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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggagctgttatacatgtctgatatatttgttccatgatcagttttcaatcactactgatctttaatttttaaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGATAGTCACGCCAGATCCCAGCCGAAGGGGGCTAACCTTGAAGACAGGGTTT

Basic information

species Zea mays
transcript GRMZM2G139894_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 3'ss of exon 13
gtttggagctgttatacatgtctgatatatttgttccatgatcagttttcaatcactactgatctttaatttttaaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGATAGTCACGCCAGATCCCAGCCGAAGGGGGCTAACCTTGAAGACAGGGTTT
||||||||||| | |   ||| | |||||||| | |  |   | | | || |||  ||||||| |||   |  |  |||||||||| ||||| || |||||||||||||||||||| ||||||||||||||||||||||| || ||||| || || ||||| |||||||||||||| |||||| 
gtttggagctgattttgctgtgtaatatatttttgcagt--cctggtatctatctgtactgatttttt-ctggtgcaaatgcagGACATTGTTGACCCATTTACAGATGAAATGCTTGCAAGGTTTGTTGTAGATAGTCATGCAAGATCTCAACCCAAGGGTGCTAACCTTGAAGATAGGGTTC
















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|211172446|gb|FL130947.1|FL130947
EST:     AATTGACGGATCCCATTATTTCACGTTTCGACGTCCTCTGTGTGGTTAAG                         GATGTTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|211174125|gb|FL130962.1|FL130962
EST:     AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAG                         GATATTGTCGATCCATTTACAGATGAAANGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|32932509|gb|CF037321.1|CF037321
EST:     AATTGACGGATCCCATTATTTCACGTTTCGACGTCCTCTGTGTGGTTAGG                         GATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|211172448|gb|FL130949.1|FL130949
EST:     AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAG                         GATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|33093214|gb|CF053208.1|CF053208
EST:     AATTGACGGATCCCATTATTTCACGTTTCGACGTCCTCTGTGTGGTTAAG                         GATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|18659890|gb|BM500576.1|BM500576
EST:     GTGTGGTTAAG                         GATGTTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: GTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|211174115|gb|FL130952.1|FL130952
EST:     AATTGACGGATCCCATTATTTCACGTTTCGACGTCCTCTGTGTGGTTAAG                         GATGTTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|211174124|gb|FL130961.1|FL130961
EST:     AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAG                         GATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|211172450|gb|FL130951.1|FL130951
EST:     AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAG                         GATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|32943927|gb|CF048746.1|CF048746
EST:     AATTGACGGATCCCATTATTTCACGTTTCGACGTCCTCTGTGTGGTTAAG                         GATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|211174121|gb|FL130958.1|FL130958
EST:     AATTGACGGATCCCATTATTTCACGTTTCGACGTCCTCTGTGTGGTTAAG                         GATGTTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|211174118|gb|FL130955.1|FL130955
EST:     AATTGACGGATCCCATTATTTCACGTTTCGACGTCCTCTGTGTGGTTAAG                         GATGTTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|32931979|gb|CF036791.1|CF036791
EST:     AATTGACGGATCCCATTATTTCACGTTTCGACGTCCTCTGTGTGGTTAAG                         GATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|30306555|gb|CD001228.1|CD001228
EST:     AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAG                         GATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|211174117|gb|FL130954.1|FL130954
EST:     AATTGACGGATCCCATTATTTCACGTTTCGACGTCCTCTGTGTGGTTNAG                         GATGTTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|29544563|gb|CB604943.1|CB604943
EST:     AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGGGGCTAAG                         GATATTGTCGATCCATTTACA
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACA
EST: gi|32934497|gb|CF039309.1|CF039309
EST:     TCACGTTTCGACGTCCTCTGTGTGGTTAAG                         GATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: TCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|211174122|gb|FL130959.1|FL130959
EST:     AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAG                         GATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|211172447|gb|FL130948.1|FL130948
EST:     AATTGACGGATCCCATTATTTCACGTTTCGACGTCCTCTGTGTGGTTAAG                         GATGTTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|18450515|gb|BM428793.1|BM428793
EST:     AA-TGACGGATCCCATTATTTCACGTTTCGACGTCCTCTGTGTGGTTAAG                         GATGTTGTTGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|32932452|gb|CF037264.1|CF037264
EST:     AATTGACGGATCCCATTATTTCACGTTTCGACGTCCTCTGTGTGGTTAAG                         GATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|32932490|gb|CF037302.1|CF037302
EST:     AATTGACGGATCCCATTATTTCACGTTTCGACGTCCTCTGTGTGGTTAAG                         GATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|211174120|gb|FL130957.1|FL130957
EST:     AATTGACGGATCCCATTATTTCACGTTTCGACGTCCTCTGTGTGGTTAAG                         GATGTTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
EST: gi|211172449|gb|FL130950.1|FL130950
EST:     AATTGACGGATCCCATTATTTCACGTTTCGACGTCCTCTGTGTGGTTAAG                         GATGTTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT
genomic: AATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 322

GTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGATAGTCACGCCAGATCCCAGCCGAAGGGGGCTAACCTTGAAGACAGGGTTT


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 78

GTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGATAGTCACGCCAGATCCCAGCCGAAGGGGGCTAACCTTGAAGACAGGGTTT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 33

GTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGATAGTCACGCCAGATCCCAGCCGAAGGGGGCTAACCTTGAAGACAGGGTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 26

GTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagct ... aaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGATAGTCACGCCAGATCCCAGCCGAAGGGGGCTAACCTTGAAGACAGGGTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttccatgatcagttttcaatcactactgatctttaatttttaaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGATAGTCACGCCAGATCCCAGCCGAAGGGGGCTAACCTTGAAGACAGGGTTT
                           tactgatctttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggagctgttatacatgtctgatatatttgttccatgatcagttttcaatcactactgatctttaatttttaaaaatgcagGATATTGTCGATCCATTTACAGATGAAATGCTCGCAAGGTTTGTTGTAGATAGTCACGCCAGATCCCAGCCGAAGGGGGCTAACCTTGAAGACAGGGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA