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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtgtttgctctttcctgatttctgtagttttgttggttgctctatgtatattttgtttggctttaaattctttggtctctctcatgtcaagta...

Basic information

species Zea mays
transcript GRMZM2G075719_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 5'ss of exon 4
TCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtgtttgctct--ttcctgatttctgtagttttgttg-gttgctctatgtatattttg-tttggctttaaattctttggtctctctcatgtcaagta
|| |||| || || || |||||||| |||||| | |||||||||||||||||||||||||||||||| ||||||||||||||||| ||||||||||||||||  |||| |||        ||| || ||||| |||   | |   |||    |   ||| |  || ||| ||| | |||  |  | ||    | |  |   |  
TCCTAAACACTTCAAAATGGATAGAGGAAGTTAGAACTGAGAGGGGCAGTGATGTTATCATTGTGCTGGTTGGGAACAAAACTGATCTTGTTGACAAGAGgtgagtggagttcaaaaaaattcttgttttctttagccctttcctgttatcttgcttatctgatgattttgctgttaataat--gatcctctttaccttctg--

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA11G04340.1 (Glycine max), 5'ss of exon 5
TCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgt-----tggtggtgtttgct-ctttcctgatttctgtagttttgttggttgctctatgtatattttgt----ttggctttaaattctttggtctctctcatgtcaagta-----------------------------
|| |||| ||||| | |||||| || || || |||| |||||| |||||||||| ||| ||||| | ||||||||||||||||||||||||  | |||||||     |||| |  |    | ||| | ||| || | | |   | |  | || || |||| |  |||      |||  || |  |  | |        || | | || |                              
TCCTAAACACATCAAGGTGGATTGAAGAGGTGCGCATTGAGAGAGGCAGTGATGCTATTATTGTTCATGTTGGGAACAAAACTGACCTTGTCAATAAGAGgtaataatggtagaatgatttgcttgcttgaattgtttggcact-tgagatgttccatgtttgctttacgttgttgttttcatgtcttgtaaaagtgttcttttaaatttacacaatttcactcatcatgagtctatag

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA01G41090.1 (Glycine max), 5'ss of exon 5
TCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgt--tggtggt-gtttgctct---ttcctgatttctgtagttttgttggttgctctatgtatattttgt----ttggctttaaattctttggtctctctcatgtcaagta-------------------------------------------------------------------
|| | || ||||| |||||||| || || || |||| |||||| |||||||||||||| ||||| |||||||||||||||||||||||||| || |||||||  |  |||| |  || | |   | | ||| || | | |   | |  |  | || |||| |  | |      |||  || |  |  | ||       || | | || |                                                                    
TCCTGAACACATCAAAGTGGATTGAAGAGGTGCGCAGTGAGAGAGGCAGTGATGTTATTATTGTTCTTGTTGGGAACAAAACTGACCTTGTCGATAAGAGgtaataatggtagaatgatttggttgcttgaattgtttggaact-tgagacgttccatgtttgctctacgttgttgttttcatgtcttgtgaaagtgttcttttaaatttcgattcatcagcccatttctggtgtcaccttatatttatgagcaatattatttgcatgcgtctatag

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA11G04330.1 (Glycine max), 5'ss of exon 4
TCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtgtttgc----------tctttcctgatttctgtagttttg--ttggttgctctatgtatattttgttt---ggctttaaattctttggtctctctcatgtcaagta---------------------------------------------------------------------------
|| |||||||  | |||||||| || || || || || ||||| ||||||||||| || ||||| |||||||||||||||||||| ||||| || || ||||   | ||  |             |        ||||  | ||  |    || |   |     | | |     ||    ||| |   ||  | || |||  || || |||                                                                               
TCCTAAATACTGCAAAGTGGATTGAAGAGGTGCGAACAGAGAGAGGCAGTGATGTCATTATTGTTCTTGTTGGGAACAAAACTGATCTTGTCGAGAAAAGgtaattagtaatgaagagaagaatgttggaatgaatttagggagactcaaattaggaacgactggcaaaaacaattcataggcatagtatagtatgttcttgct-atatcattctggagacatgctagtgttacaatctgaaatttactgttttgtttttaccaaccatcttctttgtgtgtgtctgcag

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA05G05860.1 (Glycine max), 5'ss of exon 4
TCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtgtttgctctttcctgatttctgtagttttgttggttgctctatgtatattttgtttg-gctttaaattctttggtctctctcatgtcaagta-----
|| |||| ||||| |||||||| || || || |||| ||| || ||||| ||||||||  | || |||||||||||||||||||| ||||| || || ||||      ||  |  ||  |  |  |  |  ||  ||  |  | |  | |||          ||   |   | | | || || ||| | | || | | | |     
TCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTGAAAGAGGCAGCGATGTTATTGTGGTTCTTGTTGGGAACAAAACTGATCTTGTGGATAAAAGgt----aatggctaatcaatggtagtgac--taacttcatcagatagtttatactggccggtttcatgacatgactcctatgttctgtattatctaatgaactatt

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA01G41100.1 (Glycine max), 5'ss of exon 4
TCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtgtttgctctttcctgatttctgtagttttgttggttgctctatgtatattttgtttggctttaaattctttggtctctctcatgtcaagta----------------------------------------------------------------------------------------------
||||||||||  | |||||||| || || || || || || || ||||||||||| || ||||| |||||||||||||||||||| |||||||| || ||||   | ||    |            ||    || |||   ||   ||| |  |||    | || |     | | |   | | |    | | ||    |                                                                                               
TCTTAAATACTGCTAAGTGGATTGAAGAGGTGCGAACAGAAAGAGGCAGTGATGTCATTATTGTTCTTGTTGGGAACAAAACTGATCTTGTTGAGAAAAGgtaattagtaac-gaagagaagaatgttggaaagattttagggagactcaaattatgaactattggcaaaaacaattcataggcatagtgaagtatgttctcgctatatagttctggagacatgctagtgttacaatctgaaatttactgttttgttttaccaaccaaccgccatcttctttgtgtgtctgcag

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA17G16200.1 (Glycine max), 5'ss of exon 4
TCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtgtttgctctttcctgatttctgtagttttgttggttgctctatgtatattttgtttggctttaaattctttggtctctctcatgtcaagta-----
|| |||| ||||| |||||||| || || || |||| ||| || ||||| ||||||||  |||| |||||||||||||||||||| ||||| || || ||||      ||  |  ||  |  |    |   ||  ||  |  | |  | |||   |     ||||      |      ||    ||| |  | || | |      
TCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTGAAAGAGGCAGCGATGTTATTGTTGTTCTTGTTGGGAACAAAACTGATCTTGTGGATAAAAGgt----aatggctaatcaatggtagagtgactaacttcatcagatagtttatac-tggccggtttcatgacatgactcttatgttctgtattatctaatggccta

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv02s0012g00710.t01 (Vitis vinifera), 5'ss of exon 4
TCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtgtttgctctttcctgatt--tctgtagttttgttggttgctcta--tgtatattt-tgtttggctttaaattctttggtctctctcatgtcaagta
|| |||| || || |||||||| || || |||||||||||||| || ||||||||||| || || |||||||| ||||| ||||||||||| || || ||||      |   |         ||  |  | | || |||   || |||   ||    | ||||  | |||| ||| || || | | |   || |  | | |    
TCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTGAGAGAGGTAGTGATGTTATTATCGTCCTTGTTGGAAACAAGACTGACCTTGTGGAGAAAAGgtaaagattagctaacagaagatggctaatatttaatttatatgattgtcttagtcctttattcatttttgtcttgaagttttattgaggct-ttgtttga----

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv15s0021g00640.t01 (Vitis vinifera), 5'ss of exon 4
TCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtgtttgctctttcctgatttctgtagttttgttggttgctctatgtatattttgtttggctttaaattc--tttggtctctctcatgtcaagta
|| | || ||  |||||||||| || || ||||| |||||| | |||||||||||||||||||| ||||||||||||||||| |||||||| |||||||||| | ||   | |  |||    || | | | || |||| |   |   ||| ||  |  ||      |        |   ||| | |||  | |  |    ||
TCCTTAACACTGCCAAGTGGATTGAGGAGGTTCGTACTGAGCGAGGCAGTGATGTTATCATTGTCCTTGTTGGGAACAAAACAGACCTTGTGGACAAGAGgt-gatgacttattgtctcatttgctgtttata-ttttctacttcaatctttgattgcttgtaccagtcaagggcttgtttttgactccattaaatattata

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S346_29V6.1 (Physcomitrella patens), 5'ss of exon 5
TCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtgtttgctctttcctgatttctgtagt--tttgttggttgctctatgtatattttgtttggctttaaattctttggtctctctcatgtcaagta-----------------------------------------------------
|  ||||||||||    ||||| || || || |  || ||| | || ||||||||||||||  |||||||||| ||||| ||||| |||||||| ||| |||  ||    | |||| |||     |    |||||  || |||  ||  ||  |  |    ||  |||  | |  |     |  |     | | || | | |                                                     
TTCTAAATACATCTCGATGGATTGAAGAGGTCCTAACAGAGCGTGGAAGTGATGTTATCATAATGCTTGTTGGCAACAAGACTGATCTTGTTGATAAGCGgtaagtatcttctgctatttttatttcctagtagtggttggttattttttcggtccaatgattacttgtatctgcaaatcatctttctgttgaggtgaggaatattgtaacgtgcaatttggtttattatttaattgttcttgacattttttcag

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|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|211109340|gb|FL282963.1|FL282963
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtg ... catggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
EST: gi|116822600|gb|EC866010.1|EC866010
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtg ... catggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
EST: gi|32836609|gb|CD976287.1|CD976287
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtg ... catggaacagGCAAGTCTCGATAGAGGAAGGAGAAGGCAAGGCAAAGGACCTTGGTGTCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggtgtttgctctttcctgatttctgtagttttgttggttgctctatgtatattttgtttggctttaaattctttggtctctctcatgtcaagta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctctctc