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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatcttgtagaatcagttcactttgaggtatttatgtaatttggagaagtatgtcgctcttatattcttgctaaaattctgttgcatctcatggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCATGTTTATTGAAACCAGTGCTAAAGCTGGGTTTAACATTAAG

Basic information

species Zea mays
transcript GRMZM2G075719_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 4
ttatcttgtagaatcagttcactttg-aggtatttatgtaatttggagaagtatgtcgctcttatattcttgctaaaattctgttgcatctcatggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCATGTTTATTGAAACCAGTGCTAAAGCTGGGTTTAACATTAAG
|||  ||  |  ||||     ||    |  | |||||||||  || | |  |   |   | ||    ||    | || |  |||    ||||||| |||||||||||||| |||||||||||||| ||||| || || || || ||||| ||||| ||||||||||||||||||||||| ||||||||||||
ttagatta-aatatcatcgatctccataaatttttatgtaaaatgtatatattgttgagtgttgctgtcaattttaagtcatgtactttctcatgcaacagGCAAGTCTCCATAGAGGAAGGAGAGGGCAAAGCGAAAGATCTCGGTGTGATGTTCATTGAAACCAGTGCTAAAGCTGGTTTTAACATTAAG

upper sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G04330.1 (Glycine max), 3'ss of exon 4
-----------------------------------------------------------------------------------------ttatcttgtagaatcagttcactttgaggtatttatgtaatttggagaagtatgtcgctcttatattcttgctaaaattctgttgcatctcatggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCATGTTTATTGAAACCAGTGCTAAAGCTGGGTTTAACATTAAG
                                                                                         |  | |  |      |  ||| | ||  |   |  |    ||   |   | |  |  || || | || || | ||   |||  |   | |       ||| |||||||| ||||||||||| ||||  || |||   || ||   ||||||||| |||||||| |||||||| ||||||||||| || |||
gtaattagtaatgaagagaagaatgttggaatgaatttagggagactcaaattaggaacgactggcaaaaacaattcataggcatagtatagtatgttcttgctatatcattctggagacatgctagtgttacaatctgaaatttactgttttgtttttaccaaccatcttctttgtgtgtgtctgcagACAAGTCTCTATAGAGGAAGGGGAAGCAAAAGCACGTGAGCTCAATGTCATGTTCATTGAAACTAGTGCTAAGGCTGGGTTTAATATAAAG

upper sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA01G41090.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------------------ttatcttgtagaatcagttcactttgaggtatttatgtaatttggagaagtatgtcgct--cttatattcttgctaaaattctgttgcatctcatggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCATGTTTATTGAAACCAGTGCTAAAGCTGGGTTTAACATTAAG
                                                                                 | ||||||  ||   ||   |||| |  | |  || | ||  |   |  | ||  |    ||||||||  ||   ||  |   ||||||        | ||||||||||| | ||||||||| ||||  ||| |    || ||    ||||||||||||||| | ||||| |||||||||||||| || |||
gtaataatggtagaatgatttggttgcttgaattgtttggaacttgagacgttccatgtttgctctacgttgttgttttcatgtcttgtgaaa---gtgttcttttaaatttcgat-tcatcagcccatttctggtgtcaccttatatttatgagcaatattatttgcatgcgtc--tatagGCAAGTCTCTACAGAGGAAGGGGAAGCTAAGTCTCGTGAACTAAACGTCATGTTTATTGAAGCTAGTGCCAAAGCTGGGTTTAATATAAAG

upper sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA01G41100.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------------------------------------ttatcttgtagaatcagttcactttgaggtatttatgtaatttggagaagtatgtcgctcttatattcttgctaaaattctgttgcatctcatgga-acagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCATGTTTATTGAAACCAGTGCTAAAGCTGGGTTTAACATTAAG
                                                                                              |  ||| |    || |||||     ||  |  |  ||| |      ||| | |   | | |  | | |   | ||    |   | | |    ||    ||| |||||||| ||||||||||||||||  || |||   || ||   |||||||||||||||||| |||||||| ||||||||||| || |||
gtaattagtaacgaagagaagaatgttggaaagattttagggagactcaaattatgaactattggcaaaaacaattcataggcatagtgaagtatgttctcgctatat-agttc-tggagacatgctagtgttacaatctgaaatttactgttttgttttaccaaccaaccgccatcttctttgtgtgtctgcagACAAGTCTCTATAGAGGAAGGAGAAGCAAAAGCACGTGAGCTCAATGTCATGTTTATTGAAACTAGTGCTAAGGCTGGGTTTAATATAAAG

upper sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G04340.1 (Glycine max), 3'ss of exon 5
----------------------------------------------ttatcttgtagaatcagttcactttgaggtatttatgtaatttggagaagtatgtcgctcttatattcttgctaaaattctgttgcatctcatggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCATGTTTATTGAAACCAGTGCTAAAGCTGGGTTTAACATTAAG
                                                || ||  |   |   || || |||  || || ||||   ||| | |||| |     |||| ||   || | | ||||    |     | |    | ||||||||||| | ||||||||| ||||  ||| |    || ||    ||||||||||||||| | ||||| |||||||||||||| || |||
gtaataatggtagaatgatttgcttgcttgaattgtttggcacttgagatgttccatgtttgctttacgttgttgttttcatgt--cttgtaaaagtgt-----tcttttaaatttac-acaatttcactcatcatgagtctatagGCAAGTCTCTACAGAGGAAGGGGAAGCTAAGTCTCGTGAACTGAACGTCATGTTTATTGAAGCTAGTGCCAAAGCTGGGTTTAATATAAAG

upper sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv02s0012g00710.t01 (Vitis vinifera), 3'ss of exon 4
ttatcttgtagaatcagttcactttgaggta---tttatgtaatttggagaagtatgtcgctcttatattcttgctaaa-attctgttgcatctcatggaac----agGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCATGTTTATTGAAACCAGTGCTAAAGCTGGGTTTAACATTAAG
           |  ||      ||||| ||    | |||      | |     | | |   | ||    | |  ||||| ||| |||| ||| |    ||||    ||||||||||| |||||||||||||||| ||| ||    || |||   |||||||| |||||||| ||||| |||||||| || || || |||
--------ccaagccaagaagttttgacgttcactctattctgccttgtatttttttttatttttcctctttcactaaatattttgtttcatgttggtgaacccacagGCAAGTCTCAATAGAGGAAGGAGAAGCCAAAGCTCGTGAACTTAACGTCATGTTCATTGAAACAAGTGCCAAAGCTGGCTTCAATATAAAG

upper sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S353_41V6.1 (Physcomitrella patens), 3'ss of exon 5
--ttatcttgtagaatca-gttcactttgaggtatttatgtaatttggagaagtatgtcgctct-tatattcttgctaaaattctgttgcatctcatggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCATGTTTATTGAAACCAGTGCTAAAGCTGGGTTTAACATTAAG
    || |   |   ||| || || | ||   |   |    ||    |   | | | ||||  | |   |||||   || | |   ||||     |  | ||||||||||||| ||||||||||| || | ||||||||||||  |||| |||||||| || ||||| ||| |||||||||| |||||||| |||
gtgcatttgaaactttcaagtccagtctggtttggctgctaaa---aggagaatttatcgcaatgtgagttcttatgaataata-attgctggaaaatgtacagGCAAGTCTCAATAGAGGAAGGGGATGCCAAGGCAAAGGAATTTGGAGTCATGTTCATCGAAACTAGTTCTAAAGCTGGATTTAACATCAAG

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|211458655|gb|FL157796.1|FL157796
EST:     GTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
genomic: GTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtg ... catggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
EST: gi|32836609|gb|CD976287.1|CD976287
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtg ... catggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
EST: gi|111990689|gb|EE332131.1|EE332131
EST:     GAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
genomic: GAACAAAACTGACCTTGTTGACAAGAGgttggtggtg ... catggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
EST: gi|31612410|gb|CD569032.1|CD569032
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAACCTGACCTTGTTGACAAGAG                         GCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtg ... catggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
EST: gi|211109341|gb|FL282964.1|FL282964
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtg ... catggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
EST: gi|32840351|gb|CD980032.1|CD980032
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtg ... catggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
EST: gi|14645991|gb|BI180180.1|BI180180
EST:     GGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
genomic: GGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtg ... catggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
EST: gi|32839843|gb|CD979524.1|CD979524
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtg ... catggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
EST: gi|211109340|gb|FL282963.1|FL282963
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtg ... catggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
EST: gi|60354086|gb|DN221059.1|DN221059
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtg ... catggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
EST: gi|30088223|gb|CB886428.1|CB886428
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtg ... catggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
EST: gi|116822600|gb|EC866010.1|EC866010
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtg ... catggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT

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), 48 (downstream exon)
Score: 388

TCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtg ... catggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCATGTTTATTGAAACCAGTGCTAAAGCTGGGTTTAACATTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 528

TCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtg ... catggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCATGTTTATTGAAACCAGTGCTAAAGCTGGGTTTAACATTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 603

TCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtg ... catggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCATGTTTATTGAAACCAGTGCTAAAGCTGGGTTTAACATTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 778

TCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtg ... catggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCATGTTTATTGAAACCAGTGCTAAAGCTGGGTTTAACATTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaagtatgtcgctcttatattcttgctaaaattctgttgcatctcatggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCATGTTTATTGAAACCAGTGCTAAAGCTGGGTTTAACATTAAG
                        tgctaaa  putative branch site (score: 778)
               ttatattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatcttgtagaatcagttcactttgaggtatttatgtaatttggagaagtatgtcgctcttatattcttgctaaaattctgttgcatctcatggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCATGTTTATTGAAACCAGTGCTAAAGCTGGGTTTAACATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG