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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtctgccagcattttatagaatatctatacggtttatcaccggtgatgatttttcgttcttggcttaacttttttgcttttcaaaatattgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAG

Basic information

species Zea mays
transcript GRMZM2G118316_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118316_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os12g07060.1 (Oryza sativa), 3'ss of exon 11
ggtctgccagcattttatagaatatctatacggtttatcaccg--gtgatgatttttcgttcttg--gcttaacttttttgcttttcaaaatattgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAG
    ||  | | |   |    ||||  |    ||||||| |     || |||| |||  |||| |  || | |||| |||  | ||| | | |||   ||| ||| |||||||||||| ||||| || |||||| |||||||||||||||  ||||||||||| || |||   || |
---atgtgatcctaaaactttatattcaatgagtttatctctcttatgttgatgtttgattctaggagcctgacttgttttgtattctata-atttgcttgaagAATTTTTGCAAGACATGCAAGGGTGAACAGCTAGTGAAGGGGAAAAAATCAGTCAAGCTCGACATAATGGCTG
















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|76922542|gb|DV169052.1|DV169052
EST:     CTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAG                         AGTTTTTGCAAGACTTGCA
genomic: CTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAGgtgcagtttt ... tgatttgtagAGTTTTTGCAAGACTTGCA
EST: gi|149101261|gb|EE187373.2|EE187373
EST:     GGGAAAATTGTCAAG                         AGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
genomic: GGGAAAATTGTCAAGgtgcagtttt ... tgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
EST: gi|78088193|gb|DV516586.1|DV516586
EST:     CTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAG                         AGTTTTTGCAAGACTTGCCAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
genomic: CTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAGgtgcagtttt ... tgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
EST: gi|71757145|gb|DR955082.1|DR955082
EST:     CTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAG                         AGTTTTTGCCAGACTTGCAAAGG
genomic: CTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAGgtgcagtttt ... tgatttgtagAGTTTTTGCAAGACTTGCAAAGG
EST: gi|86469547|gb|DY235917.1|DY235917
EST:     AAAATTGTCAAG                         AGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
genomic: AAAATTGTCAAGgtgcagtttt ... tgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
EST: gi|60398827|gb|DN231643.1|DN231643
EST:     CTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAG                         AGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
genomic: CTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAGgtgcagtttt ... tgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
EST: gi|91049687|gb|EB160105.1|EB160105
EST:     CTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAG                         AGTTTTTGCAAGACTTGCAAAGGAGACCAGGTAGTGAAAGGGAAAACGTCA
genomic: CTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAGgtgcagtttt ... tgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
EST: gi|211267317|gb|FL091731.1|FL091731
EST:     CTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAG                         AGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
genomic: CTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAGgtgcagtttt ... tgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
EST: gi|34391167|gb|CF384395.1|CF384395
EST:     CTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAG                         AGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
genomic: CTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAGgtgcagtttt ... tgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
EST: gi|71427930|gb|DR808980.1|DR808980
EST:     CTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAG                         AGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
genomic: CTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAGgtgcagtttt ... tgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
EST: gi|37397730|gb|CF636173.1|CF636173
EST:     AAAATTGTCAAG                         AGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
genomic: AAAATTGTCAAGgtgcagtttt ... tgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
EST: gi|32847340|gb|CD987021.1|CD987021
EST:     ACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAG                         AGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
genomic: ACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAGgtgcagtttt ... tgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
EST: gi|67040336|gb|CO466591.1|CO466591
EST:     CTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAG                         AGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
genomic: CTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAGgtgcagtttt ... tgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
EST: gi|40337178|gb|CK371248.1|CK371248
EST:     GGGAAAATTGTCAAG                         AGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA
genomic: GGGAAAATTGTCAAGgtgcagtttt ... tgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCA

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), 45 (downstream exon)
Score: 157

ATATACATGCAGAAGGGTATATTTACTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAGgtgcagtttt ... tgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 179

ATATACATGCAGAAGGGTATATTTACTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAGgtgcagtttt ... tgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 208

ATATACATGCAGAAGGGTATATTTACTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAGgtgcagtttt ... tgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 141

ATATACATGCAGAAGGGTATATTTACTGTCGAATGTACTTGCTCCCTGTGCAATGGGAGCGGGAAAATTGTCAAGgtgcagtttt ... tgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgatttttcgttcttggcttaacttttttgcttttcaaaatattgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAG
                                          tattgat  putative branch site (score: 141)
                         ttttttgcttttcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtctgccagcattttatagaatatctatacggtttatcaccggtgatgatttttcgttcttggcttaacttttttgcttttcaaaatattgatttgtagAGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - -gccagca
- - - - - - - - - - - - - - - - - - - - - - tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gttcttg