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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacataatctgttcagataatttgtgaaatgctttcatgcctttccatttgaagtggcaaacggtaatttgttgattttggctcatttattgtgtttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTACCAGCTTGAAGATCTTGAAATCGTTTCTGCTGATTATATGTTGAAGGTGG

Basic information

species Zea mays
transcript GRMZM2G178618_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 3'ss of exon 16
cacataatctgttcagataatttgtgaaatgctttcatgcctt----tccatttgaagtggcaaacggtaatttgttgattttggctcatt--tattgtgtttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTACCAGCTTGAAGATCTTGAAATCGTTTCTGCTGATTATATGTTGAAGGTGG
    |||| | ||    |  ||   || ||  ||      ||     | || |||| |  | | |||||  ||   || ||||   | | |   | |||||||||||||||||||||||| ||||||||||| |||||||| || |||||||||||||||||||||||||| |||||   |||||||||||||||||||||||| |
----taatattttttattccttgaggagattattatgcatctacatgttcagttgatgcagtagacggt--ttgactggttttatttaactggaactgtgtttcagGTTGATCCATCCACAGGTGAAGCTGATGATGATGGCGTTGAGGATGAGTACCAGCTTGAAGATCTGGAAATTACTTCTGCTGATTATATGTTGAAGGTTG

upper sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 16
-----------------------------------------------------cacataatc-tgttcagat---aattt----gtgaaa--tgctttcatgcctttccatttg--aagtggcaaacggtaatttgt--tgattttg------gctcatttattg------------tgtttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTACCAGCTTGAAGATCTTGAAATCGTTTCTGCTGATTATATGTTGAAGGTGG
                                                       ||| ||  |||| | ||   ||||     |||||   || ||| ||   ||||  || |  || | |   |   |||  | |  |  |||||       ||||| | | |            |  |||||||||| ||| |||| ||||| |||||||||||||||||||| ||||| |||||||| || ||||| || || ||| | || |||||  ||||||| ||||
gtattatcctctcttttttttttctgaacctttctggttttttattatttcatgtcatgattatgtttatattataattcaagcgtgaagcttgtttttatatttttcatttagggaatttgtggaaaataacctataatatttttgtagcaaactcatctctagattaactggatcttcttcagGTTGACCCAACCACTGGTGAGGCTGAAGATGATGGTGTCGAAGATGAATACCAGCTGGAGGATCTGGAGATTGTTGCAGCAGATTACGTGTTGAAAGTGG

upper sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 16
---------------------------------------------------cacataatc-tgttcagat---aatttg----tgaaa--tgctttcatgcctttccattt---gaagtggcaaacggtaatttgttg-attttgg-------ctcatttattg------------tgtttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTACCAGCTTGAAGATCTTGAAATCGTTTCTGCTGATTATATGTTGAAGGTGG
                                                     ||| ||  |||| | ||   ||||      ||||   || ||| ||   ||| |||||   ||| | |   |   |||| | |   ||||| |       ||||| | | |            |  |||||||||| ||| |||||||||| ||||||||||| ||||| || ||||| |||||||| || ||||| || || ||| | || |||||| ||||||| ||||
gtattatcctctttatttttgtgaagctttctggtttttttattatttgatatcatgattatgtttatattataattcaagcttgaagcttgtttttat-ttttttcatttagggaatttgtggaaaataatctataatatttttgtagcaatctcatctctagataaactgaatcttcttcagGTTGACCCAACCACGGGTGAGGCTGAAGATGACGGTGTTGAAGATGAATACCAGCTGGAGGATCTGGAGATTGTTGCAGCAGATTATGTGTTGAAAGTGG

upper sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 16
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 15
---------------------------------------------------------------------------------------caca-taatctgttcagata--atttgtgaaatgctttcatgcctttccatttgaagtggcaaacggt---aatttgttgattttggctcatttattgtgttt---cagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTACCAGCTTGAAGATCTTGAAATCGTTTCTGCTGATTATATGTTGAAGGTGG
                                                                                        |||   |    ||  || |  | |     || |  |  |     |  ||    |    | ||||  |   | |   ||| || ||  |   | | ||||||    |||||||| |||  ||| |||||||| ||||||||||| || || |||||||||||||| || ||||||||  | ||  |||  ||||| ||| |||| ||||
gtacatgttaaataggctattcacttccatctttttatttacttacactgaaaatgaccccataatactttgtggagaactcttataaacaacgactcatttggagaggagtaccagaacgactcaaattaatcacagaaaacaaagaaaactctctaactacattgtttgtgcttttatgaatgtgttaaaacagGTTGACCCAAGCACAGGTGAAGCAGAAGATGATGGAGTAGAAGATGAGTACCAGCTAGAGGATCTTGAGGTTGTAGCTGGAGATTACATGGTGAAAGTGG

upper sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 16
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 16
cacataatctgttcagataatttgtgaaatgctttcatgcctttccatttgaagt-ggcaaacggtaatttgttgattttggctcatttattgtgt-----ttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTACCAGCTTGAAGATCTTGAAATCGTTTCTGCTGATTATATGTTGAAGGTGG
|| |||        |  ||   |     |||||| ||| |   |  | |         ||||   |  |   | | |||   |   | | |||| |     | |||||||||||| | || |||||  | || || ||||||||||| || || |||||||| || || |||||| | ||| | ||||||||| |||||||||| |
caaataga------aattacactagaggatgcttccatactgatgaactaatctccaacaaaaaattctacatggttttcatcatgtgttttgtttatatttccagGTTGATCCAACTACTGGTGAGACAGAGGAAGATGGTGTCGAAGACGAATACCAGCTGGAGGACCTTGAAGTTGTTGCAGCTGATTATGTGTTGAAGGTTG

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|74235980|gb|DT643894.1|DT643894
EST:     TCATTGCCACCGGCAAGTTCTCAAATATCCTGAAATTCTTTGTTAAGGAG                         GTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTAC
genomic: TCATTGCCACCGGCAAGTTCTCAAATATCCTGAAATTCTTTGTTAAGGAGgtatgtgttt ... tgtgtttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTAC
EST: gi|40334153|gb|CK368223.1|CK368223
EST:     TTATTGCCACCGGCAAGTTCTCAAATATCCTGAAATTTTTTGTTAAGGAG                         GTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTAC
genomic: TCATTGCCACCGGCAAGTTCTCAAATATCCTGAAATTCTTTGTTAAGGAGgtatgtgttt ... tgtgtttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTAC
EST: gi|71773316|gb|DR971224.1|DR971224
EST:     TCATTGCCACCGGCAAGTTCTCAAATATCCTGAAATTCTTTGTTAAGGAG                         GTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTAC
genomic: TCATTGCCACCGGCAAGTTCTCAAATATCCTGAAATTCTTTGTTAAGGAGgtatgtgttt ... tgtgtttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTAC
EST: gi|211418624|gb|FK952670.1|FK952670
EST:     AAATATCCTGAAATTCTTTGTTAAGGAG                         GTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTAC
genomic: AAATATCCTGAAATTCTTTGTTAAGGAGgtatgtgttt ... tgtgtttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTAC
EST: gi|31364677|gb|CD449032.1|CD449032
EST:     TCATTGCCACCGGCAAGTTCTCATATATCCTGACATTCTTTGGTAAGGAG                         GTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTAC
genomic: TCATTGCCACCGGCAAGTTCTCAAATATCCTGAAATTCTTTGTTAAGGAGgtatgtgttt ... tgtgtttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTAC
EST: gi|7162448|gb|AW520070.1|AW520070
EST:     TCATTGCCACCGGCAAGTTCTCAAATATCCTGAAATTCTTTGTTAAGGAG                         GTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTAC
genomic: TCATTGCCACCGGCAAGTTCTCAAATATCCTGAAATTCTTTGTTAAGGAGgtatgtgttt ... tgtgtttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTAC
EST: gi|50337423|gb|CO532549.1|CO532549
EST:     GCCACCGGCAAGTTCTCAAATATCCTGAAATTCTTTGTTAAGGAG                         GTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTAC
genomic: GCCACCGGCAAGTTCTCAAATATCCTGAAATTCTTTGTTAAGGAGgtatgtgttt ... tgtgtttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTAC
EST: gi|211418626|gb|FK952672.1|FK952672
EST:     TCATTGCCACCGGCAAGTTCTCAAATATCCTGAAATTCTTTGTTAAGGAG                         GTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTAC
genomic: TCATTGCCACCGGCAAGTTCTCAAATATCCTGAAATTCTTTGTTAAGGAGgtatgtgttt ... tgtgtttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTAC

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), 49 (downstream exon)
Score: 262

ATATGATTCTCCTGGGCAGACCTTTGTGGCTTTTGAAAATCCAGAAGGTGTCATTGCCACCGGCAAGTTCTCAAATATCCTGAAATTCTTTGTTAAGGAGgtatgtgttt ... tgtgtttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTACCAGCTTGAAGATCTTGAAATCGTTTCTGCTGATTATATGTTGAAGGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 225

ATATGATTCTCCTGGGCAGACCTTTGTGGCTTTTGAAAATCCAGAAGGTGTCATTGCCACCGGCAAGTTCTCAAATATCCTGAAATTCTTTGTTAAGGAGgtatgtgttt ... tgtgtttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTACCAGCTTGAAGATCTTGAAATCGTTTCTGCTGATTATATGTTGAAGGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 277

ATATGATTCTCCTGGGCAGACCTTTGTGGCTTTTGAAAATCCAGAAGGTGTCATTGCCACCGGCAAGTTCTCAAATATCCTGAAATTCTTTGTTAAGGAGgtatgtgttt ... tgtgtttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTACCAGCTTGAAGATCTTGAAATCGTTTCTGCTGATTATATGTTGAAGGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

ATATGATTCTCCTGGGCAGACCTTTGTGGCTTTTGAAAATCCAGAAGGTGTCATTGCCACCGGCAAGTTCTCAAATATCCTGAAATTCTTTGTTAAGGAGgtatgtgttt ... tgtgtttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTACCAGCTTGAAGATCTTGAAATCGTTTCTGCTGATTATATGTTGAAGGTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttgaagtggcaaacggtaatttgttgattttggctcatttattgtgtttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTACCAGCTTGAAGATCTTGAAATCGTTTCTGCTGATTATATGTTGAAGGTGG
                        tgttgat  putative branch site (score: 283)
                   taatttgttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacataatctgttcagataatttgtgaaatgctttcatgcctttccatttgaagtggcaaacggtaatttgttgattttggctcatttattgtgtttcagGTTGATCCATCCACGGGTGAAGCTGAAGATGATGGTGTCGAGGATGAGTACCAGCTTGAAGATCTTGAAATCGTTTCTGCTGATTATATGTTGAAGGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - tgaaatg
- - - - - - - - - - - - - - - - -ttcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgat