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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgagctgcttcaaccactttgcatgtgttcatggtagcgatacattttgattgatttgagaagttaacatataagcatattcttctgttcctctgcagGTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGTTTGTTCTTAATGAGAAGAGTGGAAAG

Basic information

species Zea mays
transcript GRMZM2G157462_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 14
gatgagctgcttcaaccactttgc---atgtgttcatggtagcgatacattttgattgatttga--gaagttaacatataagcatattct-tctgttcctctgcagGTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGTTTGTTCTTAATGAGAAGAGTGGAAAG
      |   || ||||| || |    |||      | ||   |   |||| | |   | |  |   || |  | ||||  |   ||| | |   ||  ||| ||||||||||||| |||||||| |||||||| ||||| ||||| |  || |||||||| || |||||||| || ||||||
------ccctttgaaccatttggtgaaatgaaacatttgttttgtctcattgtaaaaaagtacatgcaaatataaatattcgttaattttgtacatttttcttcagGTTACCTTTTGAAGAAAAGTGCAAAAACAAATGGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAG

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 14
gatgagctgc-ttcaaccactttgcatgtgttcatggtagcgatacattttgattgatttgagaa-gttaacata-taagcatattcttctgt-tcctctgcagGTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGTTTGTTCTTAATGAGAAGAGTGGAAAG
   |||||    | ||  || | | || ||    |   |  |   ||   |   |  ||  | |   |||| | | |||   || | |||| | |  | | |||| |   | ||||||||||| |||||||||||||| |||||||   |||||||||| || ||||| ||||  ||||||
---gagctatgcttaaatacat-gaatttggaagttacaatgtgccaaagtatatatttcaaaattattaataaactaaaactacttttctttattgttttcagGATTTTTATTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAAAAGACAGGAAAG

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 14
gatgagctgcttcaaccactttgcatgtgttcatggtagcgatacattttgattgatttgagaa-gttaacata-taagcatattcttctgt-tcctctgcagGTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGTTTGTTCTTAATGAGAAGAGTGGAAAG
 |     ||||| ||      || || ||    | |||  |   ||   |   |  ||  | |   |||| | | |||   || | |||| | |  | |||||| |   | ||||||||||| |||||||||||||| |||||||   |||||||||| || ||||||||||  ||||||
-agctaatgcttaaatg--catgaatttggaagttgtaatgtgccaaagtatatatttcaaaattattaataaactaaaactacttttctttattgtttgcagGATTTTTGTTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAGAAGACAGGAAAG

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 14
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 14
--gatgagctgcttcaaccactttgcatgtgttca--tggtagcgatacattttgattgatttgagaagttaacatataagcatattcttctgttcctctgcagGTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGTTTGTTCTTAATGAGAAGAGTGGAAAG
   ||||  |  |     |  |||     |  |||  |   |   |         | | | ||   | ||  | | | ||  |  ||  ||| ||| | |  ||| ||| |  | |||||||| |||||||| ||||||||||| |   ||||||||||||| |||||||| | |||||||
tgcatgatttcttcatgtctttttcttctttatcacttaaaactaacttgacaaaactaacttccaaggtagata-acaaatac-ttactcttttcattt--agGGTACTTAATGAAGAAAAGTGCAAAAACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAGAAAACTGGAAAG

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|31353959|gb|CD438316.1|CD438316
EST:     AGAGGGATCAAATTTGCAAGTTGCTGGTCCTGCTGGTGAAATTACTGCAG                         GTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGT
genomic: AGAGGGATCAAATTTGCAAGTTGCTGGTCCTGCTGGTGAAATTACTGCAGgtacgaaact ... tcctctgcagGTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGT
EST: gi|31354322|gb|CD438679.1|CD438679
EST:     AGAGGGATCAAATTTGCAAGTTGCTGGTCCTGCTGGTGAAATTACTGCAG                         GTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGT
genomic: AGAGGGATCAAATTTGCAAGTTGCTGGTCCTGCTGGTGAAATTACTGCAGgtacgaaact ... tcctctgcagGTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGT
EST: gi|7031283|gb|AW461021.1|AW461021
EST:     AATTACTGCAG                         GTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGT
genomic: AATTACTGCAGgtacgaaact ... tcctctgcagGTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGT

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: 230

AGCTTAAAATCAATGAAAGACAAATCTGGCCAGCAAGATAAAGACACAAAAGAGGGATCAAATTTGCAAGTTGCTGGTCCTGCTGGTGAAATTACTGCAGgtacgaaact ... tcctctgcagGTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGTTTGTTCTTAATGAGAAGAGTGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 330

AGCTTAAAATCAATGAAAGACAAATCTGGCCAGCAAGATAAAGACACAAAAGAGGGATCAAATTTGCAAGTTGCTGGTCCTGCTGGTGAAATTACTGCAGgtacgaaact ... tcctctgcagGTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGTTTGTTCTTAATGAGAAGAGTGGAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 314

AGCTTAAAATCAATGAAAGACAAATCTGGCCAGCAAGATAAAGACACAAAAGAGGGATCAAATTTGCAAGTTGCTGGTCCTGCTGGTGAAATTACTGCAGgtacgaaact ... tcctctgcagGTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGTTTGTTCTTAATGAGAAGAGTGGAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 259

AGCTTAAAATCAATGAAAGACAAATCTGGCCAGCAAGATAAAGACACAAAAGAGGGATCAAATTTGCAAGTTGCTGGTCCTGCTGGTGAAATTACTGCAGgtacgaaact ... tcctctgcagGTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGTTTGTTCTTAATGAGAAGAGTGGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttgattgatttgagaagttaacatataagcatattcttctgttcctctgcagGTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGTTTGTTCTTAATGAGAAGAGTGGAAAG
                  agttaac  putative branch site (score: 259)
                                  tattcttctgttcctc  putative PPT
                 aagttaacatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgagctgcttcaaccactttgcatgtgttcatggtagcgatacattttgattgatttgagaagttaacatataagcatattcttctgttcctctgcagGTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGTTTGTTCTTAATGAGAAGAGTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - -gctgctt
- - - - - - caaccac
- - - - - - - - - - -tgcatgt
- - - - - - - - - - - - - - gttcatg
- - - - - - - - - - - - - - - - - - - - - tacattt
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg