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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtgatgttccatcctatcctagtcctagcgctaaatttgtttccagcacattcagttctctgaaacttgctggatgaagcaattcttccccagtcatggtagtatatattcacacccctgactatgttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG

Basic information

species Zea mays
transcript GRMZM2G031107_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031107_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os02g38840.2 (Oryza sativa), 3'ss of exon 14
-----------------------------gtgcgtgatgttcca-tcctatcctagtc-ctagcgctaaat-ttgtttccagcacattcagttctc----tgaaa----cttgctggatgaagcaattc--ttccccagtcatggta-gtatatat-----------tcacacccctgactatgttttc-acagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
                              | | |  || | || |  || | |  || || ||  |     ||||| ||| ||||| |  |   |    ||||     | || |||||| ||        ||    |  |||  ||  ||||||            | | | |     | || ||||  ||||||||||||| || ||||||||||| ||||||||||| || |||| |
gtacgtcctgttccatccttcttcccccatttctttctgctacactaataacttcttcacttgcattgcgccttgttcccaacacatgccatatccaagatgaactatccgtgttggatgtagaggccgggtttttaatccattatatatatataaaggatgaaccatgatatcatcttccatttttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
















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|14203621|gb|BG837298.1|BG837298
EST:     ACAATGACGTAAAAATCCCAGAGAGCATACGAGCGTCTCATCTTGGACAC                         GATAAGAGGAGACCAGCACGCACTTCGTTCGCCGAGATGAGCTGAGG
genomic: ACAATGGCGTCAAAATCCCAGA-AGCATACGAGCGTCTCATCTTGGATACgtgcgtgatg ... gttttcacagGATAAGAGGAGACCAGCA-GCACTTCGTTCGCCGAGATGAGCTGAGG
EST: gi|26456967|gb|CA828550.1|CA828550
EST:     TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATAC                         GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
genomic: TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATACgtgcgtgatg ... gttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
EST: gi|6031397|gb|AW076299.1|AW076299
EST:     TACAATGACGTAAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGACAC                         GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
genomic: TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATACgtgcgtgatg ... gttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
EST: gi|71596396|gb|DR907147.1|DR907147
EST:     TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATAC                         GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
genomic: TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATACgtgcgtgatg ... gttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
EST: gi|78077421|gb|DV505855.1|DV505855
EST:     TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATAC                         GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
genomic: TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATACgtgcgtgatg ... gttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
EST: gi|22521339|gb|BU080150.1|BU080150
EST:     TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATAC                         GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
genomic: TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATACgtgcgtgatg ... gttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
EST: gi|78119963|gb|DV538347.1|DV538347
EST:     TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTTTCATCTTGGATAC                         GATAAGAGGAGACCAGCAGCCCTTCGTTCGCCGAGATGAGCTGAGG
genomic: TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATACgtgcgtgatg ... gttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
EST: gi|88750685|gb|DY534826.1|DY534826
EST:     TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATAC                         GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
genomic: TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATACgtgcgtgatg ... gttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
EST: gi|109179593|gb|EC380097.1|EC380097
EST:     GGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATAC                         GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
genomic: GGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATACgtgcgtgatg ... gttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
EST: gi|51592845|gb|CV071991.1|CV071991
EST:     TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATAC                         GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
genomic: TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATACgtgcgtgatg ... gttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
EST: gi|47962266|gb|CN844975.1|CN844975
EST:     TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATAC                         GATAAGAGGAGACCAGCAGTACTTCGTTCGCCGAGATGAGCTGAGG
genomic: TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATACgtgcgtgatg ... gttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
EST: gi|76281884|gb|DV021452.1|DV021452
EST:     TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATAC                         GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
genomic: TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATACgtgcgtgatg ... gttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
EST: gi|78544145|gb|DV621643.1|DV621643
EST:     TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATAC                         GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
genomic: TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATACgtgcgtgatg ... gttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
EST: gi|78109019|gb|DV527436.1|DV527436
EST:     TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATAC                         GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
genomic: TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATACgtgcgtgatg ... gttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
EST: gi|62550472|gb|DN830892.1|DN830892
EST:     TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATAC                         GATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
genomic: TACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATACgtgcgtgatg ... gttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG

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), 46 (downstream exon)
Score: 133

TGGAAATGGCAACCGAACAAAGCGAACTGGATCTATCGTATGGGATGCGGTACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATACgtgcgtgatg ... gttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 702

TGGAAATGGCAACCGAACAAAGCGAACTGGATCTATCGTATGGGATGCGGTACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATACgtgcgtgatg ... gttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 906

TGGAAATGGCAACCGAACAAAGCGAACTGGATCTATCGTATGGGATGCGGTACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATACgtgcgtgatg ... gttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 327

TGGAAATGGCAACCGAACAAAGCGAACTGGATCTATCGTATGGGATGCGGTACAATGGCGTCAAAATCCCAGAAGCATACGAGCGTCTCATCTTGGATACgtgcgtgatg ... gttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattcttccccagtcatggtagtatatattcacacccctgactatgttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
                                   ccctgac  putative branch site (score: 327)
                                            tgttttc  putative PPT
                   tagtatatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtgatgttccatcctatcctagtcctagcgctaaatttgtttccagcacattcagttctctgaaacttgctggatgaagcaattcttccccagtcatggtagtatatattcacacccctgactatgttttcacagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA