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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcatctagtcttatatgtatttttattaattcctttcatatatcttttcttaatcatgtgaacagattgtttacattttgccttctctatgtgcacagGAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAA

Basic information

species Zea mays
transcript GRMZM2G170532_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170532_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g14510.2 (Oryza sativa), 3'ss of exon 3
aatcatctagtcttatatgtatttttattaattcctttcatatatcttttcttaatcatgtgaacagattgtttacattttgccttctctatgtgcacagGAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAA
    ||  |        |    ||||   |||     |  |  || ||||||  ||  | | || || ||||||| ||||      ||   | | ||||||| |||||  |||||||||||||||| |||||||| |||||||||||||||||||| ||||| ||
--gtataaaaaaaatcttcctcttttgcaaatcttcattgt-cattttttctgtattgtctcaagaggttgtttatatttg-----cttggtatacacagGAAAAGAACCGGATAAATAAAGATGGGGAGCTTGTGATATCTTCTACAAAAACTAGGACACAAAA

upper sequence: GRMZM2G170532_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G62850.3 (Arabidopsis thaliana), 3'ss of exon 3
aatcatctagtcttatatgtatttttattaattcctttcatatatct--tttcttaatcatgtgaacagattgtttacattttgccttctctatgtgcacagGAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAA
   |   |  |||  |  |       ||| |      |    ||| |   || ||  |  | ||    |  |  |||  ||||   || | |  ||  ||||||||||||| |||| || || ||||| || ||||| ||||||||||| ||||| ||||| |||||
tgactcttgatctggttggggccaaaatttaggataatagagtatttggctttttgtttctatgcgttgtgtagttagcttttttgttgttt--gtcaacagGAGAAGAATCGGATCAACAAGGATGGTGAACTTGTGATATCTTCTACCAAAACCAGAACGCAGAA

upper sequence: GRMZM2G170532_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv02s0241g00090.t01 (Vitis vinifera), 3'ss of exon 4
aatcatctagtcttatatgtatttttattaattcctttcatatatcttttcttaatcatgtgaacagattgtttacatt-ttgccttctcta--tgtgcacagGAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAA
  | || |  | || |   ||||||  |||  |    |    | || ||| ||    |  | | |    | |   | || ||| |||  |||  | || |||||| |||||| |||| || |||||||| ||| |||| || ||||| ||||||||||||||||||||
--ttattttttgtttttactattttatttatataaaattgggtctcgtttattgcctactt-atctttctatgagctttgttgactttcctagttatgaacagGAAAAGAATCGGATTAACAAAGATGGGGAGATTGTGATTTCTTCAACAAAAACTAGAACACAGAA

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|18164644|gb|BM334483.1|BM334483
EST:     AGGAAGCTCACTGGCTTGGGGAGAGAATCAAGGAACGGATATTACAAGCG                         GAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAA
genomic: AGGAAGCTCACTGGCTTGGGGAGAGAATCAAGGAACGGATATTACAAGCGgtaaaagaga ... atgtgcacagGAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAA
EST: gi|18168069|gb|BM337909.1|BM337909
EST:     AGGAAGCTCACTGGCTTGGGAAAAGAATCAAGGAACGGATATTACAAGCG                         GAGAAGAATAGGATAAATAAAGATGGAGAGCTGTGTTATATCTTCTACAAA
genomic: AGGAAGCTCACTGGCTTGGGGAGAGAATCAAGGAACGGATATTACAAGCGgtaaaagaga ... atgtgcacagGAGAAGAATAGGATAAATAAAGATGGAGAGCT-TGTTATATCTTCTACAAA
EST: gi|18166092|gb|BM335931.1|BM335931
EST:     AGGAAGCTCACTGGCTTGGGGAGAGAATCAAGGAACGGATATTACAAGCG                         GAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATAGTCTTCTACAAA
genomic: AGGAAGCTCACTGGCTTGGGGAGAGAATCAAGGAACGGATATTACAAGCGgtaaaagaga ... atgtgcacagGAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATA-TCTTCTACAAA
EST: gi|18173601|gb|BM348989.1|BM348989
EST:     AGGAAGCTCACTGGAAAAAGAAGAGAATCAAGGAACGGATATTACAAGCG                         GAGAAGAATAGGATAAATAAAGATGGAGAGCTTGATTATATCTTCTACAAA
genomic: AGGAAGCTCACTGGCTTGGGGAGAGAATCAAGGAACGGATATTACAAGCGgtaaaagaga ... atgtgcacagGAGAAGAATAGGATAAATAAAGATGGAGAGCTTG-TTATATCTTCTACAAA
EST: gi|18175793|gb|BM350979.1|BM350979
EST:     AGGAAGCTCACTGGCTTGGGGAGAGAATCAAGGAACGGATATTACAAGCG                         GAGAAGAATAGGATAAATAAAGATGGAGAGCTTGGTTATATCTTCTACAAA
genomic: AGGAAGCTCACTGGCTTGGGGAGAGAATCAAGGAACGGATATTACAAGCGgtaaaagaga ... atgtgcacagGAGAAGAATAGGATAAATAAAGATGGAGAGCTTG-TTATATCTTCTACAAA
EST: gi|18175280|gb|BM350651.1|BM350651
EST:     AGGAAGCTCACTGGAAAGAGAAGAGAATCAAGGAACGGATATTACAAGCG                         GAGAAGAATAGGATAAATAAAGATGGAGAGCTTGGTTATATCTTCTACAAA
genomic: AGGAAGCTCACTGGCTTGGGGAGAGAATCAAGGAACGGATATTACAAGCGgtaaaagaga ... atgtgcacagGAGAAGAATAGGATAAATAAAGATGGAGAGCTTG-TTATATCTTCTACAAA
EST: gi|17931962|gb|BM268922.1|BM268922
EST:     AGGAAGCTCACTGGCTTGGGGAGAGAATCAAGGAACGGATATTACAAGCG                         GAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATTCTTCTACAAA
genomic: AGGAAGCTCACTGGCTTGGGGAGAGAATCAAGGAACGGATATTACAAGCGgtaaaagaga ... atgtgcacagGAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATAT-CTTCTACAAA
EST: gi|17931672|gb|BM268632.1|BM268632
EST:     AGGAAGCTCACTGGCTTGGGGAGAGAATCAAGGAACGGATATTACAAGCG                         GAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATAATCTTCTACAAA
genomic: AGGAAGCTCACTGGCTTGGGGAGAGAATCAAGGAACGGATATTACAAGCGgtaaaagaga ... atgtgcacagGAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATA-TCTTCTACAAA

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), 42 (downstream exon)
Score: 87

TTAACACAAAGGTTGACATGCGATTCAATGTTAAGGAAGCTCACTGGCTTGGGGAGAGAATCAAGGAACGGATATTACAAGCGgtaaaagaga ... atgtgcacagGAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 171

TTAACACAAAGGTTGACATGCGATTCAATGTTAAGGAAGCTCACTGGCTTGGGGAGAGAATCAAGGAACGGATATTACAAGCGgtaaaagaga ... atgtgcacagGAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAA


Block sizes: 42 (upstream exon), 38 (downstream exon)
Score: 57

TTAACACAAAGGTTGACATGCGATTCAATGTTAAGGAAGCTCACTGGCTTGGGGAGAGAATCAAGGAACGGATATTACAAGCGgtaaaagaga ... atgtgcacagGAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 156

TTAACACAAAGGTTGACATGCGATTCAATGTTAAGGAAGCTCACTGGCTTGGGGAGAGAATCAAGGAACGGATATTACAAGCGgtaaaagaga ... atgtgcacagGAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttcttaatcatgtgaacagattgtttacattttgccttctctatgtgcacagGAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAA
    tcttaat  putative branch site (score: 156)
                                ttttgccttctctat  putative PPT
                      attgtttacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcatctagtcttatatgtatttttattaattcctttcatatatcttttcttaatcatgtgaacagattgtttacattttgccttctctatgtgcacagGAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - atatgta
- - - - - - - - - - - - - - - - - - ttcatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtga