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

gtagttatattccattttaaatgcaatgcataatctagtggttgatggttgcttcttgccttaccaccaccaaaggcagctagctgttctatgtgtatgagcagctctgtaatcaatatgccgtttctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATCTCTGACGAAAGGAGATGGTGAAGTAGGGATGGTAAAAATTGACAAGGAC

Basic information

species Zea mays
transcript GRMZM2G064366_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064366_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g34360.1 (Oryza sativa), 3'ss of exon 4
gtagttatattccattttaaatgcaatgcataatctagtggttgatggttgcttcttgccttaccaccaccaaaggcagctagctgttctatgtgtatgagcagctctgtaatcaatatgccgtttctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATCTCTGACGAAAGGA---GATGGTGAAGTAGGGATGGTAAAAATTGACAAGGAC
                          ||| |   | |    | ||  || |     ||  ||   ||  |  |||   | || || |            ||| |||||  |||  | ||| |    ||| || |||||| |||||||| || |||||||| ||||| || ||||| |||||||||||||||||||| ||    || ||||| ||||||||||||||  ||||||||   
-----------------------ggctgcctg--ccatcactagaaagtagtaatgtgtttttatacggcacaagaaggttatcttt---------gaaagc-gctctaaaattgacatgtcaaacctt-gtccagATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCTCAATCTCTGACGAAGGGGACCGACGGTGATGTAGGGATGGTAAAGGTTGACAAG---
















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|67024546|gb|CO453295.1|CO453295
EST:     TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
genomic: TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|21891783|gb|BQ744996.1|BQ744996
EST:     TTGCTTCTTGTGATTTGTTATCTGTGGGCCCCTTCCCAAAGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
genomic: TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|22491170|gb|BU051093.1|BU051093
EST:     AGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
genomic: AGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|148967311|gb|EE018517.2|EE018517
EST:     TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATT
genomic: TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|76289905|gb|DV029473.1|DV029473
EST:     TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATT
genomic: TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|71314489|gb|DR793872.1|DR793872
EST:     TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
genomic: TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|22491183|gb|BU051106.1|BU051106
EST:     TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
genomic: TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|83278764|gb|DV942772.1|DV942772
EST:     TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
genomic: TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|148990960|gb|EE032390.2|EE032390
EST:     TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAG                         ATATGCATATTTTGGTGAAGCTGCTGACGATGACGATGAGGATTCTCATTT
genomic: TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|211398906|gb|FL435802.1|FL435802
EST:     TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
genomic: TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|149112569|gb|EE295431.2|EE295431
EST:     TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
genomic: TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|19272383|gb|BM888639.1|BM888639
EST:     TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
genomic: TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|19272497|gb|BM888753.1|BM888753
EST:     TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
genomic: TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|148959137|gb|EE010606.2|EE010606
EST:     TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
genomic: TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|37383047|gb|CF628501.1|CF628501
EST:     CCCAAAGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
genomic: CCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|211053916|gb|FL383319.1|FL383319
EST:     TGTGGGCACCTTCCCAAAGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
genomic: TGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|71775201|gb|DR973079.1|DR973079
EST:     TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
genomic: TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|4647097|gb|AI622172.1|AI622172
EST:     TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
genomic: TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|148960354|gb|EE153613.2|EE153613
EST:     TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
genomic: TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|148971674|gb|EE022398.2|EE022398
EST:     TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
genomic: TTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
EST: gi|21331873|gb|BQ487254.1|BQ487254
EST:     CTTGTGATTTGTTATCTGTGGGCCCCTTCCCAAAGCTCGCAAAG                         ATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC
genomic: CTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATC

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), 45 (downstream exon)
Score: 98

GGCAGAGCGCATGGATCATAACTGCCTTCTGGGATGTCCTTGCGTTTGTGTTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATCTCTGACGAAAGGAGATGGTGAAGTAGGGATGGTAAAAATTGACAAGGAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 110

GGCAGAGCGCATGGATCATAACTGCCTTCTGGGATGTCCTTGCGTTTGTGTTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATCTCTGACGAAAGGAGATGGTGAAGTAGGGATGGTAAAAATTGACAAGGAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 191

GGCAGAGCGCATGGATCATAACTGCCTTCTGGGATGTCCTTGCGTTTGTGTTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATCTCTGACGAAAGGAGATGGTGAAGTAGGGATGGTAAAAATTGACAAGGAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 210

GGCAGAGCGCATGGATCATAACTGCCTTCTGGGATGTCCTTGCGTTTGTGTTGCTTCTTGTGATTTGTTATCTGTGGGCACCTTCCCAAAGCTCGCAAAGgtagttatat ... ctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATCTCTGACGAAAGGAGATGGTGAAGTAGGGATGGTAAAAATTGACAAGGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctgttctatgtgtatgagcagctctgtaatcaatatgccgtttctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATCTCTGACGAAAGGAGATGGTGAAGTAGGGATGGTAAAAATTGACAAGGAC
                                       ccgtttctttgttc  CT-rich tract
                            taatcaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttatattccattttaaatgcaatgcataatctagtggttgatggttgcttcttgccttaccaccaccaaaggcagctagctgttctatgtgtatgagcagctctgtaatcaatatgccgtttctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATCTCTGACGAAAGGAGATGGTGAAGTAGGGATGGTAAAAATTGACAAGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG