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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtgacctgtgagcatgaaaaactgcttacgccacagtttcaagtcttctttctggctgcaattgtttttacgctggcctctctttgaattcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGTCCAAGAGGGTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAG

Basic information

species Zea mays
transcript GRMZM2G009876_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009876_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 3'ss of exon 3
---ttgtgacctgtgagcatgaaaaactgcttacgccacagtttcaagtcttctt-tctggctgcaattgtttttacgctggcctctctttgaattcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGTCCAAGAGGGTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAG---
   || |||  |||||| |||  |   |  | |  |   ||| | || | | ||| | ||| |||| ||  | | | | |          || |  ||| |||||||||||||||||||||| |||| |   || ||||||||||||||||   | |||||||||||||||||||| ||||||||||| ||||||||||||||    
atattttgat-tgtgag-atgtgagcattataattcgcaagtgtaaaatttgcttgtttggttgcattt-ctgtaaagttcattcacggatgtacactt-gcagCCTGAAAATGCACGACGAGTCAACTTCTCGGCAGAAGGTTGATGATG---TTCAAGAGGGTGCTCTTCCTCCATATCTGCTGGACCGTGATCAGACACAACGT
















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|211153702|gb|FL418639.1|FL418639
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTCGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|211143002|gb|FL390386.1|FL390386
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|211516347|gb|FL407295.1|FL407295
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|211452151|gb|FL396750.1|FL396750
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|101382315|gb|EB813213.1|EB813213
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|74232800|gb|DT640714.1|DT640714
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|211129107|gb|FL371425.1|FL371425
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTCGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|211527014|gb|FL385877.1|FL385877
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|101390908|gb|EB817389.1|EB817389
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|6918424|gb|AW399954.1|AW399954
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|67038385|gb|CO464715.1|CO464715
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|101392350|gb|EB818104.1|EB818104
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|211049010|gb|FL423464.1|FL423464
EST:     AAGAGGTTCGCCAAAAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTCGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|211533317|gb|FL400722.1|FL400722
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCATATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|148953095|gb|EE152575.2|EE152575
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|31350057|gb|CD434414.1|CD434414
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|29946118|gb|CB815988.1|CB815988
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAG-AGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|211133673|gb|FL369483.1|FL369483
EST:     AAGAGGTTCGCCAAAAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTCGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|211159863|gb|FL403892.1|FL403892
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAGGGTCGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|76015209|gb|DT942379.1|DT942379
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|60351247|gb|DN218220.1|DN218220
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|88757436|gb|DY541577.1|DY541577
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|211113966|gb|FL427446.1|FL427446
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|149027253|gb|EE046450.2|EE046450
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|211258671|gb|FL369172.1|FL369172
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTCGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
EST: gi|211300841|gb|FL383944.1|FL383944
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGT

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: 231

TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGTCCAAGAGGGTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGTCCAAGAGGGTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGTCCAAGAGGGTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 110

TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcct ... ttcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGTCCAAGAGGGTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttctttctggctgcaattgtttttacgctggcctctctttgaattcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGTCCAAGAGGGTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAG
                                             ttcttcgc  CT-rich tract
                aattgttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtgacctgtgagcatgaaaaactgcttacgccacagtttcaagtcttctttctggctgcaattgtttttacgctggcctctctttgaattcttcgcagCCTGAAAATGCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGTCCAAGAGGGTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- -tgacctg
- - - - - - -gcatgaa
- - - - - - - - - - - - tgcttac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgctggc