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

...ctatggtttggttggaaaagcatctaaataaaatcaaccttatctaatgtttatccttctttgtgaattatcgaatgtttacatacattgttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGTGGCAACCCAAAGATGTTTGAGGCAAATGTGAAAAGAGCCATGACCGGAG

Basic information

species Zea mays
transcript GRMZM2G115939_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115939_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g11260.3 (Oryza sativa), 3'ss of exon 5
ctatggtttggttggaaaagcatctaaataaaatcaaccttatctaatgtttatccttctttgtgaattatcgaa----tgtttacatacattgttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGTGGCAACCCAAAGATGTTTGAGGCAAATGTGAAAAGAGCCATGACCGGAG
   | ||| | |    | |  ||  |  |     ||     ||     | |||   ||   |  || || | |       |||| | |    | ||  | ||||||||||||||| |||||||| |||||||| ||||| |||||||||||||||| |||||||||| ||||||| || ||||| ||||| || ||| ||||||
---ttgttggatgatcagattatacat-tgcttccattgccattggtgggttacagtttagtaagatttcttgtggcttagtttgcttttgattttgtccgcagCAACCAAACGATGAGGATCCGTTGAACCATGAAGCAGCAGCTGTCCTCCGTGACAACCCAAAGCTGTTTGAAGCTAATGTTAAAAGGGCAATGGCCGGAG
















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|26455341|gb|CA826924.1|CA826924
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|211060519|gb|FL179753.1|FL179753
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|21330709|gb|BQ486090.1|BQ486090
EST:     CTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|32847082|gb|CD986763.1|CD986763
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|8516401|gb|BE123127.1|BE123127
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|211378878|gb|FL474247.1|FL474247
EST:     CCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|32846744|gb|CD986425.1|CD986425
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|211441546|gb|FL398417.1|FL398417
EST:     TCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: TCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtttatccttctttgtgaattatcgaatgtttacatacattgttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGTGGCAACCCAAAGATGTTTGAGGCAAATGTGAAAAGAGCCATGACCGGAG
 atctaat  putative branch site (score: 3)
                  tgaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctatggtttggttggaaaagcatctaaataaaatcaaccttatctaatgtttatccttctttgtgaattatcgaatgtttacatacattgttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGTGGCAACCCAAAGATGTTTGAGGCAAATGTGAAAAGAGCCATGACCGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG