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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatatcggccccggtactgtgtgcgcggctcatatggcgggagcttctggcctggatctcagggttgttctgcttgttctctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAACACCATCTTCGTCTTCAAGTTCCGCACCCACTTCGGTGGAGGCAAGTCCA

Basic information

species Zea mays
transcript GRMZM2G151252_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151252_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g52490.1 (Oryza sativa), 3'ss of exon 2
gtgagatatcggccccggtactgtgtgcgcggctcatatggcgggagcttctggcctggatctcagggttgttctgcttgttctctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAACACCATCTTCGTCTTCAAGTTCCGCACCCACTTCGGTGGAGGCAAGTCCA
||||||  ||||      |  |   || |  | |  |   |     ||    ||  |||||||||| |  | |  | || | ||    ||| |||| ||| ||||||||| ||| |||||| ||||||||||||||||| | |||  ||||||||| |||||||||||||||||||||||||||||||||||||
gtgagacctcggtgtaaatcttacatgtggtggtggtgatg-atttgcggggggtttggatctcagcg--gctggggttttgct----gtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAACTGCATCTTCGTGTTCAAGTTCCGCACCCACTTCGGTGGAGGCAAGTCCA
















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|211447432|gb|FL376098.1|FL376098
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
EST: gi|211319657|gb|FL415866.1|FL415866
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGACTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
EST: gi|211450463|gb|FL416401.1|FL416401
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
EST: gi|211290632|gb|FL412736.1|FL412736
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
EST: gi|211441966|gb|FL416337.1|FL416337
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
EST: gi|166640634|gb|EG309291.1|EG309291
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTG
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTG
EST: gi|8516455|gb|BE123181.1|BE123181
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTA
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTA
EST: gi|211509382|gb|FL412052.1|FL412052
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAMC
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
EST: gi|211115282|gb|FL397762.1|FL397762
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
EST: gi|78082770|gb|DV511163.1|DV511163
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
EST: gi|211305549|gb|FL417495.1|FL417495
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGC-AACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
EST: gi|211419181|gb|FL428602.1|FL428602
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
EST: gi|211239053|gb|FL421811.1|FL421811
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGC-AACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
EST: gi|211468699|gb|FL380604.1|FL380604
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
EST: gi|93017131|gb|EB642651.1|EB642651
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
EST: gi|33095153|gb|CF055147.1|CF055147
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTAC
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTAC
EST: gi|211269039|gb|FL404034.1|FL404034
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGGACGAGGTGAGAGGACCCCAA
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGA-AGGACCCCAA
EST: gi|74237715|gb|DT645629.1|DT645629
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
EST: gi|93013352|gb|EB638872.1|EB638872
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
EST: gi|211112036|gb|FL390925.1|FL390925
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTG
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTG
EST: gi|166591684|gb|EG169185.1|EG169185
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAG
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAG
EST: gi|211496370|gb|FL389443.1|FL389443
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
EST: gi|14529566|gb|BI096699.1|BI096699
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAAC
EST: gi|211374578|gb|FL413729.1|FL413729
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGNCAACGTCTCCAAG                         GCGGAGTNGAAGGAGAGGCTTGCCAAGATGAACGAGGTGAAGG
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGG
EST: gi|33095603|gb|CF055597.1|CF055597
EST:     GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG                         GCGGAGTTGAAGGAGAGGCTTGCCAAGATGT
genomic: GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGT

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: 1697

GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAACACCATCTTCGTCTTCAAGTTCCGCACCCACTTCGGTGGAGGCAAGTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1046

GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAACACCATCTTCGTCTTCAAGTTCCGCACCCACTTCGGTGGAGGCAAGTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 888

GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAACACCATCTTCGTCTTCAAGTTCCGCACCCACTTCGGTGGAGGCAAGTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 482

GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatc ... ctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAACACCATCTTCGTCTTCAAGTTCCGCACCCACTTCGGTGGAGGCAAGTCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcgggagcttctggcctggatctcagggttgttctgcttgttctctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAACACCATCTTCGTCTTCAAGTTCCGCACCCACTTCGGTGGAGGCAAGTCCA
                                ttctgcttgttctctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatatcggccccggtactgtgtgcgcggctcatatggcgggagcttctggcctggatctcagggttgttctgcttgttctctttgtgtagGCGGAGTTGAAGGAGAGGCTTGCCAAGATGTACGAGGTGAAGGACCCCAACACCATCTTCGTCTTCAAGTTCCGCACCCACTTCGGTGGAGGCAAGTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG