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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtggttttcttcggtgtcatatttcagggccagaactgctagttacacacatctcagatgtttcttctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA

Basic information

species Zea mays
transcript GRMZM2G443985_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 12
gtcagtggttttcttcggtgt-catatttcagggccagaactgctag-ttacac-------acatctcagatgtt--tcttctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
|||||| |  |  ||   | | | | |  ||   | ||   |||| | || |||       | ||||||||| ||   |||||| ||||||||| || ||||||||||||||||| || |||||||| ||||| || || |||||||||||| |||| ||||| ||||| ||||||||||||||||||||
gtcagtcgcctcttttattctacttttagcatcccaagctttgcttgatttcactgtaacaaaatctcagatcttatgcttctattgcagATCCTACATACATGATACGTGCCATTCCTAGCAATGCATCTGACAATGTGTATTGCACACTGTTGGCACACAGTGTGGTTCATGGAGCCATGGCTGGATA

upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 11
-------------------------------------------------gtcagtggttttcttcggtgt-catatttcagggccagaactgctagttacacacatctcagatgtttcttctact--gcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
                                                      | | || | |   |||    ||| ||     | |   |  | |  ||  |||  ||  | ||| | ||| |   ||||||||||||| ||||| || ||  | ||||||||||||||||| ||||| || |||||||| || ||||| || |  || |||||||||||||| || ||
gttcgtaaagacaaaaaactatatatttatacgtatgtgtacatgtgtgcatgttcgattacatttatgtgtgcattgcatactgaaaggaggaaat--caagcattgcatttttttttactatttgacagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA

upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 11
---------------------------------------gtcagtggttttcttcggtgtcatatttcagggccagaactgctagttacacacatctcagatgtttcttctact--gcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
                                        |   || || | ||         ||| ||     | |   |  | |  ||  |||  ||  | ||| | ||| |   ||||||||||||| ||||| || ||  | ||||||||||||||||| ||||| || |||||||| || ||||| || |  || |||||||| ||||| || ||
gttcgttaagacaaactatacaattatacgtatgtgtgcatgtttgattatatttatgtatgcattgcatactgaaaggaggaaat--caagcattgcattt-tttttactatttgacagATCCAACGTATATGATCCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCGATGGCAGGTTA

upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 11
----------------gtcagtggttttcttcggtgtcatattt-cagggccagaactgctagttacacacatctcagatgtttcttctact--gcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
                 |   |||  || |  |    || |    ||  |  |  |    | | |  |    |      |  |  || |  |   |||||||||| || ||||| || || || ||||||||||||||||| ||||| || |||||||| || ||||| || |  || |||||||| ||||| || ||
gtttgtaaagattaaacttcatggaattataagtgtgcacacacacactgaaaagagcaatggctgaaagagtaatgccttctctttatgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA

upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 11
-----------------gtcagtggttttcttcggtgtcatatttcagggccagaactgctagttacacacatctcagatgtttcttctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
                 ||   |||  || |  |    || |          || | ||   |  | |   ||  |   | |||  | |  | |||||||||| || ||||| || || || ||||||||||| ||||| ||||| || |||||||| || ||||| || |  || |||||||| ||||| || ||
gtttgtaaagattaaaagttcatggaattatgtgtgtacacacactgaaaggagcaatggctgaaagagtaatgccttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA

upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 11
gtcagtggttttcttcggtgtcatatttcagggccag--aactgctagt-tacacacatctcagatgtttcttctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
||  ||        ||  | | |||| |    ||  |  ||  ||| || ||  ||  |     |  |||  ||||   ||||||| ||||| ||||| |||||  | ||||||||||| ||||| || |||||||||||||| || ||||| || |  || |||||||| ||||| || ||
gtttgtatacactatctttctaatatatagaagctgggcaatggctggtctaaccaagtgctgcactttttgtctat--cagATCCTACGTATATGATCCGTGCTGTTCCAAGCAATGCATCTGACAATGTCTATTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGGTA

upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
lower sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
-------------------------------------gtcagtggttttcttcggtg-tcatatttcagggccagaactgctagttacacacat-ctcagatgt-----ttcttc------tactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
                                      |   || ||   |   ||| |  ||| |    |  |   ||  ||||       |  ||   || |      ||  |      | |||||||||||||||||||||| || ||  | ||||||||||||||||| ||||| || |||||  |||| ||||| ||||   |||||||||| ||||| || ||
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA

upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
lower sequence: PP1S282_45V6.1 (Physcomitrella patens), 3'ss of exon 12
-----------------------------------------------------------------------------------gtcagtggttttcttcggtgtcatatttcagggccagaactgctagttacacacatctcagatgtttcttctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
                                                                                   |  | | | || | |    | ||  |    ||           | | || | ||  ||||        |  | |||||||||| ||||| ||||| || || || |||||||||||||| || || ||||| |||||| |||||||||| ||||   ||||||| || ||||| || ||
gtacagtagccgtcaactgttctaactgttgagtgatggtgatccgtcttcctggtctacatctgtcgattttttacactgtggggaattgcttacattctggccacgtccatggtgatcttgcattcgata-agactgctcattatgccatagttctgcagATCCGACGTATATGATTCGAGCAATTCCAAGCAATGCTTCGGACAATGTCTACTGCACATTGCTGGCTCATAGCGCCATCCATGGGGCTATGGCAGGGTA

upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
lower sequence: PP1S131_40V6.1 (Physcomitrella patens), 3'ss of exon 12
---------------------------------------------------------------------------------------------------------gtcagtggttttcttcggtgtcatatttcagggccagaactgctagttacacacatctcagatgtttcttctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
                                                                                                         |     |   ||   |     |   |||||  ||    |  |  | ||    |    | | ||   | |  |  |  |||||| | ||||||||| || || || || |||||||||||||| || |||||||||||  |||| |||||  | | | | ||||||||||||||||| ||
gtatgataaaatgaccaaaaccttcattggtctctctctctttctctctctttctctctctacctcacagatatcgacgtcaagtgaaaattttggactaaactagcagaagaccttgcgcttgacccagtttcaaagc----atcgagatttgactaagaataaaatcactgtggttttttagATCCTAAGTACATGATTCGAGCGATACCGAGCAATGCTTCTGACAATGTCTATTGCACCTTGCTCGCTCATGGTGCGATTCATGGAGCCATGGCTGGTTA

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|5846823|gb|AI999906.1|AI999906
EST:     GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG                         ATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
genomic: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
EST: gi|6095550|gb|AW120217.1|AW120217
EST:     GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG                         ATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
genomic: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
EST: gi|32857486|gb|CD997167.1|CD997167
EST:     GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG                         ATCTTACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
genomic: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
EST: gi|91872759|gb|EB402716.1|EB402716
EST:     GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG                         ATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
genomic: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
EST: gi|148972519|gb|EE023480.2|EE023480
EST:     GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG                         ATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
genomic: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
EST: gi|33285656|gb|CF075451.1|CF075451
EST:     GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG                         ATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
genomic: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
EST: gi|5895959|gb|AW037205.1|AW037205
EST:     GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG                         ATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
genomic: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
EST: gi|148982504|gb|EE028349.2|EE028349
EST:     GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG                         ATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
genomic: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
EST: gi|14244950|gb|BG842888.2|BG842888
EST:     GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG                         ATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
genomic: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
EST: gi|76016085|gb|DT943255.1|DT943255
EST:     GAACATTTCAAGAAAAACAAGATGACCATTAATGTGAAGTACATAG                         ATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
genomic: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
EST: gi|6020683|gb|AW065491.1|AW065491
EST:     GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG                         ATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
genomic: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
EST: gi|88747280|gb|DY531421.1|DY531421
EST:     CATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG                         ATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
genomic: CATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
EST: gi|76921243|gb|DV168509.1|DV168509
EST:     GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG                         ATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
genomic: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
EST: gi|78022684|gb|DV491071.1|DV491071
EST:     GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG                         ATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
genomic: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
EST: gi|5325011|gb|AI783202.1|AI783202
EST:     GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAG                         ATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT
genomic: GAACATTTCAAGAAAAACAAGATGACCATTAATCTGAAGTACATAGgtcagtggtt ... tctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcagggccagaactgctagttacacacatctcagatgtttcttctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA
                                        tttcttctact  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtggttttcttcggtgtcatatttcagggccagaactgctagttacacacatctcagatgtttcttctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA