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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcattattaagttacactttcttgaaatagactttgactcataattaaaattaacatatgatttcccttcacagCCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACAATTAGTAGACGCCACGAGGAGAAAGTTACTGATGGAGGTGGCAAGCCAT

Basic information

species Zea mays
transcript GRMZM2G082214_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082214_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g16940.1 (Oryza sativa), 3'ss of exon 3
gtactcattattaagttacactttcttgaaatagactttgactcataattaaaattaacatatgatttcccttcacagCCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACAATTAGTAGACGCCACGAGGAGAAAGTTACTGATGGAGGTGGCAAGCCAT
|||    || ||  ||| | ||||||  ||||  || || ||  ||||||     |||| |||||    ||||||||||||||| |||  ||||||||| |  |||| || |||||||||||||||||||||||||||||  | || |||| ||||||||| ||| ||||||||||||
gtatctgttcttgggttgccctttctgtaaatgaacctttacatataatt-----taac-tatgagactccttcacagCCCAATCAAGATAGGCAGGTTGTCTCAACTCTGTACTCACTTGAAGATACAATTAGTAGACGGAAGGAAGAGATAGTTACTGAAGGAAGTGGCAAGCCAT
















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|18163681|gb|BM333520.1|BM333520
EST:     TACTTCAGTTTATGATGCTCTACAAAGTTCAAAG                         CCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACA
genomic: TACTTCAGTTTATGATGCTCTACAAAGTTCAAAGgtactcatta ... cccttcacagCCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACA
EST: gi|32849363|gb|CD989044.1|CD989044
EST:     CAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAGGTCCAAAG                         CCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTCGAAGATACA
genomic: CAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAGgtactcatta ... cccttcacagCCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACA
EST: gi|67018853|gb|CO447602.1|CO447602
EST:     CAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAG                         CCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTNGAAGATAC
genomic: CAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAGgtactcatta ... cccttcacagCCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTT-GAAGATAC
EST: gi|78027709|gb|DV496096.1|DV496096
EST:     CAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAG                         CCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACA
genomic: CAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAGgtactcatta ... cccttcacagCCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACA
EST: gi|5108141|gb|AI739854.1|AI739854
EST:     CAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAG                         CCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACA
genomic: CAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAGgtactcatta ... cccttcacagCCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACA
EST: gi|148987058|gb|EE030883.2|EE030883
EST:     CAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAG                         CCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACA
genomic: CAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAGgtactcatta ... cccttcacagCCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACA
EST: gi|20811241|gb|BQ295719.1|BQ295719
EST:     CAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAG                         CCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACC
genomic: CAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAGgtactcatta ... cccttcacagCCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACA
EST: gi|61118955|gb|DN559916.1|DN559916
EST:     CAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAGG                         CCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACA
genomic: CAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAGgtactcatta ... cccttcacagCCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACA
EST: gi|211366681|gb|FK959526.1|FK959526
EST:     CAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAG                         CCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACA
genomic: CAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAGgtactcatta ... cccttcacagCCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACA
EST: gi|60349630|gb|DN216603.1|DN216603
EST:     CAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAG                         CCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACA
genomic: CAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAGgtactcatta ... cccttcacagCCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACA

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: 48 (upstream exon), 48 (downstream exon)
Score: 83

ATAATATACCTTGGAAAGCCAGATGGACCTACCTGCCATACAGGAGCAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAGgtactcatta ... cccttcacagCCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACAATTAGTAGACGCCACGAGGAGAAAGTTACTGATGGAGGTGGCAAGCCAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 99

ATAATATACCTTGGAAAGCCAGATGGACCTACCTGCCATACAGGAGCAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAGgtactcatta ... cccttcacagCCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACAATTAGTAGACGCCACGAGGAGAAAGTTACTGATGGAGGTGGCAAGCCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

ATAATATACCTTGGAAAGCCAGATGGACCTACCTGCCATACAGGAGCAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAGgtactcatta ... cccttcacagCCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACAATTAGTAGACGCCACGAGGAGAAAGTTACTGATGGAGGTGGCAAGCCAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 76

ATAATATACCTTGGAAAGCCAGATGGACCTACCTGCCATACAGGAGCAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAGgtactcatta ... cccttcacagCCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACAATTAGTAGACGCCACGAGGAGAAAGTTACTGATGGAGGTGGCAAGCCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgaaatagactttgactcataattaaaattaacatatgatttcccttcacagCCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACAATTAGTAGACGCCACGAGGAGAAAGTTACTGATGGAGGTGGCAAGCCAT
                             aattaac  putative branch site (score: 76)
                                          tttcccttcac  putative PPT
                 actcataattaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactcattattaagttacactttcttgaaatagactttgactcataattaaaattaacatatgatttcccttcacagCCCAATGAAGGCAGGCAGGTTATGACAACCCTATACTCACTTGAAGATACAATTAGTAGACGCCACGAGGAGAAAGTTACTGATGGAGGTGGCAAGCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG