAATCTAAAGATACTGCTGGAGCTGTTCCACTTTTAAAAACACTTCTGGAGGGTGTTGAAATGACTGAAAAACAGCTTGGAGAGgtaaactcattatttttcatttgtcatctataagtgctcagccttattaccacctttacaagtcattgattaatggttaaacagaggttcatatacacac----
















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|148933325|gb|EC876982.2|EC876982
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
EST: gi|89758965|gb|DY687943.1|DY687943
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGTTTGGA
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGA
EST: gi|94478496|gb|EB707454.1|EB707454
EST:     GAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAAGCA-CTTGCAGAG                         GTCTTCAAGAAGTTT
genomic: GAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAA-GCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTT
EST: gi|71766863|gb|DR964800.1|DR964800
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
EST: gi|148933324|gb|EC876981.2|EC876981
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
EST: gi|148938639|gb|EC882972.2|EC882972
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
EST: gi|148995403|gb|EE034608.2|EE034608
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
EST: gi|29129982|gb|CB380686.1|CB380686
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
EST: gi|5124120|gb|AI745744.1|AI745744
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
EST: gi|7162360|gb|AW519982.1|AW519982
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGGAGCAACTTGCAGAG                         GTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
EST: gi|94478060|gb|EB707018.1|EB707018
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCT
EST: gi|71770780|gb|DR968717.1|DR968717
EST:     NGAAA-CCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAAGTT-GGAGTCGAAAA-TTTGACCCGCTGAATGAGGAATT
genomic: -GAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAA-GTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATT
EST: gi|89760660|gb|DY688984.1|DY688984
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTTCA-GAAGTTTGGAGTCCAAAA-TTTGACCCGCTGAAT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTT-CAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAAT
EST: gi|101387368|gb|EB815700.1|EB815700
EST:     GAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAAGCA-CTTGCAGAG                         GTCTTTCA-GAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGGATT
genomic: GAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAA-GCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTT-CAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATT
EST: gi|71439951|gb|DR821001.1|DR821001
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
EST: gi|88755369|gb|DY539510.1|DY539510
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
EST: gi|91873051|gb|EB403008.1|EB403008
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCCAGAAGTTTGGGAGTCGAAAAATTTGACCCGCTGAATGAGGGAAT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGG-AGTCGAAAAATTTGACCCGCTGAATGAGG-AAT
EST: gi|88757877|gb|DY542018.1|DY542018
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGTTTGGAGTCGAAAAAATTGACCCGCTGAATGAGGAATTT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
EST: gi|16925262|gb|BM078330.1|BM078330
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
EST: gi|148995402|gb|EE034607.2|EE034607
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
EST: gi|71757784|gb|DR955721.1|DR955721
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
EST: gi|71434759|gb|DR815809.1|DR815809
EST:     TGATAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGATTGGAGTCGAAAAAATTGACCCGCTGAATGAGGAATTT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
EST: gi|28873855|gb|CB329788.1|CB329788
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGTCTGGAGTCGAAAAATT-GACCCGCTGAATGAGGAATTT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
EST: gi|211470275|gb|FL336875.1|FL336875
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
EST: gi|78075537|gb|DV503971.1|DV503971
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTT
EST: gi|149063793|gb|EE286381.2|EE286381
EST:     GGAAAACCCTGCTGGAGGGGGTGGACATGACTGAGAAGCACCTTGCAGAG                         GTCTTCAAGAGGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAAT
genomic: G-AAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAAT
EST: gi|89251989|gb|DY623775.1|DY623775
EST:     TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAG                         GTCTTCAAGAAGTTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATT
genomic: TGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTT-GGAGTCGAAAAATTTGACCCGCTGAATGAGGAATT

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), 47 (downstream exon)
Score: 110

CTTCTCGAAAATTGATACCTCAAAAGATTCTGCTGGAGCTGTCCCACTACTGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTTGATCCTAACAGGCATTGTGCAGTTTTTCAAATTCCTGATCCTTCAAAAC


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

CTTCTCGAAAATTGATACCTCAAAAGATTCTGCTGGAGCTGTCCCACTACTGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTTGATCCTAACAGGCATTGTGCAGTTTTTCAAATTCCTGATCCTTCAAAAC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 27

CTTCTCGAAAATTGATACCTCAAAAGATTCTGCTGGAGCTGTCCCACTACTGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTTGATCCTAACAGGCATTGTGCAGTTTTTCAAATTCCTGATCCTTCAAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

CTTCTCGAAAATTGATACCTCAAAAGATTCTGCTGGAGCTGTCCCACTACTGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatc ... atctaaacagGTCTTCAAGAAGTTTGGAGTCGAAAAATTTGACCCGCTGAATGAGGAATTTGATCCTAACAGGCATTGTGCAGTTTTTCAAATTCCTGATCCTTCAAAAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCTCGAAAATTGATACCTCAAAAGATTCTGCTGGAGCTGTCCCACTACTGAAAACCCTGCTGGAGGGTGTGGACATGACTGAGAAGCAACTTGCAGAGgtgctttatctgttatgagttttctttatctgaaaaagggttctctcctggagaaaagttttcagccatttccccttgtaaggctagtttgggaactcca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggagaaaa