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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGGTTTGACCAGCTCCCAGATTTGCATATGGAGACGCAGTGAACCAAGAAGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAGgtgtggattctgtttttattattagttaaggtagaagagctgaaccatacaaacaacacacttccaagcctataggagatcaataggaaggcagccggag...

Basic information

species Zea mays
transcript GRMZM2G087105_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087105_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os11g07970.1 (Oryza sativa), 5'ss of exon 5
TAGGTTTGACCAGCTCCCAGATTTGCATATGGAGACGCAGTGAACCAAGAAGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAGgtgtggattctgtttttattattagttaaggtagaagagctgaaccatacaaacaacacacttccaagcctataggagatcaataggaaggcagccggag
|||||||||| ||||||||| |||||||||||||||| ||||| || ||||| || ||||||||| |||||||||||||||| | ||| ||||| |||||||| |||   || ||| | | |     | |  |       ||   |  |||||  | |   |         |||    |   | |  |  | |       
TAGGTTTGACTAGCTCCCAGCTTTGCATATGGAGACGTAGTGAGCCGAGAAGTATTTTTCAATCTCGTGGAGCCTCATTCAACCGTGGCTTATGTATGAGgtgaggaacatgctttaagtttgtaaaatgacatgccttttgtttcgaacaaatgaaaagttagatgttacatatactactgaaattactgaattgctca
















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|78107838|gb|DV526256.1|DV526256
EST:     AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAG                         TTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
genomic: AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAGgtgtggattc ... cctggtgtagTTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
EST: gi|211348374|gb|FL045514.1|FL045514
EST:     AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAG                         TTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
genomic: AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAGgtgtggattc ... cctggtgtagTTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
EST: gi|76021370|gb|DT948540.1|DT948540
EST:     AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAG                         TTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
genomic: AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAGgtgtggattc ... cctggtgtagTTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
EST: gi|74238280|gb|DT646194.1|DT646194
EST:     AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAG                         TTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
genomic: AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAGgtgtggattc ... cctggtgtagTTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
EST: gi|50337804|gb|CO532930.1|CO532930
EST:     AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAG                         TTTTGCTGATCCGGAGGTTTGTA-TTGGTTGTGAGGATGGTCGAGCCTTTG
genomic: AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAGgtgtggattc ... cctggtgtagTTTTGCTGATCCGGAGGTT-GTAATTGGTTGTGAGGATGGTCGAGCCTTTG
EST: gi|211348372|gb|FL045512.1|FL045512
EST:     AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAG                         TTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
genomic: AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAGgtgtggattc ... cctggtgtagTTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
EST: gi|6021302|gb|AW066230.1|AW066230
EST:     AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAG                         CTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
genomic: AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAGgtgtggattc ... cctggtgtagTTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
EST: gi|76011998|gb|DT939168.1|DT939168
EST:     AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAG                         TTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
genomic: AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAGgtgtggattc ... cctggtgtagTTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
EST: gi|71441001|gb|DR822051.1|DR822051
EST:     AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAG                         TTTTGCTGATCCGGAGGGTGTAATTGGGTGTGAGGATGGTCGAGCCTTTGT
genomic: AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAGgtgtggattc ... cctggtgtagTTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
EST: gi|148986029|gb|EE029876.2|EE029876
EST:     AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAG                         TTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
genomic: AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAGgtgtggattc ... cctggtgtagTTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
EST: gi|148991227|gb|EE032692.2|EE032692
EST:     AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAG                         TTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
genomic: AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAGgtgtggattc ... cctggtgtagTTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
EST: gi|78085484|gb|DV513877.1|DV513877
EST:     AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAG                         TTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT
genomic: AGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAGgtgtggattc ... cctggtgtagTTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGT

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), 49 (downstream exon)
Score: 348

TAGGTTTGACCAGCTCCCAGATTTGCATATGGAGACGCAGTGAACCAAGAAGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAGgtgtggattc ... cctggtgtagTTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGTATATGATATGTACAGCAGGAGTTGCTCACGTATTTATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

TAGGTTTGACCAGCTCCCAGATTTGCATATGGAGACGCAGTGAACCAAGAAGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAGgtgtggattc ... cctggtgtagTTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGTATATGATATGTACAGCAGGAGTTGCTCACGTATTTATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 201

TAGGTTTGACCAGCTCCCAGATTTGCATATGGAGACGCAGTGAACCAAGAAGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAGgtgtggattc ... cctggtgtagTTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGTATATGATATGTACAGCAGGAGTTGCTCACGTATTTATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 236

TAGGTTTGACCAGCTCCCAGATTTGCATATGGAGACGCAGTGAACCAAGAAGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAGgtgtggattc ... cctggtgtagTTTTGCTGATCCGGAGGTTGTAATTGGTTGTGAGGATGGTCGAGCCTTTGTATATGATATGTACAGCAGGAGTTGCTCACGTATTTATCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGGTTTGACCAGCTCCCAGATTTGCATATGGAGACGCAGTGAACCAAGAAGCATATTTCAATCTGGTGGAGCCTCATTCAATCATGGGTTATGCATGAGgtgtggattctgtttttattattagttaaggtagaagagctgaaccatacaaacaacacacttccaagcctataggagatcaataggaaggcagccggag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaacaa