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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGGTGTCGCTGCTGCACTCCTTCATCCCCACGCACTGGCTCCCCTTCTCCATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtacccacctcccttccgcgtgcctcgttccccccatttgctgcggttgccgctcgttactgttcaccgcctcggcgcctccagatctggttatct...

Basic information

species Zea mays
transcript GRMZM2G078895_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078895_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g17020.1 (Oryza sativa), 5'ss of exon 1
ACGGTGTCGCTGCTGCACTCCTTCATCCCCACGCACTGGCTCCCCTTCTCCATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtacccacc---tcccttccgcgtgcctcgttccccccatttgctgcggttgccgctcgttactgt-tcaccgcctcggcgcctccagatctggttatct
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||| |||||||||||||||||||| |||||||||||||| || ||   |  |  || ||   | | ||||||    | ||| | | ||   | | ||||  |   |||||| |  | || ||    |         
ACGGTGTCGCTGCTGCACTCCTTCATCCCCACGCACTGGCTCCCCTTCTCCATCGTCGCCCGCGCCCAGCGGTGGCCGCTCTCCCGCACCCTCCTCGTCAgtcagtatcccccaaatttcccccccgcttccctttccccaatctcgcttctgctgtgccgctttacgctactaccgccccccccccccccccccaaaga----

upper sequence: GRMZM2G078895_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv06s0009g01580.t01 (Vitis vinifera), 5'ss of exon 1
ACGGTGTCGCTGCTGCACTCCTTCATCCCCACGCACTGGCTCCCCTTCTCCATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagt-acccacctcccttccgcgtgcctcgttccccccatttgctgcggttgccgctcgttactgttcaccgcctcggcgcctccagatctggttatct---
|| || ||||| || ||||||||||||||||| || |||||||| || |||||||| |  ||||| |||   ||| | ||||||   || ||| |||||||| |||   |||      | ||   | | | |  ||      |   |    ||   |  |   |    | |   | |    || | || ||||| | |  |   
ACCGTTTCGCTTCTCCACTCCTTCATCCCCACCCATTGGCTCCCTTTTTCCATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgaccaaaattttcccattttcttag--cctaatggtcatttttctttttgg-caaaaaaaataaggccatttctgcattca-atctgttcagataaa

upper sequence: GRMZM2G078895_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ20770 (Selaginella moellendorffii), 5'ss of exon 1
ACGGTGTCGCTGCTGCACTCCTTCATCCCCACGCACTGGCTCCCCTTCTCCATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtacccacctccct-tccgcgtgcctcgttccccccatttgctgcggttgccgctcgttactgttcaccgcctcggcgcctccagatctggttatct
|| ||||||||||| || || |||||||||||||||||||| |||||||| ||||||| |||||| |||   ||| || | || || || || ||||||||| ||||   |  ||    |||| | |  | |    |     ||||| || | || |                                            
ACAGTGTCGCTGCTCCATTCTTTCATCCCCACGCACTGGCTGCCCTTCTCAATCGTCGGGCGCGCACAGAAGTGGACGATTTCGCGAACGCTGCTCGTCAgtaagtagaaatttctggatccgagcgtattgaattcg----ttgct-cgatcgcag--------------------------------------------

upper sequence: GRMZM2G078895_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ32656 (Selaginella moellendorffii), 5'ss of exon 1
ACGGTGTCGCTGCTGCACTCCTTCATCCCCACGCACTGGCTCCCCTTCTCCATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtacccacctccct-tccgcgtgcctcgttccccccatttgct-gcggttgccgctcgttactgttcaccgcctcggcgcctccagatctggttatct
|| ||||||||||| || || |||||||||||||||||||| |||||||| ||||||| |||||| |||   ||| || | || || || || ||||||||| ||||   |  || |  |||| | |  | |    |     | | | || |                                                  
ACAGTGTCGCTGCTCCATTCTTTCATCCCCACGCACTGGCTGCCCTTCTCGATCGTCGGGCGCGCCCAGAAGTGGACGATTTCGCGAACGCTGCTCGTCAgtaagtagaaatttctcgatccgagcgtattgaattcgtttctcgatcgcag--------------------------------------------------

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|91873275|gb|EB403232.1|EB403232
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|148945169|gb|EC890369.2|EC890369
EST:     GGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: GGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|60337164|gb|DN204137.1|DN204137
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|211374713|gb|FL074581.1|FL074581
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|74244751|gb|DT652665.1|DT652665
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|211369405|gb|FL074563.1|FL074563
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|211369403|gb|FL074561.1|FL074561
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|78113499|gb|DV531890.1|DV531890
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|71428239|gb|DR809289.1|DR809289
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|211374716|gb|FL074584.1|FL074584
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|211434405|gb|FL298801.1|FL298801
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|211374714|gb|FL074582.1|FL074582
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|71428238|gb|DR809288.1|DR809288
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|14997229|gb|BI319243.1|BI319243
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTCCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|211372060|gb|FL074578.1|FL074578
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|211374721|gb|FL074589.1|FL074589
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|211372055|gb|FL074573.1|FL074573
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATA-
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|211374712|gb|FL074580.1|FL074580
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|148945170|gb|EC890370.2|EC890370
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|211372056|gb|FL074574.1|FL074574
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|211372047|gb|FL074565.1|FL074565
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|60350868|gb|DN217841.1|DN217841
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|211372048|gb|FL074566.1|FL074566
EST:     CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCA                         CTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: CATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
EST: gi|78025927|gb|DV494314.1|DV494314
EST:     GCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTCCTGGTCA                         TTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA
genomic: GCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAA

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: 77

ACGGTGTCGCTGCTGCACTCCTTCATCCCCACGCACTGGCTCCCCTTCTCCATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAACTGCAGTTACTATGGCAAATACTATAGCTGGCGAAGAAACAGTGCATAA


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 42

ACGGTGTCGCTGCTGCACTCCTTCATCCCCACGCACTGGCTCCCCTTCTCCATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAACTGCAGTTACTATGGCAAATACTATAGCTGGCGAAGAAACAGTGCATAA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 44

ACGGTGTCGCTGCTGCACTCCTTCATCCCCACGCACTGGCTCCCCTTCTCCATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAACTGCAGTTACTATGGCAAATACTATAGCTGGCGAAGAAACAGTGCATAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 56

ACGGTGTCGCTGCTGCACTCCTTCATCCCCACGCACTGGCTCCCCTTCTCCATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtaccc ... acttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAACTGCAGTTACTATGGCAAATACTATAGCTGGCGAAGAAACAGTGCATAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGGTGTCGCTGCTGCACTCCTTCATCCCCACGCACTGGCTCCCCTTCTCCATCGTCGCGCGCGCGCAGCGCTGGCCGCTCTCCCGCACCCTTCTCGTCAgtcagtacccacctcccttccgcgtgcctcgttccccccatttgctgcggttgccgctcgttactgttcaccgcctcggcgcctccagatctggttatct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccacctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caccgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcctcc