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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGTCATTGACACCACGGGGGCTGGTGACACATTCACCTCAGCGTTCGCTGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaaccacgtcctcttcaatatttgaccgactggtttccttgcatcttgatttgatagcttctacgttcctgaatcccag

Basic information

species Zea mays
transcript GRMZM2G178346_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178346_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g47550.1 (Oryza sativa), 5'ss of exon 3
GAAGTCATTGACACCACGGGGGCTGGTGACACATTCACCTCAGCGTTCGCTGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtac-gaaaccacgtcctcttcaatatttgaccg-actggtttccttgcatcttgat-ttgatagcttctacgt----tcctgaatcccag-------------
|||||  |||| || || || || |||||||| ||||||||||| || |||||||| || || ||||| || ||||||   ||||||||||||||||||||||| |||| |||   ||| ||   ||||||  | | | | || ||||    |  |  ||   |   | | | |         | | |||              
GAAGTTGTTGATACGACTGGTGCCGGTGACACTTTCACCTCAGCTTTTGCTGTAGCTCTAGTTGAGGGTAAACCTAAGGAAGAGTGCATGAGATTTGCTGgtactgaaagcaccctctcctcgtcatttgattgcaattgatttcttgttcttcaacattagcatactttgcttgaggcttcaatttccaatttttaatttcag
















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|71429185|gb|DR810235.1|DR810235
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|91871988|gb|EB401945.1|EB401945
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|50334100|gb|CO529226.1|CO529226
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|32838385|gb|CD978063.1|CD978063
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|71329171|gb|DR801295.1|DR801295
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|14585624|gb|BI135376.1|BI135376
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|113701953|gb|EE679457.1|EE679457
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|86468088|gb|DY234458.1|DY234458
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|89760835|gb|DY689086.1|DY689086
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|32835984|gb|CD975662.1|CD975662
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|71305902|gb|DR789076.1|DR789076
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGGGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|29945342|gb|CB815591.1|CB815591
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|78123556|gb|DV541940.1|DV541940
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|86467635|gb|DY234005.1|DY234005
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|71773042|gb|DR970960.1|DR970960
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|31909963|gb|CD651183.1|CD651183
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|71314423|gb|DR793839.1|DR793839
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|71320827|gb|DR797131.1|DR797131
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|32834864|gb|CD974542.1|CD974542
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|78124669|gb|DV543053.1|DV543053
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGC
EST: gi|32838411|gb|CD978089.1|CD978089
EST:     TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTG                         CTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATGG
genomic: TGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaacc ... tgaatcccagCTGCTGCCGCCTCTCTGTGTGTTCGAGTAAAGGGGGCTATACCCAGCATG-

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGTCATTGACACCACGGGGGCTGGTGACACATTCACCTCAGCGTTCGCTGTAGCCCTGGTCGAGGGGAAGCCTAAGAGGGAGTGCATGAGATTTGCTGgtacgaaaccacgtcctcttcaatatttgaccgactggtttccttgcatcttgatttgatagcttctacgttcctgaatcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG