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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccccaatggttaagccgatctatctaggttaatttgctcatattatcaacagagttgatgaaggttccaaagatatgattttcttttttgcgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAG

Basic information

species Zea mays
transcript GRMZM2G177914_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177914_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g12710.1 (Oryza sativa), 3'ss of exon 4
-ccccaatggttaagccgatctatctaggttaatttgctcatattatcaacagagttgatgaaggttcca-aagatatgattttcttttttgcgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAG
 |  | ||   | || | | || |       ||       |  || | | | || |||   | | |  ||  |      |  || | |||||| |||| |||||| | ||| |||||||||| |||||||||||| | ||||||||||||||||||||||||||||| || || |||||  |||| || || |||||||
tcttctatatgtcagtcaaactgtagcaaggaaacaaacaacttttttagc-gatttgtatatgatagcatgatggtcaaccttttcttttgcacttt-cagGGAGCGAAATTGGTCTACAAACATTTGGCCACATTGTACTTTGTTTTTGTCTTTGATAGCTCTGAAAATGAACTTGCGGTGCTTGATCTTGTACAAG

upper sequence: GRMZM2G177914_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g25110.1 (Oryza sativa), 3'ss of exon 3
ccccaatggttaagccgatctatctaggttaatttgctcatattatcaacagagt-tgatg--aaggttccaaagatatgattttcttttttgcgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAG
        || || | |   |    |    ||     | || |    |   |  | ||||   | | |    ||  | |  |||| ||||||    |||||||||| | ||| || ||||||| |||||||||||| | ||||| | ||||||||||||| ||||||| || || |||||  |||| || || || ||||
---tgtcagtcaaactgtagtgaggaaacaaacaactttatttagcaatttgtatatgatagcatgatgatcaacttctttttttttttttttttttttgcagGGAGCGAAATTGATCTACAAACATTTGGCCACATTGTACTTAGGTTTTGTCTTTGATGGCTCTGAAAATGAACTTGCGGTGCTTGATCTTGTGCAAG
















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|211467101|gb|FK972980.1|FK972980
EST:     GGCCCGAGAGCGCGAGGAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTT-G--
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
EST: gi|19822213|gb|BQ048237.1|BQ048237
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
EST: gi|211467096|gb|FK972975.1|FK972975
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTT
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGT-
EST: gi|149090359|gb|EE179665.2|EE179665
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
EST: gi|211467090|gb|FK972969.1|FK972969
EST:     GCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGT
genomic: GCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCC-Ggtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGT
EST: gi|211469619|gb|FK972986.1|FK972986
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
EST: gi|211467098|gb|FK972977.1|FK972977
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTT
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTT
EST: gi|5499044|gb|AI854911.1|AI854911
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
EST: gi|211472147|gb|FK972996.1|FK972996
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
EST: gi|211472153|gb|FK973002.1|FK973002
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCA
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCA
EST: gi|211472152|gb|FK973001.1|FK973001
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTT
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTT
EST: gi|211472150|gb|FK972999.1|FK972999
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCA
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCA
EST: gi|211467100|gb|FK972979.1|FK972979
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
EST: gi|211469628|gb|FK972995.1|FK972995
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTG
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTG
EST: gi|211467088|gb|FK972967.1|FK972967
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
EST: gi|211469626|gb|FK972993.1|FK972993
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
EST: gi|149073163|gb|EE161440.2|EE161440
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
EST: gi|71429421|gb|DR810471.1|DR810471
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTG
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaacagagttgatgaaggttccaaagatatgattttcttttttgcgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAG
       agttgat  putative branch site (score: 5)
                                 ttttcttttttgcgct  putative PPT
                       aaagatatgattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccccaatggttaagccgatctatctaggttaatttgctcatattatcaacagagttgatgaaggttccaaagatatgattttcttttttgcgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - tgctcat
- - - - - - - - - - - - - - - - - - - - - - - caacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaagata