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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTCTTGTTTATAGTTTTTGTTGTCTACTCAATGACCTATTATGCCGTGGAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttctataacgaaggactgtttgattgaaaccctgcaaagtcaacagtgtaactcatttatttagaatataacagtgttatgcacaccaagtaaat...

Basic information

species Zea mays
transcript GRMZM2G068557_T01
intron # 3
splice site 5'
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|148995962|gb|EE035209.2|EE035209
EST:     GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAG                         TGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
genomic: GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttcta ... tttcttgcagTGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
EST: gi|149097278|gb|EE183101.2|EE183101
EST:     GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAG                         TGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
genomic: GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttcta ... tttcttgcagTGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
EST: gi|149113069|gb|EE191505.2|EE191505
EST:     GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAG                         TGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
genomic: GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttcta ... tttcttgcagTGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
EST: gi|149080339|gb|EE169357.2|EE169357
EST:     GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAG                         TGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
genomic: GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttcta ... tttcttgcagTGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
EST: gi|50329460|gb|CO524586.1|CO524586
EST:     GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAG                         TGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
genomic: GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttcta ... tttcttgcagTGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
EST: gi|211358194|gb|FL287114.1|FL287114
EST:     GACGCTGTGAGCCTTGTCTCGAAATTTGACATCCCATCAATGACTGAGAG                         TGAATTGATACTGGATGTCATTGGCCTCCGT
genomic: GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttcta ... tttcttgcagTGAATTGATACTGGATGTCATTGGCCTCCGT
EST: gi|149014577|gb|EE044221.2|EE044221
EST:     GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAG                         TGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
genomic: GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttcta ... tttcttgcagTGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
EST: gi|148930967|gb|EC873482.2|EC873482
EST:     GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAG                         TGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGGTGTT
genomic: GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttcta ... tttcttgcagTGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
EST: gi|149088601|gb|EE177718.2|EE177718
EST:     GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAG                         TGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
genomic: GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttcta ... tttcttgcagTGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
EST: gi|148964973|gb|EC906060.2|EC906060
EST:     GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAG                         TGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
genomic: GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttcta ... tttcttgcagTGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
EST: gi|211234051|gb|FL287109.1|FL287109
EST:     GACGCTGTGAGCCTTGTCTCGAAATTTGACATCCCATCAATGACTGAGAG                         TGAATTGATACTGGATGTCAT
genomic: GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttcta ... tttcttgcagTGAATTGATACTGGATGTCAT
EST: gi|149086545|gb|EE176089.2|EE176089
EST:     GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAG                         TGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
genomic: GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttcta ... tttcttgcagTGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
EST: gi|149088071|gb|EE177251.2|EE177251
EST:     GAAGCTGTGAGCCTTGTCTTGAAATTTGATATCCCATCAATGACTGAGAG                         TGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
genomic: GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttcta ... tttcttgcagTGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
EST: gi|148949541|gb|EC895005.2|EC895005
EST:     GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAG                         TGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
genomic: GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttcta ... tttcttgcagTGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
EST: gi|148955766|gb|EC901465.2|EC901465
EST:     GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAG                         TGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT
genomic: GAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttcta ... tttcttgcagTGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTT

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: 26 (upstream exon), 45 (downstream exon)
Score: 9

TTGTCTTGTTTATAGTTTTTGTTGTCTACTCAATGACCTATTATGCCGTGGAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttcta ... tttcttgcagTGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTTCTGCATGCTCTTCCTCTTCCTGCCAGTCGCCCGAGGCTCGGTTCTCTTA


Block sizes: 38 (upstream exon), 45 (downstream exon)
Score: 23

TTGTCTTGTTTATAGTTTTTGTTGTCTACTCAATGACCTATTATGCCGTGGAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttcta ... tttcttgcagTGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTTCTGCATGCTCTTCCTCTTCCTGCCAGTCGCCCGAGGCTCGGTTCTCTTA


Block sizes: 31 (upstream exon), 19 (downstream exon)
Score: 1

TTGTCTTGTTTATAGTTTTTGTTGTCTACTCAATGACCTATTATGCCGTGGAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttcta ... tttcttgcagTGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTTCTGCATGCTCTTCCTCTTCCTGCCAGTCGCCCGAGGCTCGGTTCTCTTA


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 37

TTGTCTTGTTTATAGTTTTTGTTGTCTACTCAATGACCTATTATGCCGTGGAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttcta ... tttcttgcagTGAATTGATACTGGATGTCATTGGCCTCCGTTTAGGGGCGGTTGGGTTGTTCTGCATGCTCTTCCTCTTCCTGCCAGTCGCCCGAGGCTCGGTTCTCTTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTCTTGTTTATAGTTTTTGTTGTCTACTCAATGACCTATTATGCCGTGGAAGCTGTGAGCCTTGTCTCGAAATTTGATATCCCATCAATGACTGAGAGgtatgttctataacgaaggactgtttgattgaaaccctgcaaagtcaacagtgtaactcatttatttagaatataacagtgttatgcacaccaagtaaat

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caagtaaa