Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagcttctagcattatgttgttcagcattttttaatgtagaagatgacatcaatttgttaccttgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG

Basic information

species Zea mays
transcript GRMZM2G027307_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027307_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g58960.1 (Oryza sativa), 3'ss of exon 5
-----------------------------gcaagcttctagcattatgttgttcagcattt---tttaatgta--gaagatgacatcaatttgttaccttg-----atgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG
                              ||||  | || || | |  | || |  | ||   ||| || |    ||| ||| || |||||||||| ||       | |  |||||||||| ||||| || || ||||  ||||| |||||| |||||||||||||||||||   ||||
gcaagtatctagaatgtataattaaatactcaagtatttatcaatgt-ctattaaatacttacttttgatatctccaaggtgagattaatttgttacattatttttttatttagGCATATGAAAAGAAAACTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAG
















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|5895854|gb|AW037100.1|AW037100
EST:     TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAG                         GCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
genomic: TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAGgcaagcttct ... tgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
EST: gi|26455295|gb|CA826878.1|CA826878
EST:     TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAG                         GCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
genomic: TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAGgcaagcttct ... tgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
EST: gi|149110923|gb|EE294421.2|EE294421
EST:     TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAG                         GCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
genomic: TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAGgcaagcttct ... tgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
EST: gi|148933152|gb|EC876791.2|EC876791
EST:     TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAG                         GCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
genomic: TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAGgcaagcttct ... tgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
EST: gi|89106782|gb|DY576999.1|DY576999
EST:     TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAG                         GCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
genomic: TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAGgcaagcttct ... tgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
EST: gi|50326450|gb|CO521576.1|CO521576
EST:     TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAG                         GCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
genomic: TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAGgcaagcttct ... tgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
EST: gi|32797603|gb|CD949839.1|CD949839
EST:     TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAG                         GCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
genomic: TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAGgcaagcttct ... tgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
EST: gi|61119340|gb|DN560301.1|DN560301
EST:     TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAG                         GCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
genomic: TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAGgcaagcttct ... tgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
EST: gi|71306346|gb|DR789325.1|DR789325
EST:     TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAG                         GCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
genomic: TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAGgcaagcttct ... tgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
EST: gi|21390493|gb|BQ528542.1|BQ528542
EST:     TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAG                         GCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
genomic: TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAGgcaagcttct ... tgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
EST: gi|5917413|gb|AW054204.1|AW054204
EST:     ATACGACGACAATTGAG                         TCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
genomic: ATACGACGACAATTGAGgcaagcttct ... tgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
EST: gi|89106688|gb|DY576905.1|DY576905
EST:     TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAG                         GCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
genomic: TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAGgcaagcttct ... tgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
EST: gi|149072485|gb|EE160763.2|EE160763
EST:     TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAG                         GCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG
genomic: TTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAGgcaagcttct ... tgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAG

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: 169

TGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAGgcaagcttct ... tgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 271

TGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAGgcaagcttct ... tgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 366

TGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAGgcaagcttct ... tgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 231

TGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAGgcaagcttct ... tgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcagcattttttaatgtagaagatgacatcaatttgttaccttgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG
                                       ttacctt  CT-rich tract
        attttttaatgtagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagcttctagcattatgttgttcagcattttttaatgtagaagatgacatcaatttgttaccttgatgtacagGCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA