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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcactacataacctgcaaatctgaacattcagctttgatttttttttgtgtttcgttttatttatgcctgatcctttgctgccctcgtgtttttgcataccctacagAATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATATAGATCAAATGTCAATCGATGAAATCGAGCAGGTGGTTAATAGGGAATCA

Basic information

species Zea mays
transcript GRMZM2G162445_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162445_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os05g39850.1 (Oryza sativa), 3'ss of exon 14
gtcactacataacctgcaaatctgaacattcagctttgatttttttttgtgtttcgttttatttatgcctgatcctttgctgccctcgtgtttttgcatacc-ctacagAATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATATAGATCAAATGTCAATCGATGAAATCGAGCAGGTGGTTAATAGGGAATCA
|| ||||||| || ||  |     ||     |  | ||| | |||     | || | ||| ||| | |        |||    | || |||| |  ||||   || |||||| ||||||||||| ||  |||| |||||||||||||||||||| ||| | |||||||| ||||| || ||||| |||||    |||||||| ||  ||
gttactacatgacatg--acctcaaattgcaaaatctgaatcttta----gcttaggtttcttttt-ctcagctaattgtattcttcctgttatgtcatatttctgcagAATTGAAGCATTTGAGGCGATTCTTGGTCAGCATGTGTTGGCAAATCATCTCGATCAAATATCAATTGACGAAATTGAGCAAACTGTTAATAGAGAGGCA
















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|32932328|gb|CF037140.1|CF037140
EST:     GATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAG                         AATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATAT
genomic: GATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAGgtcactacat ... taccctacagAATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATAT
EST: gi|71444493|gb|DR825543.1|DR825543
EST:     GATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAG                         AATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATAT
genomic: GATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAGgtcactacat ... taccctacagAATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATAT
EST: gi|32930843|gb|CF035655.1|CF035655
EST:     GATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAG                         AATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATAT
genomic: GATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAGgtcactacat ... taccctacagAATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATAT
EST: gi|30704942|gb|CD058634.1|CD058634
EST:     GATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAG                         AATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATAT
genomic: GATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAGgtcactacat ... taccctacagAATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATAT
EST: gi|60401061|gb|DN233868.1|DN233868
EST:     GATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAG                         AATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATAT
genomic: GATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAGgtcactacat ... taccctacagAATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATAT
EST: gi|6012558|gb|AW061995.1|AW061995
EST:     GATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAG                         AATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATAT
genomic: GATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAGgtcactacat ... taccctacagAATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATAT
EST: gi|78543766|gb|DV621264.1|DV621264
EST:     GATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAG                         AATGGAAGCATTTGAAGCATTTTTGGGTCAGCATGTGTTGGCAAACCATAT
genomic: GATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAGgtcactacat ... taccctacagAATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATAT
EST: gi|71444494|gb|DR825544.1|DR825544
EST:     GATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAG                         AATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATAT
genomic: GATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAGgtcactacat ... taccctacagAATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATAT
EST: gi|30704945|gb|CD058635.1|CD058635
EST:     GATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAG                         AATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATAT
genomic: GATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAGgtcactacat ... taccctacagAATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATAT

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: 112

CTCCGGAAATGATCCAATGGATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAGgtcactacat ... taccctacagAATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATATAGATCAAATGTCAATCGATGAAATCGAGCAGGTGGTTAATAGGGAATCA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 19

CTCCGGAAATGATCCAATGGATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAGgtcactacat ... taccctacagAATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATATAGATCAAATGTCAATCGATGAAATCGAGCAGGTGGTTAATAGGGAATCA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 30

CTCCGGAAATGATCCAATGGATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAGgtcactacat ... taccctacagAATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATATAGATCAAATGTCAATCGATGAAATCGAGCAGGTGGTTAATAGGGAATCA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 14

CTCCGGAAATGATCCAATGGATGTGGATGTTGGGAACACTTCAAACGATCAGAATGTTCCTTTAGCGAGgtcactacat ... taccctacagAATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATATAGATCAAATGTCAATCGATGAAATCGAGCAGGTGGTTAATAGGGAATCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgttttatttatgcctgatcctttgctgccctcgtgtttttgcataccctacagAATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATATAGATCAAATGTCAATCGATGAAATCGAGCAGGTGGTTAATAGGGAATCA
             gcctgat  putative branch site (score: 14)
     ttatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcactacataacctgcaaatctgaacattcagctttgatttttttttgtgtttcgttttatttatgcctgatcctttgctgccctcgtgtttttgcataccctacagAATGGAAGCATTTGAAGCATTTCTGGGTCAGCATGTGTTGGCAAACCATATAGATCAAATGTCAATCGATGAAATCGAGCAGGTGGTTAATAGGGAATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG