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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttcttcaatgacactctaatcttattgtggtgtggtattgtgcactttgagccttgtaaaaagtgatattctgattgctccagcgtgccatcac...

Basic information

species Zea mays
transcript GRMZM2G099547_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099547_T04 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g19470.1 (Oryza sativa), 5'ss of exon 5
GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttcttcaatgacac--------------tctaatcttattg----------tggtgtggtatt-gtgcactttgagccttgtaaaaa-gtgatattctgattgctccagcgtgccatcac--------------------------------
|||||||||||||||| ||||||||||| || ||||| | |||||||||||||||||| ||||  ||  | ||||| || |||||||||||||||||||   |||  ||              | | |||||||||          | ||  | | ||  |  |||||||| | |||||||| ||| || | |         ||| | |   | |                                
GAGTGAATGCTGATGATGTTCGAGTAACAGTTGCTGCTCCTGCTGCTCGAGGGGAAGCAAACAACGAACTACTAGAGTTCATGGGCAAGgtgattttctcttatggtacctttattgggaacatgttatcttattgaattccactttcgtaggatgttcatctactttgagacatgtaaaaatgtgttaatgtttcacaataagcattctgaccctctgatgcgaacaagttcatgctatgaatcag

upper sequence: GRMZM2G099547_T04 (Zea mays), 5'ss of exon 5
lower sequence: Vv17s0000g01530.t01 (Vitis vinifera), 5'ss of exon 5
GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttcttcaatgacactctaatcttat-tgtggtgtggtattgtgcactttgagccttgtaaaaagtgatattctgattgctccagcgtgccatcac
| |||||||| ||||| |||||||| || |||||||| | ||| || || ||||||||||||| |||  |  | ||||| |||||||| ||    |     |       ||| || |||| | |  |||   ||| |    ||| ||   ||| ||   | |       | |  | ||   || |||   
GGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAAgtatcct-----agcatacttctcattttatgttttttgtcaaattatcactttttagg--tgtcaagcctaactactcaagtcttgca-tttggcatag-
















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|16926773|gb|BM079841.1|BM079841
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|60394679|gb|DN227549.1|DN227549
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|101392937|gb|EB818399.1|EB818399
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCTTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|211360252|gb|FL253401.1|FL253401
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|60348216|gb|DN215189.1|DN215189
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|12045916|gb|BF728146.1|BF728146
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGATTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|148980593|gb|EE027217.2|EE027217
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|32846204|gb|CD985885.1|CD985885
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGATTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|86471527|gb|DY237897.1|DY237897
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|71433975|gb|DR815025.1|DR815025
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|60337078|gb|DN204051.1|DN204051
EST:     TGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGGCAAG                         -TTCTTGGCCTAAG
genomic: TGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGG-CAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAG
EST: gi|60337543|gb|DN204516.1|DN204516
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|71433974|gb|DR815024.1|DR815024
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|60351167|gb|DN218140.1|DN218140
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGATTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|32928940|gb|CF033752.1|CF033752
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGATTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|16920282|gb|BM074585.1|BM074585
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|71303362|gb|DR787781.1|DR787781
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|6563795|gb|AW231327.1|AW231327
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|71757029|gb|DR954966.1|DR954966
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|16925502|gb|BM078570.1|BM078570
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|78180203|gb|DV550576.1|DV550576
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGATTGACTCAAATGACCC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCC
EST: gi|6827273|gb|AW330916.1|AW330916
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGATTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|78117103|gb|DV535490.1|DV535490
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|78075508|gb|DV503942.1|DV503942
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCNAAGAGGATGGAATAAC
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAAC
EST: gi|50325142|gb|CO520268.1|CO520268
EST:     TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG                         GTTCTTGGCCTAAGACTGACTCAG
genomic: TTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAG

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), 48 (downstream exon)
Score: 204

GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 183

GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATT


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 227

GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATT


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 116

GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttct ... gtgaaagcagGTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttcttcaatgacactctaatcttattgtggtgtggtattgtgcactttgagccttgtaaaaagtgatattctgattgctccagcgtgccatcac

- - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtaaaaag