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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttgttgaaatagaatccactcatttaatgtttgtgatcctttacagttcttatctgaacctttcttccattattactcttactgaatggatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA

Basic information

species Zea mays
transcript GRMZM2G025366_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025366_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g40310.2 (Oryza sativa), 3'ss of exon 1
--tgttgttgaaatagaatccactcatttaatgtttgtgatcctttacagttcttatctgaacctttcttccattattactcttactgaatggatttc-ctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA------------
  ||    || |||  ||| ||| | |||           |  ||| |||||||   |||| | | | ||||||  ||| ||| ||||| |   |||    ||||||| ||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||| |||||||||||||||||||            
attgccaatggaatgaaatgcaccctttt-----------ttttttccagttct---ctgagcttcttttccatc-ttagtctcactgactaacttttgtcaggtgataacaaagTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACATCATGAAGCTTG

upper sequence: GRMZM2G025366_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
tgttgttgaaatagaatccactcatttaa---tgtttgtgatcctttacagttcttatctgaacctttcttccattattactcttactgaatggatttc-ctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA
|  ||||  |  |    | |   | | ||         |  |  ||| |||||||   |||| | | | ||||||  ||| ||| ||||| |   |||    ||||||| ||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||| |||||||||||||||||||
ttgtgttacatgattgccaatggaatgaaatgcacccttttttttttccagttct---ctgagcttcttttccatc-ttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA

upper sequence: GRMZM2G025366_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G08920.1 (Glycine max), 3'ss of exon 1
---tgttgttgaaatagaatccactcatttaatgtttgtgatcctttacagttcttatctgaacctttcttccattattactcttactgaatggatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA
   | |  |  ||     |   |   || | |||    |    | ||    || | | |||    |||  |   ||    ||| |||| |     ||| |||||| || |||||||| ||||| ||| | ||||| |||||||| || |||||||||||||| || ||| ||||||| || ||||| ||||| ||||||||||
ctttttcatctaatcttcaattatatatctcatgaagttagcgccttgacattgtgaactgtgagttttatgt-ttgcacctcatactaatct--tttgctagGTAATAACAAAGTTCTGCTCAGAGCGCATTGCTAAATATGCTTTTGAGTATGCTTACCTAAATAACAGAAAGAAGGTGACTGCTGTGCACAAAGCAAACA

upper sequence: GRMZM2G025366_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G22640.1 (Glycine max), 3'ss of exon 1
tgttgttgaaatagaatccactcatttaatg---tttgtgatcctttacagttcttatctgaacctttcttccattattactcttactgaatggatttc-ctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA
      |||  |   || ||   || | |||   ||    |     ||| || || |  || |   |   |  ||  || || ||  |      ||||  |||||| || || ||||| || || ||| | ||||| |||||||||||||||||||||||||| || ||| ||||||| || ||||| ||||| |||||||| |
--catgtgatctttgatgcatatatgtcatgaagttatcaacttgatactgtcctga--tgcagtgtgggtttatgttttctgttgatcctcatattttactagGTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA

upper sequence: GRMZM2G025366_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G04780.1 (Glycine max), 3'ss of exon 1
tgttgttgaaatagaatccactcatttaatgtttgtgat-cctttacagttcttatctgaacctttcttccattattactcttactgaatggatttc-ctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA
      |||  |   ||  |   || | |||   ||    |||| | | |       || |   |   |  ||  || || ||  |      ||||  |||||| || ||||||||||| || ||| | ||||| |||||||||||||||||||||||||| || ||| ||||||| || ||||| ||||| |||||||| |
--catgtgatctttgatgtatatatgtcatgaaggtatcaccttgatactgtcctgatgcagtatgggtttatgtttgctgttgatactcatattttactagGTAATAACAAAGTTTTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA

upper sequence: GRMZM2G025366_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------tgttgttgaaatagaatccactcatttaatgt----ttgtgatcctttacagttcttatctgaacctttcttccattattactcttactgaatggattt-cctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA
                 || |  |    | | || || ||  |   |||    |  |  || ||| ||  |  | | || |  | |  |   | |||  ||| |    ||   | | | ||||||||||| ||||| || || ||| | ||||| || ||||| || |||||||| ||||| |||||| | |||||||| || || |||||||| || ||||
gtgagaattccgatttctgctcctcgttttggattcaatctgtatttgtggaatcatcttcgtttgcaagtggtctttgta--tgttatgtgtgattgttctgatcctatttctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAGTATGCCTACCTGAACAACAGGAAGAAAGTTACAGCGGTGCATAAGGCTAACA

upper sequence: GRMZM2G025366_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT4G35650.1 (Arabidopsis thaliana), 3'ss of exon 1
tgttgttgaaatagaatccactcatttaatgtttgtgatcctttacagttcttatctgaacctttcttccattattactcttactgaatggatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA
              || |||   || ||||  | | |||  |||  ||| |  ||    | |  | ||  ||   |  | ||  ||||| | ||   |||||||| ||||||||||| |||||||| || || | ||||||||| |||||||| || || |||||  | |||||||| ||||| || |||||||| ||||
------------gtaaaccat--atataattatagggattgtttttagtccaaattgtgatcccttttgtatacatgatgttgttgaattgtttgtgtagGTGATAACAAAGTTTTGTTCTGAGAGAATAGCGAGATATGCATTTGAGTATGCGTATCTAAACAATAGGAAGAAAGTGACTGCTGTTCATAAAGCTAACA

upper sequence: GRMZM2G025366_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv03s0038g03120.t01 (Vitis vinifera), 3'ss of exon 1
tgttgttgaaatagaatccactcatttaatgtttgtgatcctt-tacagttct-tatctgaacctttcttccattattactcttactga----atggatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA
     || | |||| ||  |   ||||| |||||  |||  || || |||  | | | |    |  | |   ||| |  || || ||||       | ||| ||||||||| |||||||| ||||| ||  | ||||| |||||||| || |||||| ||||||| ||||||||||||||||| || || ||||| ||||| ||||
-----tttagatagcatt-ataaatttagtgtttaagatttttataaagtgttgtttttccgacagtatggaattgtgtctgtttctgatccagctgctttgctagGTGATTACAAAGTTCTGCTCCGAACGAATTGCAAAATATGCCTTTGAGTATTCTTACCTAAACAACCGAAAGAAAGTGACAGCTGTGCACAAAGCCAACA

upper sequence: GRMZM2G025366_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S101_151V6.1 (Physcomitrella patens), 3'ss of exon 1
tgttgttgaaatagaatccactcatttaatgtttgtgatcctttacagt-tcttatctgaacctttcttccattattactct-tactgaatggatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA
  |         |   | ||  ||||       |    |  | ||| |  |  || |||     |  |||  | | | |  |  | ||    ||| | | |||| ||||| ||||| ||||| ||| | ||||| ||||| || || ||||||||||| || |||||||| |||| ||| || |||||||| || || ||||
-atctcctcgtcatgcttcatgcattgtggaaataatcttatctactgcgtggtacctgtcaaataattctgtaagtgccttacagtgccaagatgttc-agGTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTATGCTTATCTCAACAACCGCAAGACAGTAACAGCAGTGCACAAGGCCAACA

upper sequence: GRMZM2G025366_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ13705 (Selaginella moellendorffii), 3'ss of exon 1
tgttgttgaaatagaatccactcatttaatgtttgtgatcctttacagttcttatctgaacctttcttccattattactcttactgaatggatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA
                       | |  |  ||| |  |||| | |     ||    |  |  | |  | |   ||  |||| |  |         | |||||||||| ||||||||||| ||  |||||||||| || || || ||||| || ||||| |||||| ||||||  || || || ||||| || || ||||
---------------------gtactcca-atttcttctcctctgc----tttgctcggccgctccagctacgtttcttcttgcgca---------ccagGTGATCACGAAGTTTTGCTCCGAACGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA

upper sequence: GRMZM2G025366_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ29002 (Selaginella moellendorffii), 3'ss of exon 1
tgttgttgaaatagaatccactcatttaatgtttgtgatcctttacagttcttatctgaacctttcttccattattactcttactgaatggatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA
                       | |  |  ||| |  |||| | |     ||    |  |  | |  | |   ||  |||| |  |         | |||||||||| ||||||||||| ||| |||||||||| || || || ||||| || ||||| |||||| ||||||  || || || ||||| || || ||||
---------------------gtactcca-atttcttctcctctgc----tttgctcggccgctccagctacgtttcttcttgcgca---------ccagGTGATCACGAAGTTTTGCTCCGAGCGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA

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|149089013|gb|EE178164.2|EE178164
EST:     ACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAG                         -T--T-------TT--GCTCTGAGAGGATTGCCAAATATGCATTCGAGTAT
genomic: ACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAGgtactacgga ... gatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTAT
EST: gi|149105682|gb|EE291240.2|EE291240
EST:     ACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAG                         GTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTAT
genomic: ACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAGgtactacgga ... gatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTAT
EST: gi|211060059|gb|FL391389.1|FL391389
EST:     ACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAG                         GTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTAT
genomic: ACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAGgtactacgga ... gatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTAT
EST: gi|149107868|gb|EE292228.2|EE292228
EST:     ACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAG                         GTGATCACAAAGTTTTGCTC
genomic: ACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAGgtactacgga ... gatttcctagGTGATCACAAAGTTTTGCTC
EST: gi|148959185|gb|EC905302.2|EC905302
EST:     ACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAG                         GTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTAT
genomic: ACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAGgtactacgga ... gatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTAT
EST: gi|56691635|gb|CX129538.1|CX129538
EST:     ACCCGGGGTCGTTGAGAGCCTCAAG                         GTGGTCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTAT
genomic: ACCCGGGGTCGTTGAGAGCCTCAAGgtactacgga ... gatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTAT
EST: gi|76285693|gb|DV025261.1|DV025261
EST:     ACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAG                         GTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTAT
genomic: ACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAGgtactacgga ... gatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTAT

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: 105

GCACGAGGGTGTCGACATCGTCGTAATCAGGGAGAACACCGAGGGCGAGTACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAGgtactacgga ... gatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 155

GCACGAGGGTGTCGACATCGTCGTAATCAGGGAGAACACCGAGGGCGAGTACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAGgtactacgga ... gatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 239

GCACGAGGGTGTCGACATCGTCGTAATCAGGGAGAACACCGAGGGCGAGTACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAGgtactacgga ... gatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 361

GCACGAGGGTGTCGACATCGTCGTAATCAGGGAGAACACCGAGGGCGAGTACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAGgtactacgga ... gatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttcttatctgaacctttcttccattattactcttactgaatggatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA
                                ctcttac  putative branch site (score: 361)
                                               tttcct  putative PPT
                         attattact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttgttgaaatagaatccactcatttaatgtttgtgatcctttacagttcttatctgaacctttcttccattattactcttactgaatggatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
tgttgtt
- - - -gaaataga
- - - - - - - - -ccactca
- - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaatg