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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattactatccaattctaaattaattctttgttttctgttcgttgctattttgaggtgcactaaactgctaatgtgatgaagcaacctatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAAGGGGCCCCAGAAAAGAAGGCGCCGATACGGGTGAAATTTGAGATACCAT

Basic information

species Zea mays
transcript GRMZM2G436835_T04
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G436835_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g50770.1 (Oryza sativa), 3'ss of exon 9
gtaattactatccaattctaaattaattctttgttttctgttcgttgctattttgaggtgcactaaactgctaatgtgatgaagcaacctatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAAGGGGCCCCAGAAAAGAAGGCGCCGATACGGGTGAAATTTGAGATACCAT
    | | | || |   | || | |  ||||||  ||||  |   |||||  | || |||  ||||  |    ||||||          | ||   ||||| |||||||||||||| |||||||||||||| || ||||| || |||||||  || || ||||||||||| || ||||| |||||||||||||||||||
---gtaagtttcaag--ccaagtca--tctttgccttctacttcatgctacctagaagtgtgctaatat----atgtga-------gtttttctgttagGATTACATGTGCAGAGCTGAATTTAGTCTTCCAAGTATAACTGCAGAAGAAGCAGCTCCTGAAAAGAAGGCACCAATACGAGTGAAATTTGAGATACCAT

upper sequence: GRMZM2G436835_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 9
gtaattactatccaattctaaattaattctttgttttctgttcgttgctattttgaggtgcactaaactgctaatgtgatgaagcaacctatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAAGGGGCCCCAGAAAAGAAGGCGCCGATACGGGTGAAATTTGAGATACCAT--------------
    | | | || |   | || | |  ||||||  ||||  |   |||||  | || |||  ||||  |    ||||||          | ||   ||||| |||||||||||||| |||||||||||||| || ||||| || |||||||  || || ||||||||||| || ||||| |||||||||||||||||||              
---gtaagtttcaag--ccaagtca--tctttgccttctacttcatgctacctagaagtgtgctaatat----atgtga-------gtttttctgttaggattacatgtgcagAGCTGAATTTAGTCTTCCAAGTATAACTGCAGAAGAAGCAGCTCCTGAAAAGAAGGCACCAATACGAGTGAAATTTGAGATACCATATTTCACTGTGTCG
















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|110940875|gb|EE161032.1|EE161032
EST:     CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|149097147|gb|EE182959.2|EE182959
EST:     CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|32928680|gb|CF033492.1|CF033492
EST:     AAAATAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: AAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|50330278|gb|CO525404.1|CO525404
EST:     CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|60343961|gb|DN210934.1|DN210934
EST:     CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|67016089|gb|CO444838.1|CO444838
EST:     CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|32935319|gb|CF040131.1|CF040131
EST:     CCGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGCCTTCCTAGCGTAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|149072435|gb|EE160710.2|EE160710
EST:     CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|83278602|gb|DV942610.1|DV942610
EST:     CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|211094625|gb|FL030434.1|FL030434
EST:     CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|32928281|gb|CF033093.1|CF033093
EST:     CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|71433886|gb|DR814936.1|DR814936
EST:     CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|37380003|gb|CF626778.1|CF626778
EST:     CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAG                         GAATTCATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|32928313|gb|CF033125.1|CF033125
EST:     CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|60341938|gb|DN208911.1|DN208911
EST:     CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|32929943|gb|CF034755.1|CF034755
EST:     CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|149081826|gb|EE170984.2|EE170984
EST:     CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|60398404|gb|DN231220.1|DN231220
EST:     CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|14204059|gb|BG837736.1|BG837736
EST:     CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA

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: 194

TGCCACAAACCCAAATATAAGAACTTCAATGGGGTCTGCTGCATATGCTCCTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAAGGGGCCCCAGAAAAGAAGGCGCCGATACGGGTGAAATTTGAGATACCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 291

TGCCACAAACCCAAATATAAGAACTTCAATGGGGTCTGCTGCATATGCTCCTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAAGGGGCCCCAGAAAAGAAGGCGCCGATACGGGTGAAATTTGAGATACCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 304

TGCCACAAACCCAAATATAAGAACTTCAATGGGGTCTGCTGCATATGCTCCTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAAGGGGCCCCAGAAAAGAAGGCGCCGATACGGGTGAAATTTGAGATACCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 266

TGCCACAAACCCAAATATAAGAACTTCAATGGGGTCTGCTGCATATGCTCCTGAGAGAGATGCAATGGTTTGGAAAATAAAATCATTCCCTGGTGGCAAGgtaattacta ... tatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAAGGGGCCCCAGAAAAGAAGGCGCCGATACGGGTGAAATTTGAGATACCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctattttgaggtgcactaaactgctaatgtgatgaagcaacctatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAAGGGGCCCCAGAAAAGAAGGCGCCGATACGGGTGAAATTTGAGATACCAT
                        tgctaat  putative branch site (score: 266)
                                           cctatcct  putative PPT
     attttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattactatccaattctaaattaattctttgttttctgttcgttgctattttgaggtgcactaaactgctaatgtgatgaagcaacctatcctatagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAAGGGGCCCCAGAAAAGAAGGCGCCGATACGGGTGAAATTTGAGATACCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG