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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttttcatctaacgggatcatagctcatttttttttgtttctggttgctgctactgtaaggtaacaagtttagatttatgacatacctttatgtttcattgatttcattcactattgcag

Basic information

species Zea mays
transcript GRMZM2G045331_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045331_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g52340.1 (Oryza sativa), 5'ss of exon 4
GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttttcatctaacgggatcatagctcatttttttttgt-ttctggttgctgctactgtaaggtaacaagtttagatttatgacatacctttatgtttcattgatttcattcactattgcag-----------------------------------------------
|| ||| | || || ||| |  |||| |||||||| ||| ||||||| || ||||| |||||||| |||||||| ||||||||||| ||||||||   | | ||  ||  ||    ||   |        |||| |||||||||||   | |  | | |    | |||| | |    |    | |||  ||| |     ||  ||| |  |    ||                                               
GAAATTGTGTCAATCTACTCTGCACTTTCACCCCCAACATTGTCACCAGGTGCATCGAACCGAGTCTGCAATGCACTTGCACTTCTTCAGgtacataatcttatgaaatagggcggtaatgctggaaaagttgtcttctggttgcttgcatttcatgatgt--attttacagtagaaattgccttttgagttacccaagttggatttatgac-atagatttgctgattaactctttcttttttgcttttcaaaaataatttcag
















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|78123053|gb|DV541437.1|DV541437
EST:     TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAG                         TGTGTTGCATCGCACCCTGAGACCAAGATCCTTTTCCTAAATG
genomic: TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttt ... actattgcagTGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
EST: gi|76281973|gb|DV021541.1|DV021541
EST:     TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAG                         TGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
genomic: TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttt ... actattgcagTGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
EST: gi|78088708|gb|DV517101.1|DV517101
EST:     TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAG                         TGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
genomic: TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttt ... actattgcagTGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
EST: gi|60350887|gb|DN217860.1|DN217860
EST:     TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAG                         TGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTTCCTAAATG
genomic: TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttt ... actattgcagTGTGTTGCATCGCACCCTGAGACCAGGATCCTTTT-CCTAAATG
EST: gi|149048884|gb|EE048384.2|EE048384
EST:     TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAG                         TGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
genomic: TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttt ... actattgcagTGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
EST: gi|31351237|gb|CD435594.1|CD435594
EST:     TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAG                         TGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
genomic: TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttt ... actattgcagTGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
EST: gi|78091209|gb|DV519583.1|DV519583
EST:     TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAG                         TGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
genomic: TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttt ... actattgcagTGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
EST: gi|9731640|gb|BE510392.1|BE510392
EST:     TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAG                         TGTGTTGCATCGCACCCTGAGACCA
genomic: TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttt ... actattgcagTGTGTTGCATCGCACCCTGAGACCA
EST: gi|71445883|gb|DR826933.1|DR826933
EST:     TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAG                         TGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
genomic: TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttt ... actattgcagTGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
EST: gi|211374623|gb|FK958603.1|FK958603
EST:     GGCACCTGGAGCATCAAACCGAGGTTTGGA-TGCTCTTGGACTTCTGGAG                         TGTGTTGCATC
genomic: GTCACCTGGAGCATCAAACCGAG-TTTGCAATGCTCTTGCACTTCTGCAGgtacactttt ... actattgcagTGTGTTGCATC
EST: gi|31356490|gb|CD440847.1|CD440847
EST:     TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAG                         TGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
genomic: TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttt ... actattgcagTGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
EST: gi|76936740|gb|DV174858.1|DV174858
EST:     TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAG                         TGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
genomic: TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttt ... actattgcagTGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
EST: gi|31354815|gb|CD439172.1|CD439172
EST:     TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAG                         TGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
genomic: TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttt ... actattgcagTGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
EST: gi|74233595|gb|DT641509.1|DT641509
EST:     TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAG                         TGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
genomic: TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttt ... actattgcagTGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
EST: gi|91056772|gb|EB167190.1|EB167190
EST:     TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAG                         TGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG
genomic: TGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttt ... actattgcagTGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG

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: 49 (upstream exon), 43 (downstream exon)
Score: 79

GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttt ... actattgcagTGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 36

GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttt ... actattgcagTGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 68

GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttt ... actattgcagTGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 86

GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttt ... actattgcagTGTGTTGCATCGCACCCTGAGACCAGGATCCTTTTCCTAAATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAGgtacactttttcatctaacgggatcatagctcatttttttttgtttctggttgctgctactgtaaggtaacaagtttagatttatgacatacctttatgtttcattgatttcattcactattgcag

- - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG