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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacacttagtcatcatactacttgatctattcaaacctcggtgctctcactccatagccagactctaactagctagaatgtattgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGGTCGCCAAAGGAGACTAGATGGTGGTTCCATGACGACACGGTGTAATGAT

Basic information

species Zea mays
transcript GRMZM2G007381_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g44000.1 (Oryza sativa), 3'ss of exon 5
gtgacacttagtcatcatac-tacttgat-ctattcaaacctcggtgctctcactccata-gccagactctaactagctagaatgtattgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGGTCGCCAAAGGAGACTAGATGGTGGTTCCATGACGACACGGTGTAATGAT
|| || ||| || | | | ||| | | | | || || | | | | || || |||| ||||| ||||||||||||||||| ||||||||||||||||||||||| |||||||| ||||||||||| |||||||| ||||||||||||||||| |||| ||||||
----------gttattatatataactaacacccttcccattttctttcgctgaccaaaaacattaaaaggtatcttgctataatgtggtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGGTCGCCGAAGGAGACCAGATGGTGGTTCCATGATGACAAAGTGTAAGAGG

upper sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 5
gtgacacttagtcatcatactacttgatctattcaaacctcggtgctctcactccatagccag-actctaactagctaga--atgtattgttt------gcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGGTCGCCAAAGGAGACTAGATGGTGGTTCCATGACGACACGGTGTAATGAT
| ||| || |||| | || || | | | | ||| || | | | | || || || | ||| || |||||||||||| | || |||||||||||||| | ||||||| | || || || || || |||||||| || |||||||||||||| |||| || |||| |
--attatttaag-attctactggtgaatttaggtaggtcattgatccatcatcaaatgggtgtcattttggcttaataactcatttcttgatttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAA

upper sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G07810.1 (Glycine max), 3'ss of exon 5
--gtgacacttagtcatcatactacttgatctattcaaacc-tcggtgc-tctcactccatagccagactc--taactagctagaatgtattgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGGTCGCCAAAGGAGACTAGATGGTGGTTCCATGACGACACGGTGTAATGAT
|| | || || | | | || || | | ||| | | || | | || ||||| || | | | || |||||||||||| | || |||||||||||||| | ||||||| | || || || || || |||||||| || |||||||||||||| |||| || |||| ||
tggttattatttaagattcttcaggtgaatttaggtaggtcatcgatccatcatgggtgtcatttcggcttaataactctttactttatttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAT

upper sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 5
---gtgacacttagtca-tcatactacttgatctattca--aacctcggtgctctcactccatagccagactctaactagctagaat-----gtattgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGGTCGCCAAAGGAGACTAGATGGTGGTTCCATGACGACACGGTGTAATGAT
||| || || ||| ||| | | | ||| || | | || | | ||||| |||| | || | | |||||||||||| | || || || || ||||| | ||||||| ||||||||||| || || ||||| || ||||||||||||||||||| ||| |||||||
gtttctacatttgatctctcacactttgtattgttgtcacaaattcaaactttttgaccctgccacacaactcttactatgtcttattgtcgatgacaatatcagCAACGCCCGACTGATAACGATCGATATGTGAAGAACTGCAAGAACGGGAGGTCTCCTAAAGAGACAAGGTGGTGGTTCCATGACGACAAGGTTTAATGAT

upper sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------------gtgacacttagtcatcatactacttgatctattcaaacctcggtgctctcactccatagccagactctaactagctagaatgtattgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGGTCGCCAAAGGAGACTAGATGGTGGTTCCATGACGACACGGTGTAATGAT
||| | | || ||| | || | | | | | ||| | | | | | || | || || |||||||||||| ||||| || || || ||||| | |||||| || |||||||| || |||||||| || ||||||||||||||||||| ||| | |||
gttctttcttcttcttcgtgtttccctattgacaagttacccaaagtactgtgaattatgaggtctgaaactaagaatatcaatgtgttttttattccgccttatt-gcagCAACGCCCTGCGGATAACGATCGTTATGTGAAGAACTGTAAGAATGGGAGGTCTCCTAAGGAGACGAGGTGGTGGTTCCATGACGACAAGGTTTGATGCA

upper sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 5
--gtgacacttagtcatcatactacttgatctattcaaacctcggtgctctcactccatagccagac-tctaactagctagaatgta---ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGGTCGCCAAAGGAGACTAGATGGTGGTTCCATGACGACACGGTGTAATGAT
| || || || | | | | | | | || | || || || | | | | | | | | |||| |||||||||| || | || |||||||| ||||| ||||||||| | || || || || || |||||||| || ||||||||||||||||| | || ||||
gaatatcagagaggcaatgagttttcttttttttcttttttctgttttattctttaaatggcaagggattcagcctgatgcattttgaacttgtatgcagCAACGTCCTGAAGATAATGACCGTTATGTGAGGAACTGCAGGAATGGCAGATCCCCCAAGGAGACCAGGTGGTGGTTCCATGACGATAAAGTCTAATTTG

upper sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv18s0001g13180.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------gtgacacttag---tcatcatactacttgatcta--ttcaaacctcggtgctctcactccatagccagactctaactagctagaatgtattgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGGTCGCCAAAGGAGACTAGATGGTGGTTCCATGACGACACGGTGTAATGAT
| ||| | | | || ||| || | || | | | | | | | | ||| | ||| || | | | ||||||||||||| || || |||||||||||||| | || || || || || || || || |||||||||||||||||||||||||| || | |||||||
gtttggttcaaattgtcaaagttttaagttttttaaacccctcctttcttcttaattttgcttttatctttttccagcctattttagtgtgagagcattactcatgagttttttcattgtgcagCAACGCCCTGCAGATAATGACCGCTATGTGAAAAATTGTCGGAATGGCAGATCTCCCAAGGAGACTAGATGGTGGTTCCATGATGATAAAGTGTAATAGA

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|211242854|gb|FL389165.1|FL389165
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
EST: gi|71431746|gb|DR812796.1|DR812796
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
EST: gi|211172115|gb|FK994020.1|FK994020
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATGACCGCTATGTTA
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTA
EST: gi|45846873|gb|CN070816.1|CN070816
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATGGCCGCTATGTTAGGAACTGCCGCAACGGGAGG
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
EST: gi|50331624|gb|CO526750.1|CO526750
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
EST: gi|211172114|gb|FK994019.1|FK994019
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
EST: gi|116827090|gb|EC870952.1|EC870952
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
EST: gi|211421811|gb|FL084938.1|FL084938
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
EST: gi|17931977|gb|BM268937.1|BM268937
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
EST: gi|78081936|gb|DV510348.1|DV510348
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
EST: gi|71431745|gb|DR812795.1|DR812795
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
EST: gi|16925448|gb|BM078516.1|BM078516
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
EST: gi|18165814|gb|BM335659.1|BM335659
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
EST: gi|211215511|gb|FL424481.1|FL424481
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCCGCA-CGGGAG
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCC-GCAACGGGAG
EST: gi|29946817|gb|CB816340.1|CB816340
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
EST: gi|22819231|gb|BU499321.1|BU499321
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
EST: gi|16919478|gb|BM074211.1|BM074211
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
EST: gi|211172116|gb|FK994021.1|FK994021
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATTGACCGCTATGTTAGGAACTGCCGCAACGGGA
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAAT-GACCGCTATGTTAGGAACTGCCGCAACGGGA
EST: gi|29945777|gb|CB815814.1|CB815814
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
EST: gi|211172113|gb|FK994018.1|FK994018
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGG
EST: gi|211172112|gb|FK994017.1|FK994017
EST:     GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG                         CA-CGCCCGGCG-ACAATGA
genomic: GCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGA

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: 48 (upstream exon), 45 (downstream exon)
Score: 108

ATATTCTGTATGACTCGTGGTCACCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGGTCGCCAAAGGAGACTAGATGGTGGTTCCATGACGACACGGTGTAATGAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 186

ATATTCTGTATGACTCGTGGTCACCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGGTCGCCAAAGGAGACTAGATGGTGGTTCCATGACGACACGGTGTAATGAT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 158

ATATTCTGTATGACTCGTGGTCACCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGGTCGCCAAAGGAGACTAGATGGTGGTTCCATGACGACACGGTGTAATGAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 206

ATATTCTGTATGACTCGTGGTCACCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAGgtgacactta ... ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGGTCGCCAAAGGAGACTAGATGGTGGTTCCATGACGACACGGTGTAATGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcggtgctctcactccatagccagactctaactagctagaatgtattgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGGTCGCCAAAGGAGACTAGATGGTGGTTCCATGACGACACGGTGTAATGAT
                         ctctaac  putative branch site (score: 206)
 aatgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgacacttagtcatcatactacttgatctattcaaacctcggtgctctcactccatagccagactctaactagctagaatgtattgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGGTCGCCAAAGGAGACTAGATGGTGGTTCCATGACGACACGGTGTAATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG