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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttgtatgttcctgcttacattttgttttaagcatattttttaggataaagaaattgcaattctcgttttttattagttaccttacctatactcacagGCAAAGGCTTTGGCTGAGAAGAATGAACGCGACATGCAGCAACAAAGAGAGCAGGCTGAAAGACAT

Basic information

species Zea mays
transcript GRMZM5G839757_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G839757_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g36180.1 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------------------------------------tgcttgtatgttcctgcttacattttgttttaagcatattttttaggataaagaaattgcaattctcgtt----ttttattagttaccttacctatactcacagGCAAAGGCTTTGGCTGAGAAGAATGAACGCGACATGCAGCAACAAAGAGAGCAGGCTGAAAGACAT
                                                                                        | | || || ||     |||||| || ||||   |   || || ||  |   ||      ||||   |||    |   |||  ||| |||  |  |     |||||||| ||  ||||||| ||||||||||| || ||||||   ||||| ||||||||||||||||||
gtaatgttgctaatgattttagtaactaaaatagatatttgtttgtaacttgctgttataatttggtactgtggacattcattttatgttcctgaattttatcatttacatgttatttttttctatttattaagagttgtgatgcatgaatttgagttgcagtgccatttattaacttcaccgtgtatgcagGCAAAAGCCCTGGCTGAAAAGAATGAACGGGATATGCAGGTTCAAAGGGAGCAGGCTGAAAGACAT
















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|211076955|gb|FL060758.1|FL060758
EST:     AAAGAAGACGCGCTAGGATGGAACGGCATCAAAGAACTCGTGAACGAGCG                         GCAAAGGCTTTGGCTGAGAAGAATGAACGCGACATGCAGCAAACAA-GAGA
genomic: AAAGAAGACGCGCTAGGATGGAACGGCATCAAAGAACTCGTGAACGAGCGgtaatgtgct ... atactcacagGCAAAGGCTTTGGCTGAGAAGAATGAACGCGACATGCAGCAA-CAAAGAGA
EST: gi|33092165|gb|CF052159.1|CF052159
EST:     AAAGAAGACGCGCTAGGATGGAACGGCATCAAAGAACTCGTGAACGAGCG                         GCAAAGGCTTTGGCTGAGAAGAATGAACGCGACATGCAGCAACAAAGAGAG
genomic: AAAGAAGACGCGCTAGGATGGAACGGCATCAAAGAACTCGTGAACGAGCGgtaatgtgct ... atactcacagGCAAAGGCTTTGGCTGAGAAGAATGAACGCGACATGCAGCAACAAAGAGAG
EST: gi|211076956|gb|FL060759.1|FL060759
EST:     AAAGAAGACGCGCTAGGATGGAACGGCATCAAAGAACTCGTGAACGAGCG                         GCAAAGGCTTTGGCTGAGAAGAATGAACGCGACATGCAGCAACAAAGAGAG
genomic: AAAGAAGACGCGCTAGGATGGAACGGCATCAAAGAACTCGTGAACGAGCGgtaatgtgct ... atactcacagGCAAAGGCTTTGGCTGAGAAGAATGAACGCGACATGCAGCAACAAAGAGAG
EST: gi|211076954|gb|FL060757.1|FL060757
EST:     AAAGAAGACGCGCTAGGATGGAACGGCATCAAAGAACTCGTGAACGAGCG                         GCAAAGGCTTTGGCTGAGAAGAATGAACGCGACATGCAGCAACAA-GAGAG
genomic: AAAGAAGACGCGCTAGGATGGAACGGCATCAAAGAACTCGTGAACGAGCGgtaatgtgct ... atactcacagGCAAAGGCTTTGGCTGAGAAGAATGAACGCGACATGCAGCAACAAAGAGAG

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), 49 (downstream exon)
Score: 237

CTCCTACATCAGAAGAATTTCAAGAAGTAGATGGGGAGAGCGAAGAAAGAAGACGCGCTAGGATGGAACGGCATCAAAGAACTCGTGAACGAGCGgtaatgtgct ... atactcacagGCAAAGGCTTTGGCTGAGAAGAATGAACGCGACATGCAGCAACAAAGAGAGCAGGCTGAAAGACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 264

CTCCTACATCAGAAGAATTTCAAGAAGTAGATGGGGAGAGCGAAGAAAGAAGACGCGCTAGGATGGAACGGCATCAAAGAACTCGTGAACGAGCGgtaatgtgct ... atactcacagGCAAAGGCTTTGGCTGAGAAGAATGAACGCGACATGCAGCAACAAAGAGAGCAGGCTGAAAGACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 380

CTCCTACATCAGAAGAATTTCAAGAAGTAGATGGGGAGAGCGAAGAAAGAAGACGCGCTAGGATGGAACGGCATCAAAGAACTCGTGAACGAGCGgtaatgtgct ... atactcacagGCAAAGGCTTTGGCTGAGAAGAATGAACGCGACATGCAGCAACAAAGAGAGCAGGCTGAAAGACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 206

CTCCTACATCAGAAGAATTTCAAGAAGTAGATGGGGAGAGCGAAGAAAGAAGACGCGCTAGGATGGAACGGCATCAAAGAACTCGTGAACGAGCGgtaatgtgct ... atactcacagGCAAAGGCTTTGGCTGAGAAGAATGAACGCGACATGCAGCAACAAAGAGAGCAGGCTGAAAGACAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggataaagaaattgcaattctcgttttttattagttaccttacctatactcacagGCAAAGGCTTTGGCTGAGAAGAATGAACGCGACATGCAGCAACAAAGAGAGCAGGCTGAAAGACAT
                                    accttac  putative branch site (score: 206)
                       ttttttattagtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcttgtatgttcctgcttacattttgttttaagcatattttttaggataaagaaattgcaattctcgttttttattagttaccttacctatactcacagGCAAAGGCTTTGGCTGAGAAGAATGAACGCGACATGCAGCAACAAAGAGAGCAGGCTGAAAGACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
tgcttgt
- - - - - - cctgctt
- - - - - - - - - - - ttttgtt
- - - - - - - - - - - - - - - - - - - - - - - - -aaagaaa