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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagattatatgtacctgtgattgaccttttgatttgttgtttgtaacagttctgtataataatctttgagcattcttttgactgcttgattttatttcagCTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAATCAGCAGGGAAGCATCAGAAGAAGAAATTCGAGCTGCTAGGAACTATCTGAT

Basic information

species Zea mays
transcript GRMZM2G013814_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013814_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g15033.1 (Oryza sativa), 3'ss of exon 3
-tagattatatgtacctgtgattgaccttttgattt-gttgtttgtaacagttctgtataataatctttgagcattcttttgactgcttgattttatttcagCTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAATCAGCAGGGAAGCATCAGAAGAAGAAATTCGAGCTGCTAGGAACTATCTGAT
  |||| | || ||| | | |||| ||| | | ||| |||||||| |  |||||| | |  ||||  |         |||| || |||| ||||   |||||| ||||||||  |||||||||| || ||||| |||||||| || |||||||||||||||||||| |||||||||||||||||||| ||||| | ||||||
tgagatcacatatactttttattgtcctgtcggttttgttgtttggattagttcttttttgtaattatcacctcactttttaaccgcttaatttc--ttcagCCATCTTTCCTAGAATCCATGTGAAGGATCCCTATCAGCGACTTGGAATCAGCAGGGAAGCATCTGAAGAAGAAATTCGAGCTGCCAGGAATTTTCTGAT
















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|71441858|gb|DR822908.1|DR822908
EST:     CACACCACTAGCAACTGCATCATTTGGGGATATGGCTGATTCTTCAACTC                         CTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAATCA
genomic: CACACCACTAGCAACTGCATCATTTGGGGATATGGCTGATTCTTCAACTCgtgagtattt ... tttatttcagCTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAATCA
EST: gi|211077182|gb|FL069428.1|FL069428
EST:     CATACCACTAGCAACTGCATCATTTGGGGATATGGCTGATTCTTCAACTC                         CTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAATCA
genomic: CACACCACTAGCAACTGCATCATTTGGGGATATGGCTGATTCTTCAACTCgtgagtattt ... tttatttcagCTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAATCA
EST: gi|211142683|gb|FL136020.1|FL136020
EST:     CACACCACTAGCAACTGCATCATTTGGGGATATGGCTGATTCTTCAACTC                         CTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAATCA
genomic: CACACCACTAGCAACTGCATCATTTGGGGATATGGCTGATTCTTCAACTCgtgagtattt ... tttatttcagCTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAATCA
EST: gi|89754448|gb|DY685223.1|DY685223
EST:     CACACCACTAGCAACTGCATCATTTGGGGATATGGCTGATTCTTCACCTC                         CTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAATCA
genomic: CACACCACTAGCAACTGCATCATTTGGGGATATGGCTGATTCTTCAACTCgtgagtattt ... tttatttcagCTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAATCA
EST: gi|211142681|gb|FL136018.1|FL136018
EST:     CACACCACTAGCAACTGCATCATTTGGGGATATGGCTGATTCTTCAACTC                         CTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAAT
genomic: CACACCACTAGCAACTGCATCATTTGGGGATATGGCTGATTCTTCAACTCgtgagtattt ... tttatttcagCTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAAT
EST: gi|88746410|gb|DY530551.1|DY530551
EST:     CACACCACTAGCAACTGCATCATTTGGGGATATGGGTGATTCTTCAACTC                         CTATCTTTCCCCGAATCCGTGTAAAAGATCCATATCAGCGTCTCGGAATCA
genomic: CACACCACTAGCAACTGCATCATTTGGGGATATGGCTGATTCTTCAACTCgtgagtattt ... tttatttcagCTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAATCA
EST: gi|211142682|gb|FL136019.1|FL136019
EST:     CACACCACTAGCAACTGCATCATTTGGGGATATGGCTGATTCTTCAACTC                         CTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAATCA
genomic: CACACCACTAGCAACTGCATCATTTGGGGATATGGCTGATTCTTCAACTCgtgagtattt ... tttatttcagCTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAATCA

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), 48 (downstream exon)
Score: 104

CACACCAAGTATAGTACTTCTTTCTGTTATGCGCCAAGAAATGCCAGAATCACACCACTAGCAACTGCATCATTTGGGGATATGGCTGATTCTTCAACTCgtgagtattt ... tttatttcagCTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAATCAGCAGGGAAGCATCAGAAGAAGAAATTCGAGCTGCTAGGAACTATCTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

CACACCAAGTATAGTACTTCTTTCTGTTATGCGCCAAGAAATGCCAGAATCACACCACTAGCAACTGCATCATTTGGGGATATGGCTGATTCTTCAACTCgtgagtattt ... tttatttcagCTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAATCAGCAGGGAAGCATCAGAAGAAGAAATTCGAGCTGCTAGGAACTATCTGAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 47

CACACCAAGTATAGTACTTCTTTCTGTTATGCGCCAAGAAATGCCAGAATCACACCACTAGCAACTGCATCATTTGGGGATATGGCTGATTCTTCAACTCgtgagtattt ... tttatttcagCTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAATCAGCAGGGAAGCATCAGAAGAAGAAATTCGAGCTGCTAGGAACTATCTGAT


Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 89

CACACCAAGTATAGTACTTCTTTCTGTTATGCGCCAAGAAATGCCAGAATCACACCACTAGCAACTGCATCATTTGGGGATATGGCTGATTCTTCAACTCgtgagtattt ... tttatttcagCTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAATCAGCAGGGAAGCATCAGAAGAAGAAATTCGAGCTGCTAGGAACTATCTGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagttctgtataataatctttgagcattcttttgactgcttgattttatttcagCTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAATCAGCAGGGAAGCATCAGAAGAAGAAATTCGAGCTGCTAGGAACTATCTGAT
                                            ttttatttc  CT-rich tract
       tgtataataatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagattatatgtacctgtgattgaccttttgatttgttgtttgtaacagttctgtataataatctttgagcattcttttgactgcttgattttatttcagCTATCTTTCCCCGAATCCATGTAAAAGATCCATATCAGCGTCTCGGAATCAGCAGGGAAGCATCAGAAGAAGAAATTCGAGCTGCTAGGAACTATCTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - atatgta
- - - - - - - -tgtgatt
- - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttga