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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttttgcttttgtcactgccatgccacttgaatgatcatccaactaatcacttccagttcgcttggttcttctaatctttactagtgtatgtcactacatggattaatggactgctaatttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACAAAGAAATTCGAGAAGTTAATTACTGATAAGAAAGAAATTGAGGGTTTAC

Basic information

species Zea mays
transcript GRMZM2G133919_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g58340.1 (Oryza sativa), 3'ss of exon 4
gtgagttttgcttttgtcactgccatgccacttgaatgatcatccaactaatcacttccagttcgcttggttcttctaatctttactagtgtatgtcactacatggattaatggactgctaatttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACAAAGAAATTCGAGAAGTTAATTACTGATAAGAAAGAAATTGAGGGTTTAC
                |      ||||  ||||   || |||| |   || | | || |  |    ||||        || ||| ||  || || | |        ||||||||| |||||| |||||||||||||||||| ||  | ||||||||||| |||||||||||||||||||| || |||||||| ||||| ||||||||||||||||| |||||||| || ||||
---------------attctcttcatgttacttttttgttcatgc--ttatttattttctttatttttgg--------atgtttgctgatgcatatta--------attaatggaatgctaacttcatttcagGAGCTTGAGAAGTTAACACAAAAGTTCAGTGAAAATGTGCTGGATGCAACTAAGAAATTTGAGAAATTAATTACTGATAAGAATGAAATTGATGGGTTAC

upper sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA01G02480.1 (Glycine max), 3'ss of exon 4
gtgagttttgcttttgtcactgccatgccacttgaatgatcatccaactaatcacttccagttcgcttggttcttctaatctttactagtgtatgtcactacatggattaatggactgctaatttcattt-cagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACAAAGAAATTCGAGAAGTTAATTACTGATAAGAAAGAAATTGAGGGTTTAC
                        | || |  ||| ||  | ||  |  | | |     | |||  ||  |  ||||  |||||       |||||   |   |   ||  ||   |  | |||||||    ||||||| |||||  |  ||||||||||| | |||||||| |||||||| |||||||| || || ||| |||| ||||||||||  |||||||| || ||||
----------------------agaagcaaactgattggacttc--ataacttaacaaaatttcaattaatggttcttttcttt-------tatgtttattttttattttctg---tcttgatttcatccatagGAGCTGGAAAAGTTATCACAAAAGTTTGGGGAAAATGTTCTGGATGCAACAAAGAAGTTTGAAAAGCTAATCACTGATAAGACGGAAATTGAAGGATTAC

upper sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 4
gtgagttttgcttttgtcactgccatgccacttgaatgatcatccaactaatcacttccagttcgcttggttcttctaatctttactagtgtatgtcactacatggattaatggactgctaatttcattt-cagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACAAAGAAATTCGAGAAGTTAATTACTGATAAGAAAGAAATTGAGGGTTTAC
                        | || |  ||| ||  | ||  |  | | |     | |||  ||  |  | |   ||| |         | |   ||  |  |||   || |  || |||| ||    ||||||| |||||  |  ||||||||||| | || ||||| |||||||| |||||||| || || ||| |||| ||||||||||| |||||||| || ||||
---------------------cagaagcaaagtgattggacttc--ataacttaacagaatttcaattaatggtgcatttctct---------tatttttatttttattttcggtc--ctgattttatccatagGAGCTGGAAAAGTTATCACAAAAGTTTGGGGAGAATGTTCTGGATGCAACAAAGAAGTTTGAAAAGCTAATCACTGATAAGAAGGAAATTGAAGGATTAC

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|211451544|gb|FL256607.1|FL256607
EST:     GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTA-CCAAATCGAACAA                         GAGCTTGAAAAACTGACACAAAAGTTTAGCGAAAATGTGCTGGATGCC
genomic: GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAAgtgagttttg ... ttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCC
EST: gi|149009256|gb|EE041351.2|EE041351
EST:     GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAA                         GAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACA
genomic: GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAAgtgagttttg ... ttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACA
EST: gi|74240585|gb|DT648499.1|DT648499
EST:     GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAA                         GAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACA
genomic: GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAAgtgagttttg ... ttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACA
EST: gi|148950560|gb|EC896140.2|EC896140
EST:     GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAA                         GAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCAC
genomic: GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAAgtgagttttg ... ttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCAC
EST: gi|29544636|gb|CB605016.1|CB605016
EST:     GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAA                         GAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGAT
genomic: GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAAgtgagttttg ... ttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGAT
EST: gi|148960061|gb|EE153304.2|EE153304
EST:     GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAA                         GAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACA
genomic: GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAAgtgagttttg ... ttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACA
EST: gi|149072691|gb|EE160926.2|EE160926
EST:     GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAA                         GAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACA
genomic: GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAAgtgagttttg ... ttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACA
EST: gi|76020481|gb|DT947651.1|DT947651
EST:     GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAA                         GAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCCCA
genomic: GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAAgtgagttttg ... ttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACA
EST: gi|71437686|gb|DR818736.1|DR818736
EST:     GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAA                         GAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACA
genomic: GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAAgtgagttttg ... ttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACA
EST: gi|148956895|gb|EC902819.2|EC902819
EST:     GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAA                         GAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACA
genomic: GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAAgtgagttttg ... ttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACA
EST: gi|31354902|gb|CD439259.1|CD439259
EST:     GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAA                         GAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACA
genomic: GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAAgtgagttttg ... ttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACA
EST: gi|148983362|gb|EE029348.2|EE029348
EST:     GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAA                         GAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACA
genomic: GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAAgtgagttttg ... ttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACA
EST: gi|149075398|gb|EE163912.2|EE163912
EST:     GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAA                         GAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACA
genomic: GAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAAgtgagttttg ... ttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACA

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: 32 (upstream exon), 47 (downstream exon)
Score: 229

CTCAAATAAAGGAAGCTGTTCTCAGTGGAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAAgtgagttttg ... ttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACAAAGAAATTCGAGAAGTTAATTACTGATAAGAAAGAAATTGAGGGTTTAC


Block sizes: 32 (upstream exon), 49 (downstream exon)
Score: 222

CTCAAATAAAGGAAGCTGTTCTCAGTGGAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAAgtgagttttg ... ttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACAAAGAAATTCGAGAAGTTAATTACTGATAAGAAAGAAATTGAGGGTTTAC


Block sizes: 32 (upstream exon), 49 (downstream exon)
Score: 283

CTCAAATAAAGGAAGCTGTTCTCAGTGGAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAAgtgagttttg ... ttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACAAAGAAATTCGAGAAGTTAATTACTGATAAGAAAGAAATTGAGGGTTTAC


Block sizes: 32 (upstream exon), 45 (downstream exon)
Score: 160

CTCAAATAAAGGAAGCTGTTCTCAGTGGAGTTGCACTTGAGGATGAACAAAGGAAGAAATTTAACCAAATCGAACAAgtgagttttg ... ttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACAAAGAAATTCGAGAAGTTAATTACTGATAAGAAAGAAATTGAGGGTTTAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctttactagtgtatgtcactacatggattaatggactgctaatttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACAAAGAAATTCGAGAAGTTAATTACTGATAAGAAAGAAATTGAGGGTTTAC
                                      tgctaat  putative branch site (score: 160)
                                            tttcatttc  CT-rich tract
                                         taatttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttttgcttttgtcactgccatgccacttgaatgatcatccaactaatcacttccagttcgcttggttcttctaatctttactagtgtatgtcactacatggattaatggactgctaatttcatttcagGAGCTTGAAAAACTGACACAAAAGTTTAGTGAAAATGTGCTGGATGCCACAAAGAAATTCGAGAAGTTAATTACTGATAAGAAAGAAATTGAGGGTTTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA