Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattttcttaccttgcctattttctcttctctttacataaaactcaaccttagttttaccggaggcatatctcaatacttgttaattcattgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCATGGATAAGAAATTTTTGGAAAAAGTGGAAGCGGTTCGAAG

Basic information

species Zea mays
transcript GRMZM5G863152_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G863152_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g18720.1 (Oryza sativa), 3'ss of exon 4
------ttattttcttaccttgcctattttctcttctctttacataaaactcaaccttagttttaccggaggcatatctcaatacttgttaattcattgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCATGGATAAGAAATTTTTGGAAAAAGTGGAAGCGGTTCGAAG
      | |||||||  | ||| |   ||  | ||   |  | || | | |     || |||       |  | | |      |||||    | |||  | ||||||||  |  || ||| | |||  ||| ||||  |||| || |||||  |||||||||||| ||||| | |||||||||||||| ||||||||
tgaaactaattttctgtctttggca--ttgatgtttggtggatatgagattt----tttgttacttaacatacttttgctcgcacttggacttccatgttctttagGGGCACTGGACTTAGGGACTCGAAGGGAAAGTAAATATGCTAAAACTGTCATGGATAAGCAATTTCTAGAAAAAGTGGAAGCTGTTCGAAG
















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|71305070|gb|DR788672.1|DR788672
EST:     TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT                         GGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
genomic: TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATgtaagttttc ... ttgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
EST: gi|211226055|gb|FL296371.1|FL296371
EST:     TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT                         GGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
genomic: TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATgtaagttttc ... ttgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
EST: gi|211223997|gb|FL296365.1|FL296365
EST:     TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT                         GGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
genomic: TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATgtaagttttc ... ttgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
EST: gi|76920373|gb|DV168136.1|DV168136
EST:     TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT                         GGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
genomic: TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATgtaagttttc ... ttgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
EST: gi|211226059|gb|FL296375.1|FL296375
EST:     TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT                         GGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAAT
genomic: TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATgtaagttttc ... ttgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAAT
EST: gi|211226058|gb|FL296374.1|FL296374
EST:     TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT                         GGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
genomic: TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATgtaagttttc ... ttgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
EST: gi|211224000|gb|FL296368.1|FL296368
EST:     TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT                         GGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
genomic: TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATgtaagttttc ... ttgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
EST: gi|71432424|gb|DR813474.1|DR813474
EST:     TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT                         GGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
genomic: TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATgtaagttttc ... ttgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
EST: gi|211223995|gb|FL296363.1|FL296363
EST:     TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT                         GGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
genomic: TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATgtaagttttc ... ttgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
EST: gi|211226057|gb|FL296373.1|FL296373
EST:     TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT                         GGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
genomic: TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATgtaagttttc ... ttgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
EST: gi|166551775|gb|EG294357.1|EG294357
EST:     TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT                         GGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
genomic: TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATgtaagttttc ... ttgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
EST: gi|78081578|gb|DV509990.1|DV509990
EST:     TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT                         GGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
genomic: TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATgtaagttttc ... ttgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCA
EST: gi|211223993|gb|FL296361.1|FL296361
EST:     TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT                         GGGTGCCAGAATTAAGAACTGAAAGTGACAAACAAATCTGGTAAA
genomic: TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATgtaagttttc ... ttgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGA-AAACAAATCTGGTAAA

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: 38 (upstream exon), 48 (downstream exon)
Score: 86

TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATgtaagttttc ... ttgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCATGGATAAGAAATTTTTGGAAAAAGTGGAAGCGGTTCGAAG


Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 113

TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATgtaagttttc ... ttgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCATGGATAAGAAATTTTTGGAAAAAGTGGAAGCGGTTCGAAG


Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 46

TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATgtaagttttc ... ttgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCATGGATAAGAAATTTTTGGAAAAAGTGGAAGCGGTTCGAAG


Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 59

TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATgtaagttttc ... ttgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCATGGATAAGAAATTTTTGGAAAAAGTGGAAGCGGTTCGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaccttagttttaccggaggcatatctcaatacttgttaattcattgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCATGGATAAGAAATTTTTGGAAAAAGTGGAAGCGGTTCGAAG
                                   tgttaat  putative branch site (score: 59)
                                             ttgttttt  putative PPT
                                     ttaattcattgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattttcttaccttgcctattttctcttctctttacataaaactcaaccttagttttaccggaggcatatctcaatacttgttaattcattgtttttagGGGTGCCAGAATTAAGAACTGAAAGTGAAAACAAATCTGGTAAAAAAGTCATGGATAAGAAATTTTTGGAAAAAGTGGAAGCGGTTCGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - -ccttgcc
- - - - - - - - - - - - - - - - - - - - -aactcaa