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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaggctcatgtacagccccttatctaaattgatatttcttgtgaggtccttggagttcatttgtccattttctttcctttatttattgcttcctaaccttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAGAGATACTACTATTTCTGTTTTACTCGAAGACATACCAGGGGGGAGGTTG

Basic information

species Zea mays
transcript GRMZM2G098815_T04
intron # 5
splice site 3'
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|71438169|gb|DR819219.1|DR819219
EST:     AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGA                         GTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
genomic: AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGAgtatgtaggc ... accttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
EST: gi|78117671|gb|DV536058.1|DV536058
EST:     AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGA                         GTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
genomic: AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGAgtatgtaggc ... accttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
EST: gi|148952745|gb|EC898726.2|EC898726
EST:     AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGA                         GTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
genomic: AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGAgtatgtaggc ... accttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
EST: gi|71438316|gb|DR819366.1|DR819366
EST:     AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAA-TTCATCAGA                         GTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
genomic: AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGAgtatgtaggc ... accttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
EST: gi|74245464|gb|DT653378.1|DT653378
EST:     AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGA                         GTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
genomic: AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGAgtatgtaggc ... accttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
EST: gi|71433709|gb|DR814759.1|DR814759
EST:     AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGA                         GTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
genomic: AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGAgtatgtaggc ... accttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
EST: gi|76926415|gb|DV170849.1|DV170849
EST:     AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGA                         GTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
genomic: AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGAgtatgtaggc ... accttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
EST: gi|71765717|gb|DR963654.1|DR963654
EST:     AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGA                         GTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
genomic: AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGAgtatgtaggc ... accttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
EST: gi|91873215|gb|EB403172.1|EB403172
EST:     AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGA                         GTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
genomic: AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGAgtatgtaggc ... accttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
EST: gi|149076111|gb|EE164690.2|EE164690
EST:     AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGA                         GTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
genomic: AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGAgtatgtaggc ... accttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
EST: gi|14245049|gb|BG873631.1|BG873631
EST:     AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGA                         GTCTTCGATATCACCACCTGGTAGCAAACAGAAATCTGCGTCTGATGATAG
genomic: AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGAgtatgtaggc ... accttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
EST: gi|78120056|gb|DV538440.1|DV538440
EST:     AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGA                         GTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
genomic: AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGAgtatgtaggc ... accttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
EST: gi|148960798|gb|EE011460.2|EE011460
EST:     AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGA                         GTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG
genomic: AGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGAgtatgtaggc ... accttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAG

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), 46 (downstream exon)
Score: 132

GTGTACATTCCTCGCCTCAGACTAGTAGTTTCACAGCTCCTGCAGTTAGAAGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGAgtatgtaggc ... accttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAGAGATACTACTATTTCTGTTTTACTCGAAGACATACCAGGGGGGAGGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

GTGTACATTCCTCGCCTCAGACTAGTAGTTTCACAGCTCCTGCAGTTAGAAGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGAgtatgtaggc ... accttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAGAGATACTACTATTTCTGTTTTACTCGAAGACATACCAGGGGGGAGGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

GTGTACATTCCTCGCCTCAGACTAGTAGTTTCACAGCTCCTGCAGTTAGAAGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGAgtatgtaggc ... accttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAGAGATACTACTATTTCTGTTTTACTCGAAGACATACCAGGGGGGAGGTTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 105

GTGTACATTCCTCGCCTCAGACTAGTAGTTTCACAGCTCCTGCAGTTAGAAGTGCTATACCAGATCCAGACGTCCGTCAAAGTTGTGCAAATTCATCAGAgtatgtaggc ... accttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAGAGATACTACTATTTCTGTTTTACTCGAAGACATACCAGGGGGGAGGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggagttcatttgtccattttctttcctttatttattgcttcctaaccttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAGAGATACTACTATTTCTGTTTTACTCGAAGACATACCAGGGGGGAGGTTG
                                        tcctaac  putative branch site (score: 105)
                attttctttcctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtaggctcatgtacagccccttatctaaattgatatttcttgtgaggtccttggagttcatttgtccattttctttcctttatttattgcttcctaaccttataagGTCTTCGATATCACCACCTGGAAGCAAACAGAAATCTGCGTCTGATGATAGAGATACTACTATTTCTGTTTTACTCGAAGACATACCAGGGGGGAGGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA