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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caacgaaatagtgagtaatgtcaagtagtattccattatatcatttaatgtcaataatgtgaagttatgaatgtcactaataacgaaatttcatttgtagGTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATCTTCTGGAACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCA

Basic information

species Zea mays
transcript GRMZM2G020976_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020976_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g40030.1 (Oryza sativa), 3'ss of exon 7
caacgaaatagtgagtaatg--tcaagtagtattccattatatc-atttaatgtcaataatgtgaa-gttatgaatgtcactaataacgaaatttcatttgtagGTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATCTTCTGGAACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCA
  ||  |||  ||  |  |   |  ||| |         | ||| |  |  ||| | |  |  ||| | ||| ||| |||   || | |  ||| |  |||||||  ||||| ||||| ||||||||  |||| ||||| || |||||||| ||||||||||| ||||||||||||||||||||||||||||| |||||||| |
--acacaatcatgcctgttcacttcagtggaggagtgacacatccaacttctgttattcttcagaaagctatcaatatcat--atgatgttattccgattgtagGCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATCTTCTGGAATACAATCCTGAATTCTGCACTCACACAATCGATGTGTGGTA
















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|74233566|gb|DT641480.1|DT641480
EST:     ACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAG                         GTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATC
genomic: ACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAGgtaacattgg ... tcatttgtagGTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATC
EST: gi|31353270|gb|CD437627.1|CD437627
EST:     ACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAG                         GTTGTGCTTCTATTTTCGTGCATCTTAGCATTTCTACTGAACTACACCATC
genomic: ACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAGgtaacattgg ... tcatttgtagGTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATC
EST: gi|78115508|gb|DV533896.1|DV533896
EST:     ACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAG                         GTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATC
genomic: ACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAGgtaacattgg ... tcatttgtagGTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATC
EST: gi|71420100|gb|DR805010.1|DR805010
EST:     ACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAG                         GTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATC
genomic: ACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAGgtaacattgg ... tcatttgtagGTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATC
EST: gi|110210988|gb|EC892885.1|EC892885
EST:     CATGGAATTTTCCATCCCTTCATTCTCTGGGGTTTCAG                         GTTGTGCTTTTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATC
genomic: CATGGAA-TTTCCATACCTTCATTCTCTTGGGTTTCAGgtaacattgg ... tcatttgtagGTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATC
EST: gi|40303781|gb|CK348168.1|CK348168
EST:     ACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAG                         GTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATC
genomic: ACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAGgtaacattgg ... tcatttgtagGTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATC
EST: gi|71298000|gb|DR784969.1|DR784969
EST:     CCTAAAGAGGACCATGGAATTTCCATACCTTCATTTCTCTTGGGTTTCAG                         GTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATC
genomic: CCTAAAGAGGACCATGGAATTTCCATACCTTCA-TTCTCTTGGGTTTCAGgtaacattgg ... tcatttgtagGTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATC
EST: gi|31355902|gb|CD440259.1|CD440259
EST:     ACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAG                         GTTGTGCTTCTATTTTCGTGCATCTTAGCATTTCTACTGAACTACACCATC
genomic: ACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAGgtaacattgg ... tcatttgtagGTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATC
EST: gi|89760089|gb|DY688655.1|DY688655
EST:     ACCTAAAGAGGACCATGGAATTTCCATACCTTCATTTTCTTGGGTTTCAG                         GTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATC
genomic: ACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAGgtaacattgg ... tcatttgtagGTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATC

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: 48 (upstream exon), 42 (downstream exon)
Score: 51

GTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAGgtaacattgg ... tcatttgtagGTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATCTTCTGGAACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 165

GTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAGgtaacattgg ... tcatttgtagGTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATCTTCTGGAACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 323

GTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAGgtaacattgg ... tcatttgtagGTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATCTTCTGGAACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 136

GTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAGgtaacattgg ... tcatttgtagGTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATCTTCTGGAACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgtcaataatgtgaagttatgaatgtcactaataacgaaatttcatttgtagGTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATCTTCTGGAACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCA
                                taataac  putative branch site (score: 136)
                                           tttcattt  putative PPT
                                taataacgaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caacgaaatagtgagtaatgtcaagtagtattccattatatcatttaatgtcaataatgtgaagttatgaatgtcactaataacgaaatttcatttgtagGTTGTGCTTCTATTTTCATGCATCTTAGCATTTCTACTGAACTACACCATCTTCTGGAACACAATCCTGAATTCTGCACTCACACAATCTATGTGTGGCA

caacgaa
-aacgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgaatg