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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaataaaaggcttactatttgcttagtgttttgtcttttcatgggtggaccaactcagcttgtaacctgacatttcttcaccttgccatctcatag

Basic information

species Zea mays
transcript GRMZM2G108829_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g47220.3 (Oryza sativa), 5'ss of exon 5
GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaataaaaggcttactatttgcttagtgttttgtcttttcatgggtggaccaactcagcttgtaacctgacatttcttcaccttgccatctcatag
||| || ||||| |||||||||||||||||||||   |||||||||||||||||||         ||     |||||| | ||| || ||||| |   |   |     || || |||     | |   ||   | |      |||||| ||   ||
GTACCGAGCACCTGAAGTATTGCTCCAGTCATCTATCTATGATTCTGCAGTTGgta---------aagtttctactatctactttgtattttggcacatatagtacatactaagtca-----tgattggatgatcccct-ttttgccaacttgcag
















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|60349468|gb|DN216441.1|DN216441
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
EST: gi|211496286|gb|FL041698.1|FL041698
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATATGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
EST: gi|32871065|gb|CF010747.1|CF010747
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
EST: gi|32932540|gb|CF037352.1|CF037352
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
EST: gi|71304777|gb|DR788504.1|DR788504
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
EST: gi|31350422|gb|CD434779.1|CD434779
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
EST: gi|32869779|gb|CF009461.1|CF009461
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
EST: gi|47961778|gb|CN844487.1|CN844487
EST:     CGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTTG                         ATATGTGGGCAATGGGGGCCATAATGGCTGA
genomic: CGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTT-Ggtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGA
EST: gi|67011156|gb|CO439905.1|CO439905
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
EST: gi|211496285|gb|FL041697.1|FL041697
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
EST: gi|5932684|gb|AW057045.1|AW057045
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC

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: 292

GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 239

GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaataaaaggcttactatttgcttagtgttttgtcttttcatgggtggaccaactcagcttgtaacctgacatttcttcaccttgccatctcatag

- - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - CTGCAG