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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCAgtatccttttgttttctctctgcagctataacgttcattctaagtgcatattgctacttacaattttaaattattgaagtgcctaaattgtaaattttaagaattattattaaaagaaatgttgcaatgagttcctgaaaattttcctag

Basic information

species Zea mays
transcript GRMZM2G092112_T01
intron # 7
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092112_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g48920.1 (Oryza sativa), 5'ss of exon 7
GTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCAgtatccttttgttttctctctgcagctataacgttcattctaagtgcatattgctacttacaattttaaattattgaagtgcctaaattgtaaattttaagaattattattaaaagaaatgttgcaatgagttcctgaaaattttcctag
||||| |||||||||||||||||||| |||||||||||||| || || |||||||||||||||||||| ||||||||||||||  |||||||||        | |      ||||    || | |  || |  |      |  | |   |||| |   |  ||| | ||     | |    || |  || || |                                          
GTTGAATGGGATGAGATAAATGCTGCTTGGGGTCAGGCTGCTCTTCTTTTGCATACCATGGCTCAGTACTTCACCCCAAAATTTGAgtatccttga----catattgatgactatttattttactacaatt--aatccattggtcattcttttgag--aaggaattcccattgatcttcccttcatcaactagt------------------------------------------

upper sequence: GRMZM2G092112_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g44200.1 (Oryza sativa), 5'ss of exon 8
GTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCAgtatccttttgttttctctctgcagctataacgttcattcta-agtgcatattgctacttacaattttaaattattgaagtgcctaaattgtaaattttaagaattattattaaaagaaatgttgcaatgagttcctgaaaattttcctag
|| ||||||||||||||||||||||| ||||| |||||||| || ||||||||||||||||||||||| |||  |||||||||  ||||||||||           | |||  | |   ||  | ||| |||  || |||||  | |   | || |    |   | | | || || | |  |      |   | || | |                                     
GTGGAGTGGGATGAGATAAATGCTGCTTGGGGCCAGGCTGCTCTTCTGTTGCATACCATGGCTCAGTACTTCTTCCCAAAATTTGAgtatccttta----------tacagtgacattatttttgctacagtttat-ttgctggtcattctcttgagaagt---aattcatacatggcatttacctccatcaactagtta-------------------------------------
















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|50327434|gb|CO522560.1|CO522560
EST:     CACCCCAAAATTCCA                         ATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
genomic: CACCCCAAAATTCCAgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
EST: gi|71764422|gb|DR962359.1|DR962359
EST:     GCACTGCTGTTGCATACCCATGGCTCAGTATTTCACCCCCAAAATTCCA                         ATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
genomic: GCACTGCTGTTGCATA-CCATGGCTCAGTATTTCA-CCCCAAAATTCCAgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
EST: gi|86471374|gb|DY237744.1|DY237744
EST:     GCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA                         ATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
genomic: GCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCAgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
EST: gi|74242756|gb|DT650670.1|DT650670
EST:     GCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA                         ATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
genomic: GCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCAgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
EST: gi|29545091|gb|CB605269.1|CB605269
EST:     GCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA                         ATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
genomic: GCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCAgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
EST: gi|67014170|gb|CO442919.1|CO442919
EST:     CTGCACTGCTGTTGCATACCATGGGCTCAGT-TTTCACCCCAAAATTCCA                         -TACCGGATCAAGATTCACCCTATGGGAAGCTTTCCCAGAGTCACAGACAT
genomic: CTGCACTGCTGTTGCATACCATGG-CTCAGTATTTCACCCCAAAATTCCAgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
EST: gi|7238063|gb|AW573435.1|AW573435
EST:     GCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA                         ATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
genomic: GCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCAgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
EST: gi|24767878|gb|CA403013.1|CA403013
EST:     GCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA                         ATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
genomic: GCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCAgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
EST: gi|40303501|gb|CK347888.1|CK347888
EST:     GCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA                         ATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
genomic: GCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCAgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
EST: gi|211504091|gb|FL041160.1|FL041160
EST:     GTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA                         ATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
genomic: GTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCAgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT

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: 46 (upstream exon), 47 (downstream exon)
Score: 328

GTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCAgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 229

GTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCAgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 284

GTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCAgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 332

GTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCAgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCAgtatccttttgttttctctctgcagctataacgttcattctaagtgcatattgctacttacaattttaaattattgaagtgcctaaattgtaaattttaagaattattattaaaagaaatgttgcaatgagttcctgaaaattttcctag

- - - - - - - - - - - - - - - - - - - - - - GCTGTT