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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgatggtttatcattgcatcctttccagtgcttgtgccaaagaaactctacatcatcgagaaaagtctagtttgttctgttatcctgattgaccattcttatttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCA

Basic information

species Zea mays
transcript GRMZM2G123624_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123624_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os10g36870.1 (Oryza sativa), 3'ss of exon 7
gtactgatggtttatcattgcatcctttccagtgcttgtgc--caaagaaactc-tacatcatcgagaaaagtctagtttgttctg-ttatcctgattgaccattc-------ttatttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCA
||||||||| |||   |  ||||||||  ||   ||| | |   |||| ||||  |  |  ||||| |||   ||  |||||| || ||||||||||| |   |         ||| ||||  ||||||||||||||||||||||||||||||| ||||||||||| |  ||||||||||| ||||| ||||| ||| ||||||||||| | || ||| | ||||
gtactgatgattttgtacagcatccttatcaa-acttatacagaaaaggaacttgttaactatcgaaaaagaactgctttgttttggttatcctgattcagtctcttgtttctttacttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAGAGTTCTATGCCACCACCACCTTCATATGAAGAAATTAACGGTGTTTTCA
















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|60398124|gb|DN230940.1|DN230940
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
EST: gi|28985206|gb|BQ539380.2|BQ539380
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
EST: gi|78545157|gb|DV622655.1|DV622655
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
EST: gi|32919380|gb|CF024192.1|CF024192
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
EST: gi|71768413|gb|DR966350.1|DR966350
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
EST: gi|76935690|gb|DV174431.1|DV174431
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAG
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAG
EST: gi|74239023|gb|DT646937.1|DT646937
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
EST: gi|71434707|gb|DR815757.1|DR815757
EST:     GAAACTACCACCAAA-GGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGGCAAAGAATTGAAGGGGCACCTCCTCCG
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCG
EST: gi|78074542|gb|DV502976.1|DV502976
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
EST: gi|76019273|gb|DT946443.1|DT946443
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
EST: gi|60358710|gb|DN225683.1|DN225683
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
EST: gi|211409238|gb|FL441029.1|FL441029
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
EST: gi|71765023|gb|DR962960.1|DR962960
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTAGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
EST: gi|71756340|gb|DR954277.1|DR954277
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
EST: gi|149085094|gb|EE174601.2|EE174601
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
EST: gi|71328409|gb|DR800841.1|DR800841
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAG

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: 331

GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCA


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 128

GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 116

GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtactgatgg ... atttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgagaaaagtctagtttgttctgttatcctgattgaccattcttatttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCA
                               gattgac  putative branch site (score: 191)
                                     ccattcttatttttct  CT-rich tract
                                       attcttatttttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgatggtttatcattgcatcctttccagtgcttgtgccaaagaaactctacatcatcgagaaaagtctagtttgttctgttatcctgattgaccattcttatttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT