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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtttttcactcctgattcctgcaacggatgcatctatgctgcccatttgtgttttaagtgcaccaccattctactgtgacctcagtgccttccaattatgctggacatttccgaggaacttcgacatctgtttctactttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG

Basic information

species Zea mays
transcript GRMZM2G058584_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g13190.1 (Oryza sativa), 3'ss of exon 11
gtagtttttcactcctg---attcctgcaacg------------gatgcatctatgctgc-ccatttgtgttttaagt-gcaccaccattctactgtgacctcagtgccttccaattatgc------tggacatttccgaggaacttcgaca-----tctgtttctactttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG
||| || |||| |||||   | ||  | |                | |||  ||   | |  || | | |||| | || | |  |   | |  |    |     ||   |   ||||||        | | | || ||  |||   | ||||      || ||||| | || || |||| || |||||||| ||| |||||||||||||||||||||||||||| |||||||||||||| |||||||||||  |  |||| || ||||
gtaattcttcattcctgcccactctcgaattatttataatttgtaaggcacgtactatacatcactggagtttgaggtcgtagaattttgcagcatgcatgaaggtaaatgaaaattatctgatctattgccgttcccagggattgttgacaagccccctctttcttccttatgtagGCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAG

upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT5G63890.1 (Arabidopsis thaliana), 3'ss of exon 10
gtagtttttcactcctgattcctgcaacggatgcatctatgctgcccatttgtgttttaagtgcaccaccattctactgtg-acctcagtgccttccaattatgctggacatttccgaggaacttcgacatctgtttctactttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG---------
                                                            || | ||| |  | ||| ||  ||||       | | |  |       |||| |   |  | | ||    | ||||  |   || | ||||| ||||| ||||||||||| ||||| || || |||||||||||||| || || || |||||| | |||||||   | || || |||||||         
------------------------------------------------------------gtac-ccatctctttacggttcacctttactgttactatctcaaaacaacatctgt-aacatcatcactgtttgttctttaattctccagGCAATATCTTTCTCAAATCTATATGCACCCGAACATTTGATCATCAATGTCAAAGACGCTGAGAAATGGGAGGGACTGATTGAGAACGCAGGCTCGGTTT
















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|71309836|gb|DR791200.1|DR791200
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|8516559|gb|BE123284.1|BE123284
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGGTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|21331772|gb|BQ487153.1|BQ487153
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|101389917|gb|EB816889.1|EB816889
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|23357617|gb|BU645266.1|BU645266
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGCTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAAC
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAAC
EST: gi|78025141|gb|DV493528.1|DV493528
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|71432207|gb|DR813257.1|DR813257
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|76283948|gb|DV023516.1|DV023516
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|76012898|gb|DT940068.1|DT940068
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|50325709|gb|CO520835.1|CO520835
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|211059003|gb|FL461767.1|FL461767
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTAATCATCAACGTA
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|101394855|gb|EB819362.1|EB819362
EST:     GAAAGATATGGGTGAG                         GGGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: GAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|71313988|gb|DR793606.1|DR793606
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|148957295|gb|EC903330.2|EC903330
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|78179432|gb|DV549805.1|DV549805
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|93017017|gb|EB642537.1|EB642537
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|86471200|gb|DY237570.1|DY237570
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|71432206|gb|DR813256.1|DR813256
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|71774595|gb|DR972473.1|DR972473
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|211215840|gb|FL096753.1|FL096753
EST:     AAAGCACTTAGCCACAGGCTTCACTGTGTTCGCGAAAAGATATGGTTGAA                         GCGATATCAGTCNCCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGT
genomic: AAAGCACTTAGCCACAG-CTTCACTGTGTTCGCGAAA-GATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTC-AAATCTGTATGCCCCTGAGCATTTGATCATCAACGT
EST: gi|32840983|gb|CD980664.1|CD980664
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|101394357|gb|EB819113.1|EB819113
EST:     TTCGCGAAAGATATGGTTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: TTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
EST: gi|71769688|gb|DR967625.1|DR967625
EST:     CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAG                         GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA
genomic: CAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttc ... ctttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaattatgctggacatttccgaggaacttcgacatctgtttctactttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG
                                   tctgtttctacttttt  CT-rich tract
                                           tacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtttttcactcctgattcctgcaacggatgcatctatgctgcccatttgtgttttaagtgcaccaccattctactgtgacctcagtgccttccaattatgctggacatttccgaggaacttcgacatctgtttctactttttgcagGCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG