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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgctctcaatgtagagattaagcaacatcgatgacatccacgaaggcttttgctgaaatgtttttgattgtatcagtagGTCCATTCCCAGAATCTCCCCGGCTGGCTCGGTTCCCGAACCTCCCCGACATGTCTCCAAAGAAGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCT

Basic information

species Zea mays
transcript GRMZM2G033828_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033828_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os08g42600.1 (Oryza sativa), 3'ss of exon 15
------gtacgctctcaatgtagagattaagca--acatcgatgacatccacgaaggcttttgctgaaatgtttttgattgtatcagtagGTCCATTCCCAGAATCTCCCCGGCTGGCTCGGTTCCCGAACCTCCCCGACATGTCTCCAAAGAAGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCT
        | |  ||  |   | || || | ||    |  | |   ||  |  |||||||||    || || ||       ||| || ||||||||  ||||||||||| |||||  ||||||| || ||||| || ||||||||||| ||||| ||||||||| | |||||||| || || |||||   
gtatgctaatgtacttgaaaca-agtttgatcattgtactgctagaattta--aaggcttttctgaaagtgctt---gccatattagCAGGTCCATATCCAGAATCTCCTCGGCTATCTCGGTTTCCAAACCTTCCTGACATGTCTCCCAAGAAAGTTTCTGCTGCTCATAACGTATATGTTTCACC---

upper sequence: GRMZM2G033828_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os08g42600.2 (Oryza sativa), 3'ss of exon 15
------gtacgctctcaatgtagagattaagca--acatcgatgacatccacgaaggcttttgctgaaatgtttttgattgtatcagtagGTCCATTCCCAGAATCTCCCCGGCTGGCTCGGTTCCCGAACCTCCCCGACATGTCTCCAAAGAAGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCT
        | |  ||  |   | || || | ||    |  | |   ||  |  |||||||||    || || ||       ||| || ||||||||  ||||||||||| |||||  ||||||| || ||||| || ||||||||||| ||||| ||||||||| | |||||||| || || |||||  |
gtatgctaatgtacttgaaaca-agtttgatcattgtactgctagaattta--aaggcttttctgaaagtgctt---gccatattagcagGTCCATATCCAGAATCTCCTCGGCTATCTCGGTTTCCAAACCTTCCTGACATGTCTCCCAAGAAAGTTTCTGCTGCTCATAACGTATATGTTTCACCCTT
















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|76933781|gb|DV173583.1|DV173583
EST:     CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATGTAG                       
genomic: CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGA--T-Ggtacgctctc ... gtatcagt
EST: gi|76933783|gb|DV173584.1|DV173584
EST:     CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATG                         T
genomic: CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATGgtacgctctc ... gtatcagtag-
EST: gi|76933783|gb|DV173584.1|DV173584
EST:     CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATG                         T
genomic: CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATGgtacgctctc ... gtatcagtag-
EST: gi|76933783|gb|DV173584.1|DV173584
EST:     CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATG                         T
genomic: CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATGgtacgctctc ... gtatcagtag-
EST: gi|30088298|gb|CB886503.1|CB886503
EST:     CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATGTAG                       
genomic: CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGA--T-Ggtacgctctc ... gtatcagt
EST: gi|30087032|gb|CB885240.1|CB885240
EST:     CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATGTAG                       
genomic: CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGA--T-Ggtacgctctc ... gtatcagt
EST: gi|30031776|gb|CB833627.1|CB833627
EST:     CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATGTAG                       
genomic: CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGA--T-Ggtacgctctc ... gtatcagt
EST: gi|29544714|gb|CB605094.1|CB605094
EST:     CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATG                         GTCCATTCCCAGAATCTCCCCGGCTGGCTCGGTTCCCGAACCTCCCCGACA
genomic: CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATGgtacgctctc ... gtatcagtagGTCCATTCCCAGAATCTCCCCGGCTGGCTCGGTTCCCGAACCTCCCCGACA
EST: gi|30086964|gb|CB885172.1|CB885172
EST:     AGAGGAAAAAGGTCCTGCTGATGTAG                       
genomic: AGAGGAAAAAGGTCCTGCTGA--T-Ggtacgctctc ... gtatcagt
EST: gi|30088299|gb|CB886504.1|CB886504
EST:     CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATGTAG                       
genomic: CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGA--T-Ggtacgctctc ... gtatcagt
EST: gi|22935543|gb|BU571818.1|BU571818
EST:     CG---GCGCCAGCCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATG                         GTACATTCCCAGAATCTCCCCGGCTGGCTCGGTTCCCGAACCTCCCCGACA
genomic: CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATGgtacgctctc ... gtatcagtagGTCCATTCCCAGAATCTCCCCGGCTGGCTCGGTTCCCGAACCTCCCCGACA
EST: gi|27575967|gb|CA998661.1|CA998661
EST:     CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATGTAG                       
genomic: CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGA--T-Ggtacgctctc ... gtatcagt
EST: gi|30031712|gb|CB833563.1|CB833563
EST:     CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATGTAG                       
genomic: CGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGA--T-Ggtacgctctc ... gtatcagt

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), 47 (downstream exon)
Score: 142

GAAGTATTCATTCCTGCCGTCAAGTCCTTGTTGGTGGAGGTAGGGCCTGGCGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATGgtacgctctc ... gtatcagtagGTCCATTCCCAGAATCTCCCCGGCTGGCTCGGTTCCCGAACCTCCCCGACATGTCTCCAAAGAAGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCT


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 18

GAAGTATTCATTCCTGCCGTCAAGTCCTTGTTGGTGGAGGTAGGGCCTGGCGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATGgtacgctctc ... gtatcagtagGTCCATTCCCAGAATCTCCCCGGCTGGCTCGGTTCCCGAACCTCCCCGACATGTCTCCAAAGAAGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCT


Block sizes: 23 (upstream exon), 46 (downstream exon)
Score: 5

GAAGTATTCATTCCTGCCGTCAAGTCCTTGTTGGTGGAGGTAGGGCCTGGCGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATGgtacgctctc ... gtatcagtagGTCCATTCCCAGAATCTCCCCGGCTGGCTCGGTTCCCGAACCTCCCCGACATGTCTCCAAAGAAGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCT


Block sizes: 23 (upstream exon), 46 (downstream exon)
Score: 7

GAAGTATTCATTCCTGCCGTCAAGTCCTTGTTGGTGGAGGTAGGGCCTGGCGCCAGCGCCAGTCCAAAGAAGAAAGAAGAGGAAAAAGGTCCTGCTGATGgtacgctctc ... gtatcagtagGTCCATTCCCAGAATCTCCCCGGCTGGCTCGGTTCCCGAACCTCCCCGACATGTCTCCAAAGAAGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatcgatgacatccacgaaggcttttgctgaaatgtttttgattgtatcagtagGTCCATTCCCAGAATCTCCCCGGCTGGCTCGGTTCCCGAACCTCCCCGACATGTCTCCAAAGAAGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCT
                                     ttttgat  putative branch site (score: 7)
                               aaatgtttttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgctctcaatgtagagattaagcaacatcgatgacatccacgaaggcttttgctgaaatgtttttgattgtatcagtagGTCCATTCCCAGAATCTCCCCGGCTGGCTCGGTTCCCGAACCTCCCCGACATGTCTCCAAAGAAGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG