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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatgtaaaaaatcatgtaaacataacccttatcacaaaatggtcggttgtgttatccagttttcacattcgcatttaataccttcatctttggatgcagGCATTGATCCTGGCTAGGCTTCTTGGGCAACAGATAAGCATGGAGAGTATCAAT

Basic information

species Zea mays
transcript GRMZM2G151977_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151977_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g03470.1 (Oryza sativa), 3'ss of exon 8
ttatgtaaaaaa---tcatgt--aaacataacccttatcacaaaatggtcggttgtgttatccagttttcacattcgcatttaataccttcatctttggatgcagGCATTGATCCTGGCTAGGCTTCTTGGGCAACAGATAAGCATGGAGAGTATCAAT
  |  |||   |   | ||||  |     |    || |     | |  |   || | || || |  ||  |   |    | ||| |  |||||||| | ||||||||||||||| | ||||||||||| ||||||||||| |||||||||| ||| |||
--acataagggaggtttatgttcaggttcagatgttttatttgattatttcattct-ttgtcaa--ttagatgatgaggtctaacaagttcatcttggaatgcagGCATTGATCTTAGCTAGGCTTCTGGGGCAACAGATTAGCATGGAGAATATTAAT

upper sequence: GRMZM2G151977_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os12g03190.1 (Oryza sativa), 3'ss of exon 8
ttatgtaaaaaatc-atgt--aaacataacccttatcacaaaatggtcggttgtgttatccagttttcacattcgcatttaataccttcatctttggatgcagGCATTGATCCTGGCTAGGCTTCTTGGGCAACAGATAAGCATGGAGAGTATCAAT
  ||     |  |  ||||  |     |    || |     | |  |   || | || || |  ||      |    | ||| |  |||||||||| ||||||||||||||| | ||||||||||| ||||||| ||| |||||||||| ||| |||
gcataagggaggtttatgttcaggttcagatgttttatttgattatttcattct-ttgtcaa--ttaggtgatgaggtctaacaagttcatctttgaatgcagGCATTGATCTTAGCTAGGCTTCTGGGGCAACGGATCAGCATGGAGAATATTAAT
















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|86473774|gb|DY240144.1|DY240144
EST:     CAGAACCAGATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAG                         GCATTGATCCTGGCTAGGCTTCTTGGGCAACAGATAAGCATGGAGAGTATC
genomic: CAGAACCAGATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAGgttagatacc ... ttggatgcagGCATTGATCCTGGCTAGGCTTCTTGGGCAACAGATAAGCATGGAGAGTATC
EST: gi|32803400|gb|CD955636.1|CD955636
EST:     GATCCACGTGATGATCTTGGTGGAATGGATGTGGCTAGAAAG                         GCATTGATCCTGGCTAGGCTTCTTGGGCAACAGATAAGCATGGAGAGTATC
genomic: GATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAGgttagatacc ... ttggatgcagGCATTGATCCTGGCTAGGCTTCTTGGGCAACAGATAAGCATGGAGAGTATC
EST: gi|148944776|gb|EC889918.2|EC889918
EST:     ATCCACGTGATGATCTAGGTGGGATGGATGTCGCTAGAAAG                         GCATTGATCCTGGCTAGGCTTCTTG
genomic: ATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAGgttagatacc ... ttggatgcagGCATTGATCCTGGCTAGGCTTCTTG
EST: gi|31361610|gb|CD445967.1|CD445967
EST:     ATCCACGTGATGATCTTGGTGGAATGGATGTGGCTAGAAAG                         GCATTGATCCTGGCTAGGCTTCTTGGGCAACAGATAAGCATGGAGAGTATC
genomic: ATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAGgttagatacc ... ttggatgcagGCATTGATCCTGGCTAGGCTTCTTGGGCAACAGATAAGCATGGAGAGTATC
EST: gi|148936622|gb|EC880746.2|EC880746
EST:     ATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAAG                         G-ATTGATCCTGGCTAGG
genomic: ATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAA-Ggttagatacc ... ttggatgcagGCATTGATCCTGGCTAGG
EST: gi|40334075|gb|CK368145.1|CK368145
EST:     ATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAG                         GCATTGATCCTGGCTAGGCTTCTTGGGCAACAGATAAGCATGGAGAGTATC
genomic: ATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAGgttagatacc ... ttggatgcagGCATTGATCCTGGCTAGGCTTCTTGGGCAACAGATAAGCATGGAGAGTATC

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: 37 (upstream exon), 49 (downstream exon)
Score: 85

ATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAGgttagatacc ... ttggatgcagGCATTGATCCTGGCTAGGCTTCTTGGGCAACAGATAAGCATGGAGAGTATCAAT


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 100

ATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAGgttagatacc ... ttggatgcagGCATTGATCCTGGCTAGGCTTCTTGGGCAACAGATAAGCATGGAGAGTATCAAT


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 65

ATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAGgttagatacc ... ttggatgcagGCATTGATCCTGGCTAGGCTTCTTGGGCAACAGATAAGCATGGAGAGTATCAAT


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 88

ATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAGgttagatacc ... ttggatgcagGCATTGATCCTGGCTAGGCTTCTTGGGCAACAGATAAGCATGGAGAGTATCAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttgtgttatccagttttcacattcgcatttaataccttcatctttggatgcagGCATTGATCCTGGCTAGGCTTCTTGGGCAACAGATAAGCATGGAGAGTATCAAT
                            atttaat  putative branch site (score: 88)
                                    ccttcatcttt  CT-rich tract
                            atttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatgtaaaaaatcatgtaaacataacccttatcacaaaatggtcggttgtgttatccagttttcacattcgcatttaataccttcatctttggatgcagGCATTGATCCTGGCTAGGCTTCTTGGGCAACAGATAAGCATGGAGAGTATCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - aaaaaat
- - - - - - -catgtaa
- - - - - - - - - - - - - - - -atcacaa
- - - - - - - - - - - - - - - - - - - - - - - -ttgtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacattc