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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCAAGTCGGCGGCGTCGTCTCCGTGCGCGTCTGCAGGGACATCAACTCCCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactctgcagtattctcgatctgtcggttagggtttcggtgctgcggacgctgtcgaccccttgcgagaagccgtcggatttggcggttgttagt...

Basic information

species Zea mays
transcript GRMZM2G102829_T03
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102829_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os09g02700.1 (Oryza sativa), 5'ss of exon 1
AGCCAAGTCGGCGGCGTCGTCTCCGTGCGCGTCTGCAGGGACATCAACTCCCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactctgcagtat-tctcgatctg-tcggttagggtttcggtgctgcggacgctgtcgaccccttgcgagaagccgtcggatttggcggttgttagt-
|| |||||||||||||||||||||||||||||||||||| ||||| | || | ||||||||| ||||||||||||||||||| || || | ||| ||| | ||| | | |||| ||| ||| || ||| | | || | | || | | ||| | || |
GCGCAGGTCGGCGGCGTCGTCTCCGTGCGCGTCTGCAGGGACGTCAACACGCGGAGGTCGCTCGGCTACGCCTACGTCAACTACAGCAGCCCCGCCGATGgt---acctccccgatccgcctcgccctgctcgattgctgttcttttcccacgaatctagcatctaggtttaggtggattgcttttttttccttttcccaaga
















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|18963395|gb|BM660411.1|BM660411
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
EST: gi|32795710|gb|CD947946.1|CD947946
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGC
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGC
EST: gi|94478793|gb|EB707751.1|EB707751
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
EST: gi|76287722|gb|DV027290.1|DV027290
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
EST: gi|87152528|gb|DY397317.1|DY397317
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         TTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
EST: gi|32802614|gb|CD954850.1|CD954850
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTA
EST: gi|32802522|gb|CD954758.1|CD954758
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTA
EST: gi|6526941|gb|AW216188.1|AW216188
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACCTGCTTAACTTCACTCCTATCAATGGAAAGCCT
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAAC-TGCTTAACTTCACTCCTATCAATGGAAAGCCT
EST: gi|37420628|gb|CF648009.1|CF648009
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
EST: gi|91872653|gb|EB402610.1|EB402610
EST:     GGGTACGCGTACGTCAAATACAACATCCAGGGCGGCG                         CTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCGA
genomic: GGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
EST: gi|32802269|gb|CD954505.1|CD954505
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTA
EST: gi|19770298|gb|BQ035019.1|BQ035019
EST:     CCGCAAGTCGCTCGGGTTCGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
EST: gi|50339950|gb|CO535076.1|CO535076
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
EST: gi|60291829|gb|DN190068.1|DN190068
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
EST: gi|89247208|gb|DY618994.1|DY618994
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
EST: gi|71757068|gb|DR955005.1|DR955005
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
EST: gi|50339951|gb|CO535077.1|CO535077
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
EST: gi|91872652|gb|EB402609.1|EB402609
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
EST: gi|60400258|gb|DN233065.1|DN233065
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
EST: gi|61119220|gb|DN560181.1|DN560181
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
EST: gi|32804742|gb|CD956978.1|CD956978
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTACTTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTA
EST: gi|30705350|gb|CD058755.1|CD058755
EST:     GTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
genomic: GTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
EST: gi|89249056|gb|DY620842.1|DY620842
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
EST: gi|76291689|gb|DV031257.1|DV031257
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
EST: gi|78119331|gb|DV537715.1|DV537715
EST:     CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACG                         CTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA
genomic: CCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTA

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: 933

AGCCAAGTCGGCGGCGTCGTCTCCGTGCGCGTCTGCAGGGACATCAACTCCCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTATCAGGATCATGTATTCTAACCGTGACCCTAGCTCGCGCAAAAGCGGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 806

AGCCAAGTCGGCGGCGTCGTCTCCGTGCGCGTCTGCAGGGACATCAACTCCCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTATCAGGATCATGTATTCTAACCGTGACCCTAGCTCGCGCAAAAGCGGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 533

AGCCAAGTCGGCGGCGTCGTCTCCGTGCGCGTCTGCAGGGACATCAACTCCCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTATCAGGATCATGTATTCTAACCGTGACCCTAGCTCGCGCAAAAGCGGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 548

AGCCAAGTCGGCGGCGTCGTCTCCGTGCGCGTCTGCAGGGACATCAACTCCCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactc ... tttattgcagCTGCACGAGCACTTGAACTGCTTAACTTCACTCCTATCAATGGAAAGCCTATCAGGATCATGTATTCTAACCGTGACCCTAGCTCGCGCAAAAGCGGCAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCAAGTCGGCGGCGTCGTCTCCGTGCGCGTCTGCAGGGACATCAACTCCCGCAAGTCGCTCGGGTACGCCTACGTCAACTACAACAACCAGGGCGACGgtgagaactctgcagtattctcgatctgtcggttagggtttcggtgctgcggacgctgtcgaccccttgcgagaagccgtcggatttggcggttgttagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgacccc