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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATCGCTTTGCGTGAAGAGGCTAGTCTACACCAACGATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGTgtcagttctctttctctatctcgtttgtatgtatactagctacatgatattcctcttaattattagcagctttcagtaagcacatcattctcatgttcaa...

Basic information

species Zea mays
transcript GRMZM2G059191_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059191_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g01340.2 (Oryza sativa), 5'ss of exon 2
GTATCGCTTTGCGTGAAGAGGCTAGTCTACACCAACGATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGTgtcagttctctttctctatctcgtttgtatgtatactagctacatgatattcctcttaattattagcagctttcagtaagcacatcattctcatgttcaa
|||||||| |||||||||||||| || ||||||||||||||||| ||||| ||||||||||||||||| |||||||| ||| || |     |||       | |  | |  |||  || || ||  || |  | |   | ||||   |  |  | |                       
GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCTgtaagctaggagtct-------gatcatgta-atagcagttagattgtacttgtgt-gctaattaatggagtataatttag-------------------
















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|149073444|gb|EE161749.2|EE161749
EST:     TCAAAGGAGTCTGCTCAAACTTCCTGT                         GTGACTTGAAACCTGGGGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: TCAAAGGAGTCTGCTCAAACTTCCTGTgtcagttctc ... gtgcatgcagGTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|71297722|gb|DR784813.1|DR784813
EST:     CACCAACGATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGT                         GTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: CACCAACGATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGTgtcagttctc ... gtgcatgcagGTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|71763164|gb|DR961101.1|DR961101
EST:     CAAACTTCCTGT                         GTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: CAAACTTCCTGTgtcagttctc ... gtgcatgcagGTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|71313358|gb|DR793225.1|DR793225
EST:     GGGGAGATTTTCAAAGGAGTCTGCTCAAACTTCCTGT                         GTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: GGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGTgtcagttctc ... gtgcatgcagGTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|71436411|gb|DR817461.1|DR817461
EST:     CCAACGATCAGGGGGAGA-TGTCAAAGGAGTTTGCTCAAACTTCCTGT                         GTGACTTGAAACCTGGCGCCGAAGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: CCAACGATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGTgtcagttctc ... gtgcatgcagGTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|89248692|gb|DY620478.1|DY620478
EST:     GGAGTTTGCTCAAACTTCCTGT                         GTGAC-TGAAACCCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAG
genomic: GGAGTCTGCTCAAACTTCCTGTgtcagttctc ... gtgcatgcagGTGACTTGAAA-CCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAG
EST: gi|13178509|gb|BG349767.1|BG349767
EST:     CACCAACGATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGT                         GTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: CACCAACGATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGTgtcagttctc ... gtgcatgcagGTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|71326435|gb|DR799900.1|DR799900
EST:     TGTCAAAGGAGTCTGCTCAAACTTCCTGT                         GTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: TGTCAAAGGAGTCTGCTCAAACTTCCTGTgtcagttctc ... gtgcatgcagGTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|13178183|gb|BG349441.1|BG349441
EST:     CACCAACGATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGT                         GTGACTTGAAACCTGGCGCCGATGTGAAGATCAC
genomic: CACCAACGATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGTgtcagttctc ... gtgcatgcagGTGACTTGAAACCTGGCGCCGATGTGAAGATCAC
EST: gi|13125967|gb|BG316642.1|BG316642
EST:     GATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGT                         GTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: GATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGTgtcagttctc ... gtgcatgcagGTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|94479916|gb|EB708874.1|EB708874
EST:     CGATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGT                         GTGAC-TGAAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAG
genomic: CGATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGTgtcagttctc ... gtgcatgcagGTGACTTG-AAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAG
EST: gi|13315903|gb|BG410251.1|BG410251
EST:     CACCAACGATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGT                         GTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: CACCAACGATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGTgtcagttctc ... gtgcatgcagGTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|110219228|gb|EC901126.1|EC901126
EST:     AGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGT                         GTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: AGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGTgtcagttctc ... gtgcatgcagGTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGG

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: 46 (upstream exon), 36 (downstream exon)
Score: 4

GTATCGCTTTGCGTGAAGAGGCTAGTCTACACCAACGATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGTgtcagttctc ... gtgcatgcagGTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 138

GTATCGCTTTGCGTGAAGAGGCTAGTCTACACCAACGATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGTgtcagttctc ... gtgcatgcagGTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG


Block sizes: 27 (upstream exon), 39 (downstream exon)
Score: 3

GTATCGCTTTGCGTGAAGAGGCTAGTCTACACCAACGATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGTgtcagttctc ... gtgcatgcagGTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 108

GTATCGCTTTGCGTGAAGAGGCTAGTCTACACCAACGATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGTgtcagttctc ... gtgcatgcagGTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATCGCTTTGCGTGAAGAGGCTAGTCTACACCAACGATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGTgtcagttctctttctctatctcgtttgtatgtatactagctacatgatattcctcttaattattagcagctttcagtaagcacatcattctcatgttcaa

- - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG