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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggtcttacatcacattgtcaatctcagtcatgtcatcggtctctggtttgcactaccaattataacatctctcgacttttgaaccttttgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGTAGGGATCGTACGGAGATGGAAAACATTATATTCAAGCTTTTTGAAAGGC

Basic information

species Zea mays
transcript GRMZM2G049091_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G049091_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g43450.1 (Oryza sativa), 3'ss of exon 4
taggtcttacatcacattgtcaa-tctcagtcatgtcatcggtctct--ggtttgcactac-------caattataacatctctcgac-ttttgaaccttttgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGTAGGGATCGTACGGAGATGGAAAACATTATATTCAAGCTTTTTGAAAGGC
            ||  ||| ||| |  || ||||||  |||| ||||     ||| |||||       || ||| |   ||||   ||   || ||  || ||||   ||||| |||||||| ||| ||||| | |||||||| ||||  |||||||  ||||||||||| | |||  ||||||| ||||||||||||||||||||||| |
-----------ccatgttgccaaatgccaatcatgtggtcggcctcttcatcttgaactactcatcatcagttaaagtttctcataacacatttaattttgtgctcttcagGAGAAGAAGAAGCAAACACCAACCAAACCATCTGATGCAAAAAGAATACGTAGGGATCGCAGGGAACTGGAAAATATTATATTCAAGCTTTTTGAAAGAC

upper sequence: GRMZM2G049091_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0001g13370.t01 (Vitis vinifera), 3'ss of exon 4
taggtcttacatcacattgtcaatctcagtcatgtcatcggtctctggtttgcactaccaattataa-catctctcgacttttgaaccttttgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGTAGGGATCGTACGGAGATGGAAAACATTATATTCAAGCTTTTTGAAAGGC
|   | ||  ||    ||  || |  |   ||     ||     ||   |   || |  |   | ||  || | |    | | |       |   || ||||| |||||||||   || ||||  ||    || ||  | ||||||||| | |||||||||  |||  ||||| | ||||| |||||||||||||||||||
tttattttttattttttt-ccatttgctaccaaaatttccaagactatatcctacgaagagcgaaaaatatgtattatttatggtcaaccatctctggcagGATAAGAAGAAAACTGCGCCAGTTAAGGGCTCTGACATGAAAAGAACTAGAAGGGATCGTGGGGAACTGGAAGATATTATGTTCAAGCTTTTTGAAAGGC
















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|149087889|gb|EE177157.2|EE177157
EST:     GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAG                         GAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCCAAAGAACTCGT
genomic: GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
EST: gi|60394867|gb|DN227736.1|DN227736
EST:     GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAG                         GAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
genomic: GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
EST: gi|71321698|gb|DR797541.1|DR797541
EST:     GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAG                         GAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
genomic: GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
EST: gi|71330940|gb|DR802278.1|DR802278
EST:     GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAG                         GAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
genomic: GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
EST: gi|71321696|gb|DR797540.1|DR797540
EST:     GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAG                         GAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
genomic: GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
EST: gi|149087888|gb|EE287172.2|EE287172
EST:     GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAG                         GAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
genomic: GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
EST: gi|149111893|gb|EE191049.2|EE191049
EST:     GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAG                         GAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
genomic: GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
EST: gi|110532526|gb|EE036710.1|EE036710
EST:     GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAG                         GAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
genomic: GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
EST: gi|148942185|gb|EC887190.2|EC887190
EST:     GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAG                         GAAAAGAAGAAACAAGCACCAGCGAAAACCATCCGATGTCAAAAGAACTCG
genomic: GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAA-CCATCCGATGTCAAAAGAACTCG
EST: gi|148999712|gb|EE036711.2|EE036711
EST:     GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAG                         GAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
genomic: GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
EST: gi|91869046|gb|EB400256.1|EB400256
EST:     GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAG                         GAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTC
genomic: GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTC
EST: gi|60341247|gb|DN208220.1|DN208220
EST:     GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAG                         GAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
genomic: GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
EST: gi|6307892|gb|AW163859.1|AW163859
EST:     GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAG                         GAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
genomic: GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
EST: gi|120480832|gb|EH211048.1|EH211048
EST:     GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAG                         GAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
genomic: GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
EST: gi|211422720|gb|FL461576.1|FL461576
EST:     GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAG                         GWAAAGAAGAWACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
genomic: GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
EST: gi|78078666|gb|DV507078.1|DV507078
EST:     GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAG                         GAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
genomic: GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
EST: gi|6056902|gb|AW091307.1|AW091307
EST:     GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAG                         GAAAAGAAGAACCAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
genomic: GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
EST: gi|78083456|gb|DV511849.1|DV511849
EST:     GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAG                         GAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT
genomic: GCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGT

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), 46 (downstream exon)
Score: 93

GTACTTGACAATGACCACGGTATGAGCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGTAGGGATCGTACGGAGATGGAAAACATTATATTCAAGCTTTTTGAAAGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 54

GTACTTGACAATGACCACGGTATGAGCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGTAGGGATCGTACGGAGATGGAAAACATTATATTCAAGCTTTTTGAAAGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 66

GTACTTGACAATGACCACGGTATGAGCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGTAGGGATCGTACGGAGATGGAAAACATTATATTCAAGCTTTTTGAAAGGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 96

GTACTTGACAATGACCACGGTATGAGCATGAGACCAATGCCTGGCTTGGTTGGTCTCATACCTTCTGGTTCAAAGgtagtttcgt ... tgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGTAGGGATCGTACGGAGATGGAAAACATTATATTCAAGCTTTTTGAAAGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtttgcactaccaattataacatctctcgacttttgaaccttttgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGTAGGGATCGTACGGAGATGGAAAACATTATATTCAAGCTTTTTGAAAGGC
                ttataac  putative branch site (score: 96)
                                        ccttttgctt  putative PPT
              aattataacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taggtcttacatcacattgtcaatctcagtcatgtcatcggtctctggtttgcactaccaattataacatctctcgacttttgaaccttttgcttgccagGAAAAGAAGAAACAAGCACCAGCGAAACCATCCGATGTCAAAAGAACTCGTAGGGATCGTACGGAGATGGAAAACATTATATTCAAGCTTTTTGAAAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT