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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgctgctgtgcttgtgctccgttccattcatttcattaccttatcagttcttattctgaaaaaaaaacgtgggcttgcattgcatccttgtgttgtattctcacacgcaccctgggtctacttaattactgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGCATCGATACTCCCTCGAGGTTTGAAGCTCCCCAGGAGTCTTGATCTCTCC

Basic information

species Zea mays
transcript GRMZM2G179737_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179737_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g03380.1 (Oryza sativa), 3'ss of exon 8
gtgagttgctgctgtgcttgtgctccgttccattcatttcattaccttatcagttcttattctgaaaaaaaaacgtgggcttgcattgcatccttgtgttgtattctcacacgcaccctgggtctacttaattactgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGCATCGATACTCCCTCGAGGTTTGAAGCTCCCCAGGAGTCTTGATCTCTCC
                                  |     ||||| |  |   | |||   ||| ||||     ||     |  ||   ||   |||      |   ||   |     |      | |||  || |   ||||||| |||||||| || |||||| |||||||||||||||  || |||||||| || ||||| || || | ||| || ||||||| ||| || | | | |   
---------------------------------actgcgaattacatctttgctacttcacctgtaaaa----tgtttatctctatca-atatctgt------tatccaagagttattttctcacagttatgtattatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGAATTGATACCCCATCAAAGTTCGACGCTCCCCCGGAATCATAAGCCCATT

upper sequence: GRMZM2G179737_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os12g03060.2 (Oryza sativa), 3'ss of exon 8
gtgagttgctgctgtgcttgtgctccgttccattcatttcattaccttatcagttcttattctgaaaaaaaaacgtgggcttgcattgcatccttgtgttgtattctcacacgcaccctgggtctacttaattactgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGCATCGATACTCCCTCGAGGTTTGAAGCTCCCCAGGAGTCTTGATCTCTCC
                                         ||  ||| ||  || ||    | |    ||||  |    ||  ||  ||   || |||| |  |   |       |          |   |||     ||||||| |||||||| || |||||| |||||||||||||||  || |||||||| || ||||| || || | ||| || ||||||| ||| || | | | |   
----------------------------------------gttgacttctc--ttattgactttactgcaaaatttta-tttctatatcactatt-tgttatcctagaattattttctcacaatagttcgtttatgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGAATTGATACCCCATCAAAGTTCGATGCTCCCCCGGAATCGTAAGCCCATT
















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|149110591|gb|EE190498.2|EE190498
EST:     GCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTT                         GGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
genomic: GCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTTgtgagttgct ... ctgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
EST: gi|101390191|gb|EB817028.1|EB817028
EST:     GCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTT                         GGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
genomic: GCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTTgtgagttgct ... ctgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
EST: gi|60353776|gb|DN220749.1|DN220749
EST:     GCGATGGCGAGTGCCTCGTCAAATCGAGTCTCCTCGAAGGAACTTTCGTT                         GGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
genomic: GCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTTgtgagttgct ... ctgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
EST: gi|83279335|gb|DV943343.1|DV943343
EST:     GCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTT                         GGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
genomic: GCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTTgtgagttgct ... ctgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
EST: gi|13178640|gb|BG349898.1|BG349898
EST:     GCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTT                         GGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
genomic: GCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTTgtgagttgct ... ctgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
EST: gi|78087095|gb|DV515488.1|DV515488
EST:     GCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTT                         GGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
genomic: GCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTTgtgagttgct ... ctgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
EST: gi|60398214|gb|DN231030.1|DN231030
EST:     GCGATGGCGAGTGCCTCGTCAAATCGAGTCTCCTCGAAGGAACTTTCGTT                         GGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
genomic: GCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTTgtgagttgct ... ctgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
EST: gi|4609573|gb|AI600412.1|AI600412
EST:     GCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTT                         GGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
genomic: GCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTTgtgagttgct ... ctgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
EST: gi|78087096|gb|DV515489.1|DV515489
EST:     GCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTT                         GGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
genomic: GCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTTgtgagttgct ... ctgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
EST: gi|91048207|gb|EB158625.1|EB158625
EST:     GCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTT                         GGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
genomic: GCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTTgtgagttgct ... ctgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
EST: gi|60398588|gb|DN231404.1|DN231404
EST:     GCGATGGCGAGTGCCTCGTCAAATCGAGTCTCCTCGAAGGAACTTTCGTT                         GGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC
genomic: GCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTTgtgagttgct ... ctgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGC

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: 30 (upstream exon), 49 (downstream exon)
Score: 8

TCTCGCGGAGAAGAAGACTAACGGCACGAAAGCTGTCCAGGGCGAAAAATGCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTTgtgagttgct ... ctgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGCATCGATACTCCCTCGAGGTTTGAAGCTCCCCAGGAGTCTTGATCTCTCC


Block sizes: 28 (upstream exon), 45 (downstream exon)
Score: 13

TCTCGCGGAGAAGAAGACTAACGGCACGAAAGCTGTCCAGGGCGAAAAATGCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTTgtgagttgct ... ctgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGCATCGATACTCCCTCGAGGTTTGAAGCTCCCCAGGAGTCTTGATCTCTCC


Block sizes: 46 (upstream exon), 39 (downstream exon)
Score: 5

TCTCGCGGAGAAGAAGACTAACGGCACGAAAGCTGTCCAGGGCGAAAAATGCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTTgtgagttgct ... ctgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGCATCGATACTCCCTCGAGGTTTGAAGCTCCCCAGGAGTCTTGATCTCTCC


Block sizes: 28 (upstream exon), 30 (downstream exon)
Score: 6

TCTCGCGGAGAAGAAGACTAACGGCACGAAAGCTGTCCAGGGCGAAAAATGCGATGGCGAGTGCCTCGTCAAGTCGAGTCTCCTCGAAGGAACTTTCGTTgtgagttgct ... ctgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGCATCGATACTCCCTCGAGGTTTGAAGCTCCCCAGGAGTCTTGATCTCTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccttgtgttgtattctcacacgcaccctgggtctacttaattactgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGCATCGATACTCCCTCGAGGTTTGAAGCTCCCCAGGAGTCTTGATCTCTCC
                                   tacttaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgctgctgtgcttgtgctccgttccattcatttcattaccttatcagttcttattctgaaaaaaaaacgtgggcttgcattgcatccttgtgttgtattctcacacgcaccctgggtctacttaattactgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGCATCGATACTCCCTCGAGGTTTGAAGCTCCCCAGGAGTCTTGATCTCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC