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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggactgtcttgttcatatcggtgtgccatatcattatgcttgaggtggtggtatgtaccttccattagggaggcctcttgacaacttatgtctcagcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG

Basic information

species Zea mays
transcript GRMZM2G086489_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086489_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os04g55960.1 (Oryza sativa), 3'ss of exon 12
tggactgtcttgttcatatcggtgtgccatatcattatgcttgaggtggtggtatgtaccttccattagggaggcctc-ttgacaacttatgtctcagcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG
||     |  |||   | | |  || |  | | |  ||       |  ||  ||| |    ||     |  ||  ||   |       |||||| |  |||||||||||| ||||||||||||||||||||||||||||||||||| ||| ||||||| |||||||| ||||||||||||||||| ||||||||||||
tgtctgataatgtattttttgtggt-cattttgaggatatgacttgctgttctatttgttctcttgctgcaagatctgactccttgaatatgtccctacagGATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAG
















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|32929509|gb|CF034321.1|CF034321
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... gtctcagcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTC
EST: gi|32832265|gb|CD971943.1|CD971943
EST:     ATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTC
genomic: ATCATCTCCAAAgtaagtattt ... gtctcagcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTC
EST: gi|40334433|gb|CK368503.1|CK368503
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... gtctcagcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTC
EST: gi|31351811|gb|CD436168.1|CD436168
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTACTTTATGGGCCTTC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... gtctcagcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTC
EST: gi|32929744|gb|CF034556.1|CF034556
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... gtctcagcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTC
EST: gi|32929783|gb|CF034595.1|CF034595
EST:     ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... gtctcagcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTC
EST: gi|67033233|gb|CO461982.1|CO461982
EST:     ATTGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTC
genomic: ATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... gtctcagcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTC
EST: gi|32835719|gb|CD975397.1|CD975397
EST:     CACGATACTACTCAATTTCATCATCTCCAAA                         GATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTC
genomic: CACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... gtctcagcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTC
EST: gi|13316176|gb|BG410623.1|BG410623
EST:     CTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAACA                        
genomic: CTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCC-AA-Agtaagtattt ... gtctcagca
EST: gi|13316176|gb|BG410623.1|BG410623
EST:     CTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAACA                        
genomic: CTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCC-AA-Agtaagtattt ... gtctcagca

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: 589

TGGCCGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTTGCAGCAATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... gtctcagcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 749

TGGCCGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTTGCAGCAATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... gtctcagcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 965

TGGCCGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTTGCAGCAATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... gtctcagcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1120

TGGCCGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTTGCAGCAATAGCTCCTCGTCTGCAACCACGATACTACTCAATTTCATCATCTCCAAAgtaagtattt ... gtctcagcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggtggtatgtaccttccattagggaggcctcttgacaacttatgtctcagcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG
                               tcttgac  putative branch site (score: 1120)
                                      aacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggactgtcttgttcatatcggtgtgccatatcattatgcttgaggtggtggtatgtaccttccattagggaggcctcttgacaacttatgtctcagcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
tggactg
- - - - - - ttcatat
- - - - - - - - - - - - tgccata
- - - - - - - - - - - - - - - - - - -tgcttga
- - - - - - - - - - - - - - - - - - - - - - ggtggtg