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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccactaagcaataagattagttctgcttaatggctgcattgctctaatttattgcttctcatcttttcatcctttgaaaatatgcag

Basic information

species Zea mays
transcript GRMZM2G130034_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130034_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g40550.1 (Oryza sativa), 5'ss of exon 5
GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccacta--------agcaataagattagttctgcttaatggctgcattgctctaatttattgcttctcatcttttcatcctttgaaaatatgcag
||||| ||||| |||||||||||||||||||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||  | |   |        | |   ||| |||| |  |  |||| |   ||    | |  ||| ||| || | |||||||||    | |||||| |||||
GTCTGGTTTCCAGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCGGAGGAGCCTACAAGATTTGGAATTAGCTGCTTGGGAAGgttgagcctcactcgcactaacttgaagcttagcttggactaattgtgccacaattatgttttgttggttattatcttttcacttctggaaaatgtgcag
















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|148941174|gb|EC886056.2|EC886056
EST:     ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG                         CCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
genomic: ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
EST: gi|71775247|gb|DR973125.1|DR973125
EST:     ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG                         CCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
genomic: ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
EST: gi|78086441|gb|DV514834.1|DV514834
EST:     ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG                         CCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
genomic: ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
EST: gi|148969605|gb|EE020450.2|EE020450
EST:     ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG                         CCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
genomic: ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
EST: gi|213178277|gb|FM185022.1|FM185022
EST:     ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG                         CCGCTTAATGGCAGGGATTGAAGAACTTG
genomic: ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTG
EST: gi|31359313|gb|CD443670.1|CD443670
EST:     ATGTTTACATCAGAGGAGGCGACACGATTTGGAATTAGCTGCTTGGGAAG                         CCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
genomic: ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
EST: gi|76015424|gb|DT942594.1|DT942594
EST:     ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG                         CCGCTTAATGGCAGGGATTGAAGAACTTGCTNCA-TCCCTCCGAAAAGTAG
genomic: ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTGCT-CAATCCCTCCGAAAAGTAG
EST: gi|50323473|gb|CO518599.1|CO518599
EST:     ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG                         CCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
genomic: ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
EST: gi|50324880|gb|CO520006.1|CO520006
EST:     ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG                         CCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
genomic: ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
EST: gi|91874398|gb|EB404355.1|EB404355
EST:     ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG                         CCGCTTAATGGCAGGGATT
genomic: ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATT
EST: gi|31361617|gb|CD445974.1|CD445974
EST:     ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG                         CCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
genomic: ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
EST: gi|148983478|gb|EE029496.2|EE029496
EST:     ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG                         CCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
genomic: ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
EST: gi|149103753|gb|EE289159.2|EE289159
EST:     ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG                         CCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
genomic: ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
EST: gi|71427278|gb|DR808328.1|DR808328
EST:     ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG                         CCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
genomic: ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
EST: gi|148940595|gb|EC885401.2|EC885401
EST:     ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG                         CCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
genomic: ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
EST: gi|78107618|gb|DV526036.1|DV526036
EST:     ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG                         CCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
genomic: ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT
EST: gi|148944452|gb|EC889567.2|EC889567
EST:     ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG                         CCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGACAAGTAGT
genomic: ATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGT

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), 46 (downstream exon)
Score: 117

GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGTTGACAATCAGAATGTGTCATTTTTGGATGCTGCAGAATCTGCTGGCTAT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 130

GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGTTGACAATCAGAATGTGTCATTTTTGGATGCTGCAGAATCTGCTGGCTAT


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 126

GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGTTGACAATCAGAATGTGTCATTTTTGGATGCTGCAGAATCTGCTGGCTAT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 93

GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccact ... aaatatgcagCCGCTTAATGGCAGGGATTGAAGAACTTGCTCAATCCCTCCGAAAAGTAGTTGACAATCAGAATGTGTCATTTTTGGATGCTGCAGAATCTGCTGGCTAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAGgtaaaccactaagcaataagattagttctgcttaatggctgcattgctctaatttattgcttctcatcttttcatcctttgaaaatatgcag

- - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT