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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAGgttagttatcttatatgtatcctacatggcatcctctgaattggtttactcctgtgagcaatctacatatttgtcgattagttacatacacaactctttt...

Basic information

species Zea mays
transcript GRMZM2G028307_T02
intron # 13
splice site 5'
intron type U2

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|211332968|gb|FL315995.1|FL315995
EST:     GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG                         GAGAAATCTATCTCGCGTTCTTCAATCTCGACTCCATGAGCAGGAAGATGA
genomic: GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAGgttagttatc ... catggtgcagGAGAAATCTATCTCGCATTCTTCAATCTCGACTCCATGAGCAGGAAGATGA
EST: gi|50328270|gb|CO523396.1|CO523396
EST:     GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG                         GAGAAATCTATCTCGCATTCTTCAATCTCGACTCCATGAGCAGGAAGATGA
genomic: GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAGgttagttatc ... catggtgcagGAGAAATCTATCTCGCATTCTTCAATCTCGACTCCATGAGCAGGAAGATGA
EST: gi|74237283|gb|DT645197.1|DT645197
EST:     GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG                         GAGAAATCTATCTCGCATTCTTCAATCTCGACTCCATGAGCAGGAAGATGA
genomic: GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAGgttagttatc ... catggtgcagGAGAAATCTATCTCGCATTCTTCAATCTCGACTCCATGAGCAGGAAGATGA
EST: gi|211028161|gb|FL322650.1|FL322650
EST:     GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG                         GAGAAATCTATCTCGCGTTCTTCAATCTCGACTCCATGAGCAGGAAGATGA
genomic: GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAGgttagttatc ... catggtgcagGAGAAATCTATCTCGCATTCTTCAATCTCGACTCCATGAGCAGGAAGATGA
EST: gi|32934104|gb|CF038916.1|CF038916
EST:     ACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG                         GAGAAATCTATCTCGCGTTCTTCAATCTCGACTCCATGAGCAGGAAGATGA
genomic: ACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAGgttagttatc ... catggtgcagGAGAAATCTATCTCGCATTCTTCAATCTCGACTCCATGAGCAGGAAGATGA
EST: gi|211010841|gb|FL363378.1|FL363378
EST:     GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG                         GAGAAATCTATCTCGCGTTCTTCAATCTCGACTCCATGAGCAGGAAGATGA
genomic: GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAGgttagttatc ... catggtgcagGAGAAATCTATCTCGCATTCTTCAATCTCGACTCCATGAGCAGGAAGATGA
EST: gi|89760464|gb|DY688865.1|DY688865
EST:     GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG                         GAGAAATCTATCTCGCATTCTTCAATCTCGACTCCATGAGCAGGAAGATGA
genomic: GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAGgttagttatc ... catggtgcagGAGAAATCTATCTCGCATTCTTCAATCTCGACTCCATGAGCAGGAAGATGA
EST: gi|211483893|gb|FL352028.1|FL352028
EST:     GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG                         GAGAAATCTATCTCGCGTTCTTCAATCTCGACTCCATGAGCAGGAAGATGA
genomic: GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAGgttagttatc ... catggtgcagGAGAAATCTATCTCGCATTCTTCAATCTCGACTCCATGAGCAGGAAGATGA
EST: gi|32834923|gb|CD974601.1|CD974601
EST:     GTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG                         GAGAAATCTATCTCGCGTTCTTCAATCTCGACTCCATGAGCAGGAAGATGA
genomic: GTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAGgttagttatc ... catggtgcagGAGAAATCTATCTCGCATTCTTCAATCTCGACTCCATGAGCAGGAAGATGA

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: 42 (upstream exon), 49 (downstream exon)
Score: 255

GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAGgttagttatc ... catggtgcagGAGAAATCTATCTCGCATTCTTCAATCTCGACTCCATGAGCAGGAAGATGACCGTTCAAATATCAGACCTTGGAAAGGTTCTCGGAAGAAACCTTTTGGA


Block sizes: 42 (upstream exon), 43 (downstream exon)
Score: 64

GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAGgttagttatc ... catggtgcagGAGAAATCTATCTCGCATTCTTCAATCTCGACTCCATGAGCAGGAAGATGACCGTTCAAATATCAGACCTTGGAAAGGTTCTCGGAAGAAACCTTTTGGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 77

GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAGgttagttatc ... catggtgcagGAGAAATCTATCTCGCATTCTTCAATCTCGACTCCATGAGCAGGAAGATGACCGTTCAAATATCAGACCTTGGAAAGGTTCTCGGAAGAAACCTTTTGGA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 320

GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAGgttagttatc ... catggtgcagGAGAAATCTATCTCGCATTCTTCAATCTCGACTCCATGAGCAGGAAGATGACCGTTCAAATATCAGACCTTGGAAAGGTTCTCGGAAGAAACCTTTTGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAGgttagttatcttatatgtatcctacatggcatcctctgaattggtttactcctgtgagcaatctacatatttgtcgattagttacatacacaactctttt

- -  AGTGGA
- - - GTGGAG
- - -  TGGAGG
- - - - - - - - - CATGGA
- - - - - - - - - - - - - - -  TGGAAG