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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccaagccatatcaccagcatgtcttaaatctggttacgtataataatactgcaataggagtcaaaggggtctgatctatttttacttctttcagCTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTG

Basic information

species Zea mays
transcript GRMZM2G170326_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170326_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g44150.1 (Oryza sativa), 3'ss of exon 3
gtaccaagccatatcaccagcatgtcttaaatctggttacgtataataatactgcaataggagtcaaaggg-gtctgatctatttttacttctttcagCTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTG
|||   | |||  || ||   |  ||  ||   |  |   || |   | ||||     || ||| | |||  |||||| ||   |||   |||||||||| || ||||||||||||||||||||||| || |||||||||||| ||
gtaatgaaccacctctccccaaaatcccaa--ttaatcttgtttttcattact-----agcagttacaggatgtctgaccttcattt---tctttcagCTGAAGGAGTACATTGATGACACTGAAGATTTTATCAACATTCAGTTG

upper sequence: GRMZM2G170326_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G44820.1 (Glycine max), 3'ss of exon 4
gtaccaagccatatcaccagcatgtcttaaatctggttacgtataataatactgcaataggagtcaaaggggtctgatctatttttacttctttcagCTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTG
             | | ||   |||  |  |        | |    |  |      |||  |||  |          | |  |  |  || |||||| | ||||| |||||||||||||| ||||| |||||||||||||| |||
------------gtaaacatagtgttatctacactaactctttcctttctggcttcataacagtttatcaaccactgtttcctgctttttgtttcagTTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG

upper sequence: GRMZM2G170326_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G00510.1 (Glycine max), 3'ss of exon 4
gtaccaagccatatcaccagcatgtcttaaatctggttacgtataataatactgcaataggagtcaaaggggtctgatctatttttacttctttcagCTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTG
             | | ||   |    || | ||     | | |  |  |      |||  |||  |          | |  |  |  || |||||| | ||||| |||||||||||||| ||||| |||||||||||||| |||
------------gtaaacactgttatctaca-ctaacc-cttttccttctggcttcataacagtttagcaaccactgtttcctgctttttgtttcagTTGAAAGAATACATTGATGACACCGAAGATTTCATCAACATTCAACTG

upper sequence: GRMZM2G170326_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 5
gtaccaagccatatcaccagcatgtcttaaatctggttacgtataataatactgcaatagg-agtcaaaggggtctgatctatttttacttcttt-cagCTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTG
          |  | |   ||   ||| |  |    |||| | | ||  | || |  |||  ||    |    ||||   |  | |   | |||| ||| | || ||||||||||||||||||||||| ||||| |||||||| |||
--------gtactttaatggctcctctcattt----ttacttttgatctttcttcgctagacagctttaatcatctgtgttcctctctttactttacagTTAAAGGAGTACATTGATGACACTGAAGATTTCATTAACATTCAACTG

upper sequence: GRMZM2G170326_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0018g00570.t01 (Vitis vinifera), 3'ss of exon 3
gtaccaagccatatcaccagcatgtcttaaatctggttacgtataataatactgcaataggagtcaaaggggtctgatctatttttacttc------tttcagCTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTG----------------------------------------------------
||| |  ||    |      ||| | |  |  || ||  | | ||||| |||| ||   || ||  |     | |  |   |  || ||||      |||||||| || || |||||||||||||| ||||| ||||| ||||||||||||                                                    
gtatcctgcatctttctttacatttgtagacccttgt--cttttaata-tacttcaggtggggtggagaaaatttattagttagtttcttcatgtcgtttcagCTGAAGGAATACATTGATGACACAGAAGATTTCATTAACATTCAGCTGGTACGTGTTGTTTCTTTCTTATATGTTTGGTTCCCAGAAAGTATTAAGAAAA

upper sequence: GRMZM2G170326_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0018g00600.t01 (Vitis vinifera), 3'ss of exon 3
gtaccaagccatatcaccagcatgtcttaaatctggttacgtataataatactgcaataggagtcaaaggggtctgatctatttttacttc------tttcagCTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTG
||| |  ||    |      ||| | |  |  || ||  | | ||||| |||| ||   || ||  |     | |  |   |  || ||||      |||||||| || || |||||||||||||| ||||| ||||| ||||||||||||
gtatcctgcatctttctttacatttgtagacccttgt--cttttaata-tacttcaggtggggtggagaaaatttattagttagtttcttcatgtcgtttcagCTGAAGGAATACATTGATGACACAGAAGATTTCATTAACATTCAGCTG

upper sequence: GRMZM2G170326_T02 (Zea mays), 3'ss of exon 3
lower sequence: PP1S423_14V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------------------------gtaccaagcc---atatcaccagcatgtcttaaatctggttacgtataataatactgcaataggagtcaaaggggtctgatctatttttacttctttcagCTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTG
                                                                                     | |    |     |||||  |  |||    | |    | ||| ||    |   |     || |         | |     | | |  |   | | | ||| | || ||||| || ||||||||||| |||||||||||||| ||||||
gtagctatccatccatcccccccccttttttttttttttttttttttttttttttgtgtgtgtgtgtgtgtgtgttaatgggctggcaatgggtttatatatcgtct-cattctctgaggacgtttaggtcctttttcaacatcatggacacatggagtgatgcgtttgtggtggatgcatgcagTTGAAGGAGTATATAGATGACACTGAGGACTTCATCAACATACAGCTG

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|78104709|gb|DV523127.1|DV523127
EST:     GGGAGCTTATTTCGTTGTTATCGACAGCACTCTCAAACA-GCTGACATCG                         CTTAAAGAGTACATTGATGACACTG
genomic: GGAAGCTTATTTCGTTGTTATCGACAGCACTCTCAA-CAAGCTGACATCGgtaccaagcc ... cttctttcagCTTAAAGAGTACATTGATGACACTG
EST: gi|5847172|gb|AW000251.1|AW000251
EST:     TGGAAGCTTATTTCGTTGNTATCGACAGCACTCTCAACAAGCTGACATCG                         CTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTGGAC
genomic: TGGAAGCTTATTTCGTTGTTATCGACAGCACTCTCAACAAGCTGACATCGgtaccaagcc ... cttctttcagCTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTGGAC
EST: gi|5847068|gb|AW000147.1|AW000147
EST:     TGGAAGCTTATTTCGTTGTTATCGACAGCACTCTCAACAAGCTGACATCG                         CTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTG
genomic: TGGAAGCTTATTTCGTTGTTATCGACAGCACTCTCAACAAGCTGACATCGgtaccaagcc ... cttctttcagCTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTG

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), 40 (downstream exon)
Score: 23

GAGCTCCGATAACACAACGACAGATCATATCCAAGAGTTGGAGATGTTACTGGAAGCTTATTTCGTTGTTATCGACAGCACTCTCAACAAGCTGACATCGgtaccaagcc ... cttctttcagCTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 14

GAGCTCCGATAACACAACGACAGATCATATCCAAGAGTTGGAGATGTTACTGGAAGCTTATTTCGTTGTTATCGACAGCACTCTCAACAAGCTGACATCGgtaccaagcc ... cttctttcagCTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 27

GAGCTCCGATAACACAACGACAGATCATATCCAAGAGTTGGAGATGTTACTGGAAGCTTATTTCGTTGTTATCGACAGCACTCTCAACAAGCTGACATCGgtaccaagcc ... cttctttcagCTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 19

GAGCTCCGATAACACAACGACAGATCATATCCAAGAGTTGGAGATGTTACTGGAAGCTTATTTCGTTGTTATCGACAGCACTCTCAACAAGCTGACATCGgtaccaagcc ... cttctttcagCTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataataatactgcaataggagtcaaaggggtctgatctatttttacttctttcagCTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTG
                             gtctgat  putative branch site (score: 19)
                                   tctatttttacttctt  CT-rich tract
                                     tatttttacttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccaagccatatcaccagcatgtcttaaatctggttacgtataataatactgcaataggagtcaaaggggtctgatctatttttacttctttcagCTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG