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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttgatgtagtattttgttatcttcatcttctgttgcttttcctataaaaacgaagcaataactgcctttgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACT

Basic information

species Zea mays
transcript GRMZM2G370852_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G370852_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g03260.2 (Oryza sativa), 3'ss of exon 8
gtctgttgatgtagtattttgttatcttcatc--ttctgttgcttttcctataaaaa-----cgaagcaataactgcctttgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACT
|| |||| || |||| |  |||||||||   |  |    |   |||   |||| |||     | ||||  | | |    | || |||||||||||||| |||||||||||||| ||||||||||| ||||||||||||||||| ||||| |||||||| ||||| || ||||| || || ||||||||||
gtttgttcatatagt-tactgttatcttttgcaatctcatcaatttcattatacaaaagagtcaaagctgttattttggtggacctgcagCCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAGATTGACCGGGTCTATATCGGTTCTTGTACTGGAGGTAAAACTGAGGACT

upper sequence: GRMZM2G370852_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 13
-------------------------------------------------gtctgttgatgtagtattttgttatcttcatcttctgttgcttttc-ctataaaaacgaagcaataactgcctttgatc-tgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACT
                                                    |||| |   | | || |||| |       |  | |||  |||   |   || |  | |||||   |       | | | ||||||||||| || || || |||||  | ||||||||||||||  |||| || || ||| |||| || ||||| |||||||||||||| |||||||| || |
gtacttttactttaacttaatcatatttttatcttcattttgccataaaaagtgttaa--gaattttgtgttgtaaaagattctttttgagtttgattgctaatataatgcaatgtgtttgaaccaccatacagCCACATTCCCCCGATAATCGTGCTTTGGCAAGAGAATGCAACAATGTGAAAATTGACAGAGTATACATTGGATCCTGCACTGGTGGGAAGACTGAAGATT

upper sequence: GRMZM2G370852_T02 (Zea mays), 3'ss of exon 10
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 11
gtctgttgatg--tagtattttgttatcttcatcttctgttgcttttcctataaaaacgaagcaataactgcctttgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACT
||  ||| | |  ||  | |||   |   | |  |  |  |||   | | |    |   |     | | || ||||  | | ||||| ||||| ||||||||||| || ||||| |||||||||||||| || || || ||| |||| || || ||||| || |||||||| ||||| ||||| |
gtgggtttacgattaccaatttaa-acactgagttatttctgccacttc-aggttacttattttgttaatgtctttttttt-cagCCTCATTCTCCTGACAACCGAGCTCTAGCTAGAGAATGCAAAGACGTGAAAATTGACAGAGTATACATCGGTTCTTGTACTGGTGGGAAGACAGAGGATT

upper sequence: GRMZM2G370852_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 3'ss of exon 11
-----------------gtctgttgatgtagtattttgttatcttcatcttctgttgcttttcctataaaaacgaagcaataactgcctttgat--ctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACT
                    |||  |   |        | |  |  ||  | ||  | ||||    ||  ||  ||  | ||  || | |   |  ||| |||| ||||| ||||| || |||||  | |||||||||||||||||||| || || ||| | || |||||||| || ||||||||||| || |||||||| |
aatgattattacgtaaaacatgtcaaataaactccaaataacttcaataatatgcaggttttta-gtagtaatcaa-tagtatttgtcatatgtttctgtagCCTCATTCACCTGATAATCGTGCTTTGGCAAGAGAATGCAAAGATGTGAAAATTGACAGGGTATATATTGGATCTTGCACTGGTGGAAAAACTGAGGATT

upper sequence: GRMZM2G370852_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------------------------------gtctgttgatgtagtattttgttatcttcatcttctgttgct----------tttcctataaaaacgaagcaataactgcctttgat--ctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACT
                                                            | | | |   |||||   |||    ||   ||||| |          ||  |  |  | |   |  |||| ||||| |   |  |||||||| ||||| ||||| ||  ||||  | ||||||||||||||||| || || || ||| | || |||||||| || || |||||||| || |||||||| |
gtgagtgattttatatagccttaagtgaaatcatcttaagtttttaaactgtagaccaaataggtatttcattttaaaatccatttcaagtgttgataagtggcaaattcacactttatattgaataatatctgccatatgtttctgcagCCTCATTCACCTGATAAATGTGCTTTGGCAAGAGAATGCAAAGACGTGAAAATTGACAGGGTGTATATTGGATCTTGTACTGGTGGAAAAACTGAGGATT

upper sequence: GRMZM2G370852_T02 (Zea mays), 3'ss of exon 10
lower sequence: EFJ16664 (Selaginella moellendorffii), 3'ss of exon 5
gtctgttgatgtagtattttgttatcttcatcttctgttgcttttcctataaaaacgaagcaataactgcctttgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACT
                                   |  ||   ||  | | |  |||       |    | |||  | ||||||| ||||| || || || || ||  |||| ||  | ||||||||||| |||||||||||||| || ||||| |||||||| || |||||||| |||||| 
----------------------------------gtactgtagttgttttgaccacgtgcagtcagtctctttttgtgtgcagCCGCATTCTCCGGATAAACGAGCATTAGCCAGGAACTGCAAAGATGTGAAGATCGACCGAGTGTACATTGGCTCCTGCACGGGAGGCAAGACGGAGGACG

upper sequence: GRMZM2G370852_T02 (Zea mays), 3'ss of exon 10
lower sequence: EFJ32611 (Selaginella moellendorffii), 3'ss of exon 9
gtctgttgatgtagtattttgttatcttcatcttctgttgcttttcctataaaaacgaagcaataactgcctttgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACT
          |||   | |  || |||| | |   ||   ||    || |            |||| |   |||  | ||||||| ||||| || || || || |   |||| || || ||||||||||| |||||||||||||| || ||||| |||||||| || |||||||| |||||||
----------gtaac-tgtaattgtcttgaccacttgc-actcggtctgt----------ttataatt--tttttgtgtgcagCCGCATTCTCCGGATAAACGAGTATTAGCCAGGGACTGCAAAGATGTGAAGATCGACCGAGTGTACATTGGCTCCTGCACGGGAGGCAAGACGGAGGACT

upper sequence: GRMZM2G370852_T02 (Zea mays), 3'ss of exon 10
lower sequence: EFJ16666 (Selaginella moellendorffii), 3'ss of exon 10
gtctgttgatgtagtattttgttatcttcatcttctgttgcttttcctataaaaacgaagcaataactgcctttgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACT
          |||   | |  || |||| | |   ||   |||   || |  |        |||   |   | || | ||||||| ||||| || || || || ||  |||| || || ||||||||||| |||||||||||||| || ||||| |||||||| || |||||||| || ||||
----------gtaac-tgtaattgtcttgaccacttgc-acttggtctgttta-------taatttttttgtgtg-tgtgcagCCGCATTCTCCGGATAAACGAGCGTTAGCCAGGGACTGCAAAGATGTGAAGATCGACCGAGTGTACATTGGCTCCTGCACGGGAGGCAAGACGGAAGACT

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|76282892|gb|DV022460.1|DV022460
EST:     AGTAGTTGCCAAG                         CCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
genomic: AGTAGTTGCCAAGgtctgttgat ... tgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
EST: gi|32840108|gb|CD979789.1|CD979789
EST:     TTAGTGACTACCGGNTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAG                         CCACATTCGCCT
genomic: TTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAGgtctgttgat ... tgatctgcagCCACATTCGCCT
EST: gi|16916456|gb|BM072849.1|BM072849
EST:     TTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAG                         CCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
genomic: TTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAGgtctgttgat ... tgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
EST: gi|32846022|gb|CD985703.1|CD985703
EST:     TTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAG                         CCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
genomic: TTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAGgtctgttgat ... tgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
EST: gi|31350830|gb|CD435187.1|CD435187
EST:     TAGTGACTACCGGTTTGATGTATCGAAACT-GAGCCCAGTAGTTGCCAAG                         CCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
genomic: TAGTGACTACCGGTTTGATGTATCGAAACTGGAG-CCAGTAGTTGCCAAGgtctgttgat ... tgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
EST: gi|60341015|gb|DN207988.1|DN207988
EST:     TTGATGTATCGAAACTGGAGCCAGGTAGTTGCCAAG                         CCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
genomic: TTGATGTATCGAAACTGGAGCCA-GTAGTTGCCAAGgtctgttgat ... tgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
EST: gi|32840107|gb|CD979788.1|CD979788
EST:     TTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAG                         CCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
genomic: TTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAGgtctgttgat ... tgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
EST: gi|211090106|gb|FL396339.1|FL396339
EST:     TTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAG                         CCACATTCGCCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAA
genomic: TTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAGgtctgttgat ... tgatctgcagCCACATTCG-CCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAA
EST: gi|32840106|gb|CD979787.1|CD979787
EST:     TTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAG                         CCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
genomic: TTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAGgtctgttgat ... tgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
EST: gi|211011802|gb|FL408548.1|FL408548
EST:     TTAGTGACTA-CGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAG                         CCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
genomic: TTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAGgtctgttgat ... tgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
EST: gi|211350370|gb|FL368852.1|FL368852
EST:     TTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAG                         CCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
genomic: TTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAGgtctgttgat ... tgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
EST: gi|148971978|gb|EE022780.2|EE022780
EST:     ACTGGAGCCAGTAGTTGCCAAG                         CCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
genomic: ACTGGAGCCAGTAGTTGCCAAGgtctgttgat ... tgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
EST: gi|149079940|gb|EE168953.2|EE168953
EST:     GTAGTTGCCAAG                         CCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGGATGTCAA
genomic: GTAGTTGCCAAGgtctgttgat ... tgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAA-GATGTCAA
EST: gi|211524232|gb|FL397627.1|FL397627
EST:     TTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAG                         CCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG
genomic: TTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAGgtctgttgat ... tgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAG

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: 46 (upstream exon), 48 (downstream exon)
Score: 49

ATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAGgtctgttgat ... tgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 132

ATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAGgtctgttgat ... tgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACT


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

ATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAGgtctgttgat ... tgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACT


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 78

ATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAGgtctgttgat ... tgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcttctgttgcttttcctataaaaacgaagcaataactgcctttgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACT
                                      ctgccttt  CT-rich tract
             ttttcctataaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgttgatgtagtattttgttatcttcatcttctgttgcttttcctataaaaacgaagcaataactgcctttgatctgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA