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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactctcctatgtgtttgaggaaaaaaatacatgatgttccttccaaagttttgtattaatcggcaacctaactgcttttgttctctgtaactgttttagTGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAATGACACAGAAGAGGCAAGGAAGAAGATAAGAAAATTCAAGGAATCAGCTT

Basic information

species Zea mays
transcript GRMZM2G444643_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G444643_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 1
-------aactctcctatgtgtttgaggaaaaaaatacatgatgttccttccaaagttttgtattaatcggcaacctaactgcttttgttctctgtaactgttttagTGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAATGACACAGAAGAGGCAAGGAAGAAGATAAGAAAATTCAAGGAATCAGCTT------
          |    ||  |  || |       |||   | ||||   ||| |||| ||  | || |    ||   | | || |||| || | | |    |||| ||||| ||| ||  |  ||||||  |||  ||| |      |  | | || |||| |  || ||  |||| ||||||||||||||||| |||||||||||||      
tagatatttttactttaaataattaacattttcaattgttaatgtaa-ttctaaagcttaatgttga----cactttcattgtttttcttttattt--tcgtttcagTGGATTGGAAGAAAACTTATATTTGGAAAGGAA------AAGGTTGATTATGAGAAGGAGGAAACAAGAAAGAAGATAAGAAAATTTAAGGAATCAGCTTGGAAAT
















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|211231830|gb|FL279445.1|FL279445
EST:     TTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAG                         TGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAAT
genomic: TTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAGgtgcgactgc ... actgttttagTGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAAT
EST: gi|211233878|gb|FL279446.1|FL279446
EST:     TTCTCTTCTWCCCTACCGTCCGCTTYCTCCTCGACCGCTTCGTCTTCAAG                         TGGGTTGCAATGAGGCTTATACATGGGCAGGGGACATCAGAGAGCTAATAA
genomic: TTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAGgtgcgactgc ... actgttttagTGGGTTGCAATGAGGCTTATACATGGGCAGGG-ACATCAGAGAGCTAATAA
EST: gi|211233880|gb|FL279448.1|FL279448
EST:     TTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAG                         TGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAAT
genomic: TTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAGgtgcgactgc ... actgttttagTGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAAT
EST: gi|211233879|gb|FL279447.1|FL279447
EST:     TTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAG                         TGGGT-GCAATGAGGCTTATAACATGGGCAGGGACATCAGAGAGCTAATAA
genomic: TTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAGgtgcgactgc ... actgttttagTGGGTTGCAATGAGGCTTATA-CATGGGCAGGGACATCAGAGAGCTAATAA
EST: gi|211231827|gb|FL279442.1|FL279442
EST:     TTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAG                         TGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAAT
genomic: TTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAGgtgcgactgc ... actgttttagTGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAAT
EST: gi|71767992|gb|DR965929.1|DR965929
EST:     TTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAG                         TGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAAT
genomic: TTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAGgtgcgactgc ... actgttttagTGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAAT
EST: gi|211231825|gb|FL279440.1|FL279440
EST:     TTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAG                         TGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAAT
genomic: TTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAGgtgcgactgc ... actgttttagTGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAAT
EST: gi|78104263|gb|DV522681.1|DV522681
EST:     TTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAG                         TGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAAT
genomic: TTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAGgtgcgactgc ... actgttttagTGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAAT
EST: gi|78086491|gb|DV514884.1|DV514884
EST:     TTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAG                         TGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAAT
genomic: TTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAGgtgcgactgc ... actgttttagTGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAAT

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: 47 (upstream exon), 44 (downstream exon)
Score: 142

GCGCGAGGCCTACCCTGCGTACGACGACTTCCTCGCGCTCCCCGCCTTCGTTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAGgtgcgactgc ... actgttttagTGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAATGACACAGAAGAGGCAAGGAAGAAGATAAGAAAATTCAAGGAATCAGCTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 172

GCGCGAGGCCTACCCTGCGTACGACGACTTCCTCGCGCTCCCCGCCTTCGTTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAGgtgcgactgc ... actgttttagTGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAATGACACAGAAGAGGCAAGGAAGAAGATAAGAAAATTCAAGGAATCAGCTT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 210

GCGCGAGGCCTACCCTGCGTACGACGACTTCCTCGCGCTCCCCGCCTTCGTTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAGgtgcgactgc ... actgttttagTGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAATGACACAGAAGAGGCAAGGAAGAAGATAAGAAAATTCAAGGAATCAGCTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 135

GCGCGAGGCCTACCCTGCGTACGACGACTTCCTCGCGCTCCCCGCCTTCGTTCTCTTCTTCCCTACCGTCCGCTTCCTCCTCGACCGCTTCGTCTTCAAGgtgcgactgc ... actgttttagTGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAATGACACAGAAGAGGCAAGGAAGAAGATAAGAAAATTCAAGGAATCAGCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagttttgtattaatcggcaacctaactgcttttgttctctgtaactgttttagTGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAATGACACAGAAGAGGCAAGGAAGAAGATAAGAAAATTCAAGGAATCAGCTT
                                              ctgtttt  CT-rich tract
     tttgtattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactctcctatgtgtttgaggaaaaaaatacatgatgttccttccaaagttttgtattaatcggcaacctaactgcttttgttctctgtaactgttttagTGGGTTGCAATGAGGCTTATACATGGGCAGGGACATCAGAGAGCTAATAATGACACAGAAGAGGCAAGGAAGAAGATAAGAAAATTCAAGGAATCAGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - tgtgttt
- - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - tgatgtt