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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgttccggtctccttaatataatatcgggagggtggtctttccctcccctgattttttttttatcgttgctgaatttctgttgcatctcatggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCATGTTTATTGAAACCAGTGCTAAGGCTGGGTTTAACATTAAG

Basic information

species Zea mays
transcript GRMZM2G169694_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 4
--------catgtt-ccggtctccttaatataatatcgggagggtggtctttccctcccctgattttttttttatcgttgctgaatttctgttgcatctcatggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCATGTTTATTGAAACCAGTGCTAAGGCTGGGTTTAACATTAAG
         || |   || ||||| |||  |  |||    |  ||      |   |       | ||  | | |   ||    || |  |||    ||||||| |||||||||||||| ||||||||||| |||||||| ||||| || || || || ||||| ||||||||||||||||| ||||| ||||||||||||
ttagattaaatatcatcgatctccataaatttttatgtaaaatgta-----tatattgttgagtgttgctgtcaatttt----aagtcatgtactttctcatgcaacagGCAAGTCTCCATAGAGGAAGGAGAGGGCAAAGCGAAAGATCTCGGTGTGATGTTCATTGAAACCAGTGCTAAAGCTGGTTTTAACATTAAG

upper sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G04330.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------------------------catgttccggtct--ccttaatataatat-cgggag----ggtggtctttccctcccctgattttttttttatcgttgctgaatttctgttgcatctcatggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCATGTTTATTGAAACCAGTGCTAAGGCTGGGTTTAACATTAAG
                                                                                  |||  |   || |   |||  ||||  || | ||||    | | || || |  ||      ||  | |||| |  || |  |   |||  |   | |       ||| |||||||| |||||||||||||| |  || ||    || ||    |||||||| |||||||| |||||||||||||||||||| || |||
gtaattagtaatgaagagaagaatgttggaatgaatttagggagactcaaattaggaacgactggcaaaaacaattcataggcatagtatagtatgttcttgctatatcattctggagacatgctagtgttacaatctgaaatttactgttttgtttttaccaaccatcttctttgtgtgtgtctgcagACAAGTCTCTATAGAGGAAGGGGAAGCAAAAGCACGTGAGCTCAATGTCATGTTCATTGAAACTAGTGCTAAGGCTGGGTTTAATATAAAG

upper sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA01G41100.1 (Glycine max), 3'ss of exon 4
---------------------------------------------------------------------------------------catgttccggtctccttaatataatatcgggagggtggtctttccctcccctgattttttttttatcgtt--gctgaatttctgttgcatctcatgga-----acagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCATGTTTATTGAAACCAGTGCTAAGGCTGGGTTTAACATTAAG
                                                                                            |  | ||||  || |||| |   ||     || |  |        ||||  |||  | | | |||   |  |    | |     |    ||        ||| |||||||| ||||||||||| || |  || ||    || ||    ||||||||||||||||| |||||||||||||||||||| || |||
gtaattagtaacgaagagaagaatgttggaaagattttagggagactcaaattatgaactattggcaaaaacaattcataggcatagtgaagtatgttctcgcta-tatagttctggagacatgctagtgttacaatctgaaatttactgttttgttttaccaaccaaccgccatcttctttgtgtgtctgcagACAAGTCTCTATAGAGGAAGGAGAAGCAAAAGCACGTGAGCTCAATGTCATGTTTATTGAAACTAGTGCTAAGGCTGGGTTTAATATAAAG

upper sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv02s0012g00710.t01 (Vitis vinifera), 3'ss of exon 4
catgttccggtctccttaatataatatcgggagggtggtctttccctcccctgattttttttttatcgtt--------gctgaat-ttctgttgcatctcatggaac----agGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCATGTTTATTGAAACCAGTGCTAAGGCTGGGTTTAACATTAAG
             ||     |  |  |   || | |     |   || || ||  |||||||||||  ||         || ||| || |||| ||| |    ||||    ||||||||||||||||||||||| || | ||| ||    || |||   |||||||| |||||||| ||||| || ||||| || || || |||
-------------ccaagccaagaagttttgacgttcactctattctgccttgtatttttttttatttttcctctttcactaaatattttgtttcatgttggtgaacccacagGCAAGTCTCAATAGAGGAAGGAGAAGCCAAAGCTCGTGAACTTAACGTCATGTTCATTGAAACAAGTGCCAAAGCTGGCTTCAATATAAAG

upper sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S12_267V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------catgttccggtctccttaatataatatcgggagggtggtctttccctcccctgattttttttttatcgttgctgaatttctgttgcatctcatggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCATGTTTATTGAAACCAGTGCTAAGGCTGGGTTTAACATTAAG
                           |  |   ||||  ||     ||  ||   |   | |  |       |    |   | | || |    |      |   ||||| |     | |  |||||| ||||||||||||||||| || | |||||| |||||  |   ||||||||| || ||||| ||| |||||||||| |||||||| |||
gtcagtaaattcacaatattagatgagtaattttgtctttttgg-ggaacttcacaaaattagcatccagaatcaacaacgctatgttgacttataaactgtgaatgttggaaaatcttg--cagGCAGGTCTCAATAGAGGAAGGAGACGCCAAGGCCAAGGAATTACAAGTCATGTTCATCGAAACAAGTTCTAAGGCTGGATTTAACATCAAG

upper sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S353_41V6.1 (Physcomitrella patens), 3'ss of exon 5
-catgttccggtctccttaatataatatcgggagggtggtctttccctcccctgattttttttttatcgttgctgaatttctgttgcatctcatggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCATGTTTATTGAAACCAGTGCTAAGGCTGGGTTTAACATTAAG
     ||     ||    | |  | |   ||   ||  |             | ||     | | |    |  |||||     ||||     |  | |||||||||||||||||||||||||||| | |||||| |||||  ||||||||||||| || ||||| ||| |||| ||||| |||||||| |||
gtgcatttgaaactttcaagtccagt-ctggtttggctgctaaaaggagaatttatcgcaatgtgagttcttatgaataataattgctggaaaatgtacagGCAAGTCTCAATAGAGGAAGGGGATGCCAAGGCAAAGGAATTTGGAGTCATGTTCATCGAAACTAGTTCTAAAGCTGGATTTAACATCAAG

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|149104596|gb|EE290046.2|EE290046
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
EST: gi|71333156|gb|DR803613.1|DR803613
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
EST: gi|148970042|gb|EE020962.2|EE020962
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
EST: gi|213172892|gb|FM183005.1|FM183005
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
EST: gi|33093555|gb|CF053549.1|CF053549
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
EST: gi|37397830|gb|CF636223.1|CF636223
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
EST: gi|33092315|gb|CF052309.1|CF052309
EST:     ATCATTGTGCTTGTTGGGAACCAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
genomic: ATCATTGTGCTTGTTGGGAA-CAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
EST: gi|149085277|gb|EE174782.2|EE174782
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
EST: gi|71333158|gb|DR803614.1|DR803614
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
EST: gi|56462112|gb|CK986410.1|CK986410
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCGAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
EST: gi|211355171|gb|FL139763.1|FL139763
EST:     TTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
genomic: TTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
EST: gi|213167949|gb|FM194944.1|FM194944
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
EST: gi|148954186|gb|EC899590.2|EC899590
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCAATAGGGGAAGGGGAGGGCAAGGCGAAGGCCCTTGGAGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
EST: gi|148960910|gb|EE011595.2|EE011595
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
EST: gi|213169870|gb|FM180689.1|FM180689
EST:     AAACTGACCTTGTTGACAAGAG                         GCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
genomic: AAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
EST: gi|213169997|gb|FM189153.1|FM189153
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
EST: gi|87152147|gb|DY396936.1|DY396936
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCAATAGAG
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAG
EST: gi|32870836|gb|CF010518.1|CF010518
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGT-GACAAGAG                         G-A-GTA--AATAAGAGGGAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCA
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATA-GAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCA
EST: gi|149085276|gb|EE174781.2|EE174781
EST:     GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAG                         GCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT
genomic: GATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCAT

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), 49 (downstream exon)
Score: 408

TCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCATGTTTATTGAAACCAGTGCTAAGGCTGGGTTTAACATTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 500

TCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCATGTTTATTGAAACCAGTGCTAAGGCTGGGTTTAACATTAAG


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

TCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCATGTTTATTGAAACCAGTGCTAAGGCTGGGTTTAACATTAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 648

TCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCTTGTTGACAAGAGgttggtggta ... catggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCATGTTTATTGAAACCAGTGCTAAGGCTGGGTTTAACATTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcccctgattttttttttatcgttgctgaatttctgttgcatctcatggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCATGTTTATTGAAACCAGTGCTAAGGCTGGGTTTAACATTAAG
   ccctgat  putative branch site (score: 648)
        attttttttttatcgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgttccggtctccttaatataatatcgggagggtggtctttccctcccctgattttttttttatcgttgctgaatttctgttgcatctcatggaacagGCAAGTCTCAATAGAGGAAGGGGAGGGCAAGGCGAAGGACCTTGGAGTCATGTTTATTGAAACCAGTGCTAAGGCTGGGTTTAACATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
catgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttgc