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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtcataaacatcgaaatatacagttccagattgacaaagaaataaaagctacagcggttgcccaaaatgtctgataatcttaattgcatatgcttttctccctctctagGGCTAACGGAAACCTGTGCTGGGTCCTTTGTTTCCCTGCCGAACAACATGTCCATGCTGGGAACTGTCGGCCCTCCAGTCCCGTATGTCGAAGTACGCCT

Basic information

species Zea mays
transcript GRMZM2G152127_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 14
gtattgtcataaacatcgaaatatacagttccagattgacaaagaaataaaagctacagcggttgcccaaaatgtctgataatcttaattgcatatgcttttctccctc--tctagGGCTAACGGAAACCTGTGCTGGGTCCTTTGTTTCCCTGCCGAACAACATGTCCATGCTGGGAACTGTCGGCCCTCCAGTCCCGTATGTCGAAGTACGCCT
||||  |  | || | |     |   |  |    ||| | ||| |||| | | ||  ||   || || || |   ||  |    |||||| | | |||||   | | ||  |  ||| || || || ||||||||||||||||| |||||||| || ||||||||||| |||||||||||||| |||||||||||||| ||||||||||||| |||
gtatgcttgtgaa-accacgtcaatgatcttataattaaaaaaaaaatgatatctcgag---ttcccaaagacacctagtg--tttaatttcgtttgcttgctttcttcattgcagGTCTTACTGAGACCTGTGCTGGGTCCTTCGTTTCCCTTCCAAACAACATGTCGATGCTGGGAACTGTAGGCCCTCCAGTCCCCTATGTCGAAGTACACCT
















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|71768490|gb|DR966427.1|DR966427
EST:     TGAGGAGTATCTGCGTGTGGTAACATGCTCCCATGTCCTTCAAGGATACG                         GGCTAACGGAAACCTGTGCTGGGTCCTTTGTTTCCCTGCCGAACAACATGT
genomic: TGAGGAGTATCTGCGTGTGGTAACATGCTCCCATGTCCTTCAAGGATACGgtattgtcat ... ccctctctagGGCTAACGGAAACCTGTGCTGGGTCCTTTGTTTCCCTGCCGAACAACATGT
EST: gi|211036305|gb|FL124438.1|FL124438
EST:     TGAGGAGTATCTGCGTGTGGTAACATGCTCCCATGTCCTTCAAGGATACG                         GGCTCACGGAAACCTGCGCTGGGTCCTTTGTTTCCCTGCCGAACAACATGT
genomic: TGAGGAGTATCTGCGTGTGGTAACATGCTCCCATGTCCTTCAAGGATACGgtattgtcat ... ccctctctagGGCTAACGGAAACCTGTGCTGGGTCCTTTGTTTCCCTGCCGAACAACATGT
EST: gi|76011816|gb|DT938986.1|DT938986
EST:     TGAGGAGTATCTGCGTGTGGTAACATGCTCCCATGTCCTTCAAGGATACG                         GGCTAACGGAAACCTGTGCTGGGTCCTTTGTTTCCCTGC
genomic: TGAGGAGTATCTGCGTGTGGTAACATGCTCCCATGTCCTTCAAGGATACGgtattgtcat ... ccctctctagGGCTAACGGAAACCTGTGCTGGGTCCTTTGTTTCCCTGC
EST: gi|211444856|gb|FL116921.1|FL116921
EST:     TGAGGAGTATCTGCGTGTGGTAACATGCTCCCATCTCCTTCAAGGATACG                         GGCTAACGGAAACCTGTGCTGGGTCCTTTGTTTCCCTGCCGAACAACATGT
genomic: TGAGGAGTATCTGCGTGTGGTAACATGCTCCCATGTCCTTCAAGGATACGgtattgtcat ... ccctctctagGGCTAACGGAAACCTGTGCTGGGTCCTTTGTTTCCCTGCCGAACAACATGT

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), 47 (downstream exon)
Score: 115

GGAAGGGTTCGCCTGATTCTATCTGGCGCAGCTCCCCTATCTAGACATGTTGAGGAGTATCTGCGTGTGGTAACATGCTCCCATGTCCTTCAAGGATACGgtattgtcat ... ccctctctagGGCTAACGGAAACCTGTGCTGGGTCCTTTGTTTCCCTGCCGAACAACATGTCCATGCTGGGAACTGTCGGCCCTCCAGTCCCGTATGTCGAAGTACGCCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 80

GGAAGGGTTCGCCTGATTCTATCTGGCGCAGCTCCCCTATCTAGACATGTTGAGGAGTATCTGCGTGTGGTAACATGCTCCCATGTCCTTCAAGGATACGgtattgtcat ... ccctctctagGGCTAACGGAAACCTGTGCTGGGTCCTTTGTTTCCCTGCCGAACAACATGTCCATGCTGGGAACTGTCGGCCCTCCAGTCCCGTATGTCGAAGTACGCCT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 33

GGAAGGGTTCGCCTGATTCTATCTGGCGCAGCTCCCCTATCTAGACATGTTGAGGAGTATCTGCGTGTGGTAACATGCTCCCATGTCCTTCAAGGATACGgtattgtcat ... ccctctctagGGCTAACGGAAACCTGTGCTGGGTCCTTTGTTTCCCTGCCGAACAACATGTCCATGCTGGGAACTGTCGGCCCTCCAGTCCCGTATGTCGAAGTACGCCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 169

GGAAGGGTTCGCCTGATTCTATCTGGCGCAGCTCCCCTATCTAGACATGTTGAGGAGTATCTGCGTGTGGTAACATGCTCCCATGTCCTTCAAGGATACGgtattgtcat ... ccctctctagGGCTAACGGAAACCTGTGCTGGGTCCTTTGTTTCCCTGCCGAACAACATGTCCATGCTGGGAACTGTCGGCCCTCCAGTCCCGTATGTCGAAGTACGCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggttgcccaaaatgtctgataatcttaattgcatatgcttttctccctctctagGGCTAACGGAAACCTGTGCTGGGTCCTTTGTTTCCCTGCCGAACAACATGTCCATGCTGGGAACTGTCGGCCCTCCAGTCCCGTATGTCGAAGTACGCCT
                       tcttaat  putative branch site (score: 169)
                                catatgcttttctccc  putative PPT
                 tgataatcttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtcataaacatcgaaatatacagttccagattgacaaagaaataaaagctacagcggttgcccaaaatgtctgataatcttaattgcatatgcttttctccctctctagGGCTAACGGAAACCTGTGCTGGGTCCTTTGTTTCCCTGCCGAACAACATGTCCATGCTGGGAACTGTCGGCCCTCCAGTCCCGTATGTCGAAGTACGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG