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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacaatttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG

Basic information

species Zea mays
transcript GRMZM2G165357_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 7
gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacaatttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
|||  | ||||| | | | || |  | |  ||||    |   ||||| |||  ||  |   |||||| |||||    || | || | ||  ||   |||||| || |||||||| ||||| |||||||||||||| ||||| || |||||||| |||||||||||||||||||||||||
gtacgtctgttc-tatcacaaatacactacatttatcctatattttcttaatctag-tgcaaagttcacttac----ttgaattgatttacttc--atcagGAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttac----aatttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
  ||   |  ||  ||  ||  |  |  |||| ||   |  ||| |||| |  | |   |    | || |||     |   |  |  |||   | | |  | |||| ||| ||||||||||||||||||| |||||||| ||||| ||  ||||||| || ||||| |||||||| || || |
--aatgatcatcgactttaatatataccttatctgtcct--tttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgca-cagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 7
-gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacaatttttatttaactttttttct-atcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
    ||||||      |||  || ||  || || |        |  | ||   ||    |     ||     | |   |  |  |||   | | | | | |||| ||| ||||||||||||||||||| |||||||| ||||| ||  ||||||| || ||||| ||||||||||| || |
taggaatttg---gaatgaccatcgactttaatatataccatatcattatctcttggaatgttgctttatcaatagcctaaacataaaaatatgtatgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacaattttt--atttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
               |   | |  | | ||||  |||||   || ||  || ||||||  |  ||    | ||| | ||   | ||   || | || |   |||||||||||| ||||||||||| || |||||||| || |||||  ||||||| ||||| |||||||| ||||| ||||
--------------gtaggagtaaacacttatcagcttttaattctc--aacttatctg-cgtgtcaattcacattcttataacttggtttctattatgatagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 3'ss of exon 7
--gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacaatttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
  | | | |      | ||     |    |   |||   | ||      | | |   | | || |  | |  | | || |   ||    | | | | |  |||| || |||||||| ||||||||||| ||||| || || || || |||||||| || ||||||||||||||||| || |
tagcagactgacatttttggcggctctgttaattttatgtaggaaa---aaagaccttttctctaactatgattctatatgccttccgttatatatattacagGAGTCAGGAGTTGCTATGATGAGGGAAAGCGAGTGGCTGAAACTCTGATGTTTGATTATCACAGGCAGCATGGAATAG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 6
lower sequence: EFJ17446 (Selaginella moellendorffii), 3'ss of exon 6
gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacaatttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
                                       |    | ||  |  ||| | ||   || |||   | |   |  | |   || |  | | ||||||||||||| || || || ||||| || || || || || ||| ||||||| ||||||||||||||||| || ||||
---------------------------------------gtacgtgcaccagatatttgtc---ttgtct---actgcctgctca---ttgtgccgagcagGTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 6
lower sequence: EFJ35029 (Selaginella moellendorffii), 3'ss of exon 6
gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacaatttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
                                       |    | ||  |  ||| | ||   || |||   | |   |  | |   || | || | ||||||||||||| || || || ||||| || || || || || ||| ||||||| ||||||||||||||||| || ||||
---------------------------------------gtacgtgcaccagatatttgtc---ttgtct---actgcctgctca---ttgtgtcaagcagGTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTG

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|148939205|gb|EC883670.2|EC883670
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|149065532|gb|EE286652.2|EE286652
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|32838870|gb|CD978551.1|CD978551
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|211102135|gb|FL378499.1|FL378499
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGGTAACCCGATTG                         GTGTTAGGAGTTG
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTG
EST: gi|211182716|gb|FL410032.1|FL410032
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGGTA-GCGTGTAGCAGAGACGCTGATG
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGG-TAAGCGTGTAGCAGAGACGCTGATG
EST: gi|32850602|gb|CD990283.1|CD990283
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|211264125|gb|FL402706.1|FL402706
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|211355257|gb|FL372995.1|FL372995
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTCTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|60394382|gb|DN227252.1|DN227252
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|71444250|gb|DR825300.1|DR825300
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|149082965|gb|EE172201.2|EE172201
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|71449953|gb|DR831003.1|DR831003
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|149070980|gb|EE159385.2|EE159385
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|60339871|gb|DN206844.1|DN206844
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|211108221|gb|FL373168.1|FL373168
EST:     ACTTGAGCATCCTCAAACTGAGGNCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATG
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATG
EST: gi|149070503|gb|EE158907.2|EE158907
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|15100352|gb|BI396143.1|BI396143
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT

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: 355

GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 634

GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 717

GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1459

GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataaattatctttcaagttctcttacaatttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
                                  atttaac  putative branch site (score: 1459)
                             tttttatttaactttt  CT-rich tract
                  ttctcttacaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacaatttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT