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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAACTTCGGGTCGGAGGTCCGCTCTGGCAACCTGAAGAACCTCGGCCTCATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAAgtaagtgccctccatccttctttcgtcgccatgagaagactaatgttggcaactgttctcgtattcatcgtttccctcggtttcctggaccactgtgctttgtttaccag

Basic information

species Zea mays
transcript GRMZM2G098714_T01
intron # 2
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|26455797|gb|CA827380.1|CA827380
EST:     ACGTCGTC-AAGGCAAAGATGACAA                         AGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
genomic: ACGTCGTCAAAGGCAAAGATGACAAgtaagtgccc ... tgtttaccagAGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
EST: gi|211341515|gb|FL063181.1|FL063181
EST:     ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAA                         AGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCG
genomic: ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAAgtaagtgccc ... tgtttaccagAGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCG
EST: gi|29945007|gb|CB815421.1|CB815421
EST:     ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAA                         AGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
genomic: ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAAgtaagtgccc ... tgtttaccagAGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
EST: gi|211339122|gb|FL063170.1|FL063170
EST:     ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAA                         AGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
genomic: ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAAgtaagtgccc ... tgtttaccagAGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
EST: gi|211343901|gb|FL063190.1|FL063190
EST:     ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAA                         AGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
genomic: ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAAgtaagtgccc ... tgtttaccagAGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
EST: gi|211343898|gb|FL063187.1|FL063187
EST:     TCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGANCAA                         AGTCTTGGTTGTCATCAAATGCNGAGCTTGTGTGCCAAGCGCTTGACGCC
genomic: TCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGA-CAAgtaagtgccc ... tgtttaccagAGTCTTGGTTGTCATCAAATGC-GAGCTTGTGTGCCAAGCGCTTGACGCC
EST: gi|5555566|gb|AI881517.1|AI881517
EST:     ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAA                         AGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
genomic: ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAAgtaagtgccc ... tgtttaccagAGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
EST: gi|211343899|gb|FL063188.1|FL063188
EST:     TCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGNACAA                         AGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCG
genomic: TCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATG-ACAAgtaagtgccc ... tgtttaccagAGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCG
EST: gi|211343902|gb|FL063191.1|FL063191
EST:     ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAA                         AGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
genomic: ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAAgtaagtgccc ... tgtttaccagAGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
EST: gi|211343905|gb|FL063194.1|FL063194
EST:     ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAA                         AGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
genomic: ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAAgtaagtgccc ... tgtttaccagAGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
EST: gi|29945326|gb|CB815583.1|CB815583
EST:     ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAA                         AGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
genomic: ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAAgtaagtgccc ... tgtttaccagAGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
EST: gi|71438959|gb|DR820009.1|DR820009
EST:     ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAA                         AGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
genomic: ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAAgtaagtgccc ... tgtttaccagAGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
EST: gi|5268729|gb|AI770693.1|AI770693
EST:     ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAA                         AGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
genomic: ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAAgtaagtgccc ... tgtttaccagAGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
EST: gi|211341513|gb|FL063179.1|FL063179
EST:     ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAA                         AGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA
genomic: ATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAAgtaagtgccc ... tgtttaccagAGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGA

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: 48 (upstream exon), 49 (downstream exon)
Score: 88

CCAACTTCGGGTCGGAGGTCCGCTCTGGCAACCTGAAGAACCTCGGCCTCATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAAgtaagtgccc ... tgtttaccagAGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGAGATCAACGGCGAGGCCAAAAAAGAGGAGCCTCCAATTGTGCTGAAGCCT


Block sizes: 27 (upstream exon), 25 (downstream exon)
Score: 3

CCAACTTCGGGTCGGAGGTCCGCTCTGGCAACCTGAAGAACCTCGGCCTCATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAAgtaagtgccc ... tgtttaccagAGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGAGATCAACGGCGAGGCCAAAAAAGAGGAGCCTCCAATTGTGCTGAAGCCT


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 6

CCAACTTCGGGTCGGAGGTCCGCTCTGGCAACCTGAAGAACCTCGGCCTCATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAAgtaagtgccc ... tgtttaccagAGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGAGATCAACGGCGAGGCCAAAAAAGAGGAGCCTCCAATTGTGCTGAAGCCT


Block sizes: 26 (upstream exon), 30 (downstream exon)
Score: 2

CCAACTTCGGGTCGGAGGTCCGCTCTGGCAACCTGAAGAACCTCGGCCTCATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAAgtaagtgccc ... tgtttaccagAGTCTTGGTTGTCATCAAATGCGAGCTTGTGTGCCAAGCGCTTGACGCCGAGATCAACGGCGAGGCCAAAAAAGAGGAGCCTCCAATTGTGCTGAAGCCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAACTTCGGGTCGGAGGTCCGCTCTGGCAACCTGAAGAACCTCGGCCTCATCCGCATCATCGACTACACTTGCAACGTCGTCAAAGGCAAAGATGACAAgtaagtgccctccatccttctttcgtcgccatgagaagactaatgttggcaactgttctcgtattcatcgtttccctcggtttcctggaccactgtgctttgtttaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG