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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttttttcagggcatataaaaatataggatatatactctgatcttctcttgaattaacacattattgttgttgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTA

Basic information

species Zea mays
transcript GRMZM2G086030_T01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086030_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os04g55230.1 (Oryza sativa), 3'ss of exon 20
----gttcttttttcagggcatataaaaatataggatatatactctgatcttctcttgaatta--acacattattgtt-----gttgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTA
     || |   ||||    ||  ||  |   ||   | |||||   || |||||||| | ||  | |||| ||  ||     | |||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||| || ||||| ||||| ||||||||||| |||||||||||||| |
gttttttttcccttcaaaatatgcaatgacg-agtccaaatactgctatgttctcttggactattagacatgataattttcctgctgcagGATGCTGCTGCATGGCTTGAGTATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCCGCCCGAAGGGGCATCCCAAAACCTGACTCATCTATTGCAAGCA

upper sequence: GRMZM2G086030_T01 (Zea mays), 3'ss of exon 20
lower sequence: GLYMA08G22850.1 (Glycine max), 3'ss of exon 19
------------------------------------------------------------gttcttttttcagggcatataaaaat--ataggatatatactctgatcttctc--ttgaattaacacattattgttgttgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTA
                                                              |     ||       |||    ||  ||||  |   |  | | || ||  |  ||  || ||    || |      |||||||||||||||||||||| || |||||||| ||||||||  |||| || ||||| || |||  ||  || |  ||||| |||||| |||| ||||||||||
gtcatttccttttctgatagtagtgctagaatacgtcaaagaatattggtctaggattgaactacgcattggcaaactatggggattgatagattgatttgtttaatgttaccattttcatgaaagttttttccccaatgcagGATGCTGCTGCATGGCTTGAGTATTTTGAATCAAAAGCCCTAGAGCAGCAAGAAGCAGCTAAAAATGGAACTCCAAAGCCTGATGCATCCATTGCAAGTA

upper sequence: GRMZM2G086030_T01 (Zea mays), 3'ss of exon 20
lower sequence: GLYMA07G03250.1 (Glycine max), 3'ss of exon 21
------------------------------------------------gttcttttttcagggcatataaaaat--ataggatatatactctgatcttctc---ttgaattaacacattattgttgt--tgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTA
                                                  |     ||      ||||     |  ||||    | |   || || ||  |   ||  || ||    || || ||    ||||||||||||| || ||||| ||||||||||| ||||||||  |||| || ||||| ||  ||  ||  || |  ||||| |||||| |||| ||||||||||
gtcatttccttttctgattgtagtactagaattctggtctaggattgaactaagcattggcaaaatatgggggttgatagatggttttggctaatgttaccatttttcatgaaaggtttttttttccaatgcagGATGCTGCCGCGTGGCTTGAATATTTTGAATCAAAAGCCATAGAGCAGCAAGAAGCAACTAAAAATGGAACTCCAAAGCCTGATGCATCCATTGCAAGTA

upper sequence: GRMZM2G086030_T01 (Zea mays), 3'ss of exon 20
lower sequence: AT1G15290.1 (Arabidopsis thaliana), 3'ss of exon 18
---------------------------------------------------gttcttttttcagggcatataaaaatataggatatatactctgatcttctcttgaattaacacattattg--ttgttgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTA
                                                    ||  ||  |       ||  ||| |  | | | |  |||||||      | ||  |     |   |||    | |  |||||||||||||||||||| ||||||||||| |||| |||  |||| || || || || |  ||||  || || ||||| |||||| | || || || || |
gtgattgatttgcttctggttcattcgcatacaaatctcagacgaatattaatttcttactagcaaagtaacaaagtgaacgttttgaactctgagacatacatgtttgttttctccatttgtctctcacagGATGCTGCTGCATGGCTCGAATATTTTGAATCAAGAGCCATAGAGCAGCAGGAAGCAGGCCGAAATGGAATCCCAAAGCCTGATGCTTCCATCGCGAGCA

upper sequence: GRMZM2G086030_T01 (Zea mays), 3'ss of exon 20
lower sequence: Vv09s0002g07530.t01 (Vitis vinifera), 3'ss of exon 20
----------------------gttcttttttcagggcatataaaaatatagg-atatatactctgatcttctcttgaattaacacattattgttgttgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTA
                        | |||    |   || ||   | |||||  | ||| | |    || ||  ||||     |   |   |  |  |||||||||||||||||||||| ||||||||||| |||||||| ||||| || ||||| || ||  |||  || |  ||||| || ||| ||||||||||||| |
atgcgaccaattgagctaagggcatgtttagctaataca-atgtcactatagatacataaaatggagtcatcaattga-cgggcgtgtgtgttctcatgcagGATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAAGAAGCAGCAAGAAATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCA

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|31353676|gb|CD438033.1|CD438033
EST:     CCTTGCAGATACTTCAGGAGAAACTAGGGCAAGATGACCTCCGAACTCAG                         GATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTACAACAACAA
genomic: CCTTGCAGATACTTCAGGAGAAACTAGGGCAAGATGACCTCCGAACTCAGgttctttttt ... gttgttgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAA
EST: gi|211017605|gb|FL188943.1|FL188943
EST:     CCTTGCAGATACTTCAGGAGAAACTAGGGCAAGATGACCTCCGAACTCAG                         GATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAA
genomic: CCTTGCAGATACTTCAGGAGAAACTAGGGCAAGATGACCTCCGAACTCAGgttctttttt ... gttgttgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAA
EST: gi|67035470|gb|CO464003.1|CO464003
EST:     CCTTGCAGATACTTCAGGAGAAACTAGGGCAAGATGACCTCCGAACTCAG                         GATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAA
genomic: CCTTGCAGATACTTCAGGAGAAACTAGGGCAAGATGACCTCCGAACTCAGgttctttttt ... gttgttgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAA
EST: gi|31354896|gb|CD439253.1|CD439253
EST:     CCTTGCAGATCCTTCAAGAGAAACTAGGGCAAGATGACCTCCGAACTCAG                         GATGCTGCTGCATGGCTAGAATATTTTGAGTCACCAGCATTAGAACAACAA
genomic: CCTTGCAGATACTTCAGGAGAAACTAGGGCAAGATGACCTCCGAACTCAGgttctttttt ... gttgttgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAA

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: 114

CCTTTCAATGATGGACGCGTACTCCCTAAGCGTGCAACATGAACAAACAACCTTGCAGATACTTCAGGAGAAACTAGGGCAAGATGACCTCCGAACTCAGgttctttttt ... gttgttgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 256

CCTTTCAATGATGGACGCGTACTCCCTAAGCGTGCAACATGAACAAACAACCTTGCAGATACTTCAGGAGAAACTAGGGCAAGATGACCTCCGAACTCAGgttctttttt ... gttgttgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTA


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

CCTTTCAATGATGGACGCGTACTCCCTAAGCGTGCAACATGAACAAACAACCTTGCAGATACTTCAGGAGAAACTAGGGCAAGATGACCTCCGAACTCAGgttctttttt ... gttgttgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 394

CCTTTCAATGATGGACGCGTACTCCCTAAGCGTGCAACATGAACAAACAACCTTGCAGATACTTCAGGAGAAACTAGGGCAAGATGACCTCCGAACTCAGgttctttttt ... gttgttgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atataggatatatactctgatcttctcttgaattaacacattattgttgttgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTA
                              aattaac  putative branch site (score: 394)
                              aattaacacattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttttttcagggcatataaaaatataggatatatactctgatcttctcttgaattaacacattattgttgttgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG