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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatttccaagaaaactgccccgcgtgtcttccgtacgactagacgatcaaagcttgtttacgaatctgtgatgctgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGCAACCAAGTCCAGAATAGCCAGCCGTATGCCGCAGATGAGCGGGATGGAC

Basic information

species Zea mays
transcript GRMZM2G074790_T03
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074790_T03 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os05g46290.1 (Oryza sativa), 3'ss of exon 16
----gtacatttcc-aagaaaactgccccgcgtgtcttccgtacgactagacgatcaaagcttgtttacgaatctgtgatgctgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGCAACCAAGTCCAGAATAGCCAGCCGTATGCCGCAGATGAGCGGGATGGAC
    | || || |  |||   | | |      | || |  | |  |||| |   || |  |||| |||  ||  |||| |  ||||   |||||||||  |||||||| |||| || ||||| |||||  | |||| ||| ||| | ||| ||||||| || || || ||||||||||||||||||||||| 
gtacgcacgttccttaagttgattact--atttttcctttgcattactaaaatttccacacttgcttaataacttgtgtttttgttt--cagTGTTTCTTTGCTGATGACAACGACAGAGGCAGCTGTTGCTGAGCCCCCAGCAGCAAAGGCCAGAATGGCTAGTCGGATGCCGCAGATGAGCGGGATGGAT
















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|211267531|gb|FL446292.1|FL446292
EST:     ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAG                         TGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
genomic: ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAGgtacatttcc ... tgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
EST: gi|5688540|gb|AI941555.1|AI941555
EST:     ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAG                         TGTTTCCCTGCTGATGGCAACCCCGGAGGCCGCTGTCTCCGAGCTCCCGGC
genomic: ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAGgtacatttcc ... tgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
EST: gi|67028320|gb|CO457069.1|CO457069
EST:     ATCATCGATCCGGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAG                         TGTTTCCCTGCTGATGGCA-CCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
genomic: ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAGgtacatttcc ... tgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
EST: gi|5006206|gb|AI712268.1|AI712268
EST:     ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAG                         TGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
genomic: ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAGgtacatttcc ... tgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
EST: gi|31997582|gb|CD661667.1|CD661667
EST:     ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAG                         TGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
genomic: ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAGgtacatttcc ... tgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
EST: gi|76911014|gb|DV164129.1|DV164129
EST:     ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAG                         TGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
genomic: ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAGgtacatttcc ... tgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
EST: gi|211184128|gb|FL012625.1|FL012625
EST:     ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAG                         TGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
genomic: ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAGgtacatttcc ... tgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
EST: gi|166455871|gb|EG161281.1|EG161281
EST:     ATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAAG                         TGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGG
genomic: ATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGC-AAGgtacatttcc ... tgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGG
EST: gi|60394409|gb|DN227279.1|DN227279
EST:     ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAG                         TGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
genomic: ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAGgtacatttcc ... tgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
EST: gi|24764724|gb|CA399887.1|CA399887
EST:     ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAG                         TGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
genomic: ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAGgtacatttcc ... tgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
EST: gi|149072567|gb|EE044214.2|EE044214
EST:     ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAG                         TGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
genomic: ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAGgtacatttcc ... tgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
EST: gi|74242337|gb|DT650251.1|DT650251
EST:     ATCATCGATCCCGTGAAGGTGATCCGCCCCGCACTTCAAGACGCTGCAAG                         TGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
genomic: ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAGgtacatttcc ... tgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
EST: gi|8666121|gb|BE186937.1|BE186937
EST:     ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAG                         TGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
genomic: ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAGgtacatttcc ... tgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
EST: gi|61118980|gb|DN559941.1|DN559941
EST:     ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAG                         TGTTTCCCTGTTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
genomic: ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAGgtacatttcc ... tgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
EST: gi|71759820|gb|DR957757.1|DR957757
EST:     ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAG                         TGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
genomic: ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAGgtacatttcc ... tgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
EST: gi|78117876|gb|DV536263.1|DV536263
EST:     ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAG                         TGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
genomic: ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAGgtacatttcc ... tgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
EST: gi|31352804|gb|CD437161.1|CD437161
EST:     ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAG                         TGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC
genomic: ATCATCGATCCCGTGAAGGTGATCCGCACCGCACTTCAAGACGCTGCAAGgtacatttcc ... tgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgtacgactagacgatcaaagcttgtttacgaatctgtgatgctgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGCAACCAAGTCCAGAATAGCCAGCCGTATGCCGCAGATGAGCGGGATGGAC
                        ttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatttccaagaaaactgccccgcgtgtcttccgtacgactagacgatcaaagcttgtttacgaatctgtgatgctgttgggcagTGTTTCCCTGCTGATGGCAACCACGGAGGCCGCTGTCTCCGAGCTCCCGGCAACCAAGTCCAGAATAGCCAGCCGTATGCCGCAGATGAGCGGGATGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA