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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgccactttgtctcctatatttcatataatattcatatctgtctactagttatgacattagttctatgtccaaacttctctcttgccttcataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAGCAGGAGAGATGATTTGGAGTCACTTGCCTATACACTAGTATTCCTTCAC

Basic information

species Zea mays
transcript GRMZM2G017835_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017835_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA10G44050.1 (Glycine max), 3'ss of exon 8
--------------gtttgccactttgtctcctatatttcatataatattcatatctgtctactagttatgacattagttctatgtccaaacttctctcttgcct-tcataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAGCAGGAGAGATGATTTGGAGTCACTTGCCTATACACTAGTATTCCTTCAC
                   || | || |||  | | || |   |  || |  | | | | || ||||| |        |  | | || |   |  |   |  ||| |  | || ||||||||| ||  ||||||||||||| ||||| ||||| || ||||| ||||| || ||||||||| | || || ||||| || |||||||| ||||| || 
gttttcttcccccccaccccctccttttcttttcttttcccccttgtagttctctttttttaatagttttcttgcatatggt-tatcaatgttcttgagtctcctctttttatgtagAGGAACTGTTCGATATGCTAGTGTTCATGCTCATTTGGGGAGAACTGCTAGTAGAAGAGATGATCTTGAATCTCTTGCATACACACTAGTCTTCCTCCAT

upper sequence: GRMZM2G017835_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 8
----gtttgccactttgtctcctatatttcatataatattcatatctg---tctactagttatgacattagttctatgtccaaacttctc---tcttgccttcataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAGCAGGAGAGATGATTTGGAGTCACTTGCCTATACACTAGTATTCCTTCAC
      || || |  |  | ||    |||| | |  | |||   |      |||  |  || | |   |  |  | |   |||  ||||     |||  |||  | || ||||||||| ||  ||||||||||||| ||||| ||||| || ||||| ||||| || ||||||||| | || || ||||| || ||||||||||||||||| 
gtattcttccccccctccccccctcttttcttttcttcttccccttgcagttctcttctttttaatggttttcttgttatcaatgttcttgaaccttatcttt-ttatgtagAGGAACTGTTCGATATGCTAGTGTTCATGCTCATTTGGGGAGAACTGCTAGTAGAAGAGATGATCTTGAATCTCTTGCATACACACTAGTATTCCTTCAT

upper sequence: GRMZM2G017835_T03 (Zea mays), 3'ss of exon 8
lower sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 8
gtttgccactttgtctcctatatttcatataatattcat-atctgtctactagttatgacattagttctatgtccaaacttctctcttgccttcataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAGCAGGAGAGATGATTTGGAGTCACTTGCCTATACACTAGTATTCCTTCAC
    |  | ||  | |  | | | |     |   ||  | || | |  |||  || |         |  ||     |   | | |  ||  | | | ||| || ||||| || |||||||||||||| ||||| || || |||||||| || ||||| ||||| ||| | ||||| ||||| ||||||||  | |||||||| 
----gtgaattgatgttgtgtttgtgggccatgctttgtgatttttgaacttattttttttaatccttcattcttgattatttttactgtttgcttcatccagGGGAACTGTGAGATATGCTAGTGTTCATGCTCACTTGGGAAGAACTGCCAGCAGAAGAGACGATCTAGAGTCTCTTGCATATACACTCATCTTCCTTCAT

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|211242969|gb|FL282602.1|FL282602
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|22819487|gb|BU499577.1|BU499577
EST:     ACTGCTAATGGGCAGCATGTTAGCTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATAATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTA
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATA-TGCTAGTGTCCATGCACATTTAGGAAGAACCGCTA
EST: gi|211242967|gb|FL282600.1|FL282600
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|76015692|gb|DT942862.1|DT942862
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|32832258|gb|CD971936.1|CD971936
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|87156608|gb|DY401397.1|DY401397
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|31440950|gb|CD510381.1|CD510381
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|32832272|gb|CD971950.1|CD971950
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|211242968|gb|FL282601.1|FL282601
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|26559748|gb|CA831983.1|CA831983
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|32832300|gb|CD971978.1|CD971978
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|148988749|gb|EE031658.2|EE031658
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|60345255|gb|DN212228.1|DN212228
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|32832043|gb|CD971721.1|CD971721
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|32835538|gb|CD975216.1|CD975216
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|32835900|gb|CD975578.1|CD975578
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actagttatgacattagttctatgtccaaacttctctcttgccttcataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAGCAGGAGAGATGATTTGGAGTCACTTGCCTATACACTAGTATTCCTTCAC
                              cttctctcttgccttc  CT-rich tract
                                           ttcataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgccactttgtctcctatatttcatataatattcatatctgtctactagttatgacattagttctatgtccaaacttctctcttgccttcataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAGCAGGAGAGATGATTTGGAGTCACTTGCCTATACACTAGTATTCCTTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG