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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attactgggtgtgcgtgccaagctggccctcttttctgaattctggaggcagcaggatcatcatctcacttcgctttgcttttgttggcattgcatgcagGTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAGGAGGAGTTCATCCGGGCGACGGCCGGCGTGTGGAAGGAGCAGAAGCTGC

Basic information

species Zea mays
transcript GRMZM5G843914_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G843914_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g55890.1 (Oryza sativa), 3'ss of exon 11
---attactgggtgtgcgtgccaagctggccctcttttctgaattctggaggcag-caggatcatcatctcacttcgctttgcttttgttggcattgcatgcagGTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAGGAGGAGTTCATCCGGGCGACGGCCGGCGTGTGGAAGGAGCAGAAGCTGC
    ||||||     || |    |  |||   |     ||  | |    || ||| ||    | |    ||||     | |       |   | ||   |||||||||| ||||||||||| ||| |||||||||| || |||||| | ||||||||||||||||||||||| ||||  ||| | ||||||||||||||  | |
aaagttactg--caggcattattacttggtggtgccaact--actgccaagccagtcaatcccctttagtcacaatcatctcacaaactcctctttttctgcagGTGAGAGTGTACACTCCAAAGAGGCTGTTCCATCAACTGGAGGCTGCCAAGGAGGAGTTCATCCGGGCAACGGTGGGCATCTGGAAGGAGCAGAAAATAC
















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|29576777|gb|CB616889.1|CB616889
EST:     AGCCTCTTTTGCGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCG                         GTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAG
genomic: AGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCGgtaagcaaca ... ttgcatgcagGTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAG
EST: gi|71431420|gb|DR812470.1|DR812470
EST:     AGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCG                         GTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAG
genomic: AGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCGgtaagcaaca ... ttgcatgcagGTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAG
EST: gi|74241581|gb|DT649495.1|DT649495
EST:     AGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCG                         GTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAG
genomic: AGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCGgtaagcaaca ... ttgcatgcagGTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAG
EST: gi|71431421|gb|DR812471.1|DR812471
EST:     AGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCG                         GTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAG
genomic: AGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCGgtaagcaaca ... ttgcatgcagGTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAG
EST: gi|88756881|gb|DY541022.1|DY541022
EST:     AGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCG                         GTGAGGGTGTACACTCCGAAGCGGCTGTT
genomic: AGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCGgtaagcaaca ... ttgcatgcagGTGAGGGTGTACACTCCGAAGCGGCTGTT
EST: gi|89760782|gb|DY689054.1|DY689054
EST:     AGCTTCTTTTACGTTTTGCGTTTTGTTCCGGCAGCCATTCTGATCCCGCG                         GTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAG
genomic: AGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCGgtaagcaaca ... ttgcatgcagGTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAG
EST: gi|78123668|gb|DV542052.1|DV542052
EST:     AGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCG                         GTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAG
genomic: AGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCGgtaagcaaca ... ttgcatgcagGTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAG
EST: gi|166692809|gb|EG322476.1|EG322476
EST:     AGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCG                         GTGAGGGTGTACACTCCGAAGCGTCTGTTCCACCAGCTGG
genomic: AGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCGgtaagcaaca ... ttgcatgcagGTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGG
EST: gi|211322727|gb|FL462751.1|FL462751
EST:     TGTTCCGGCAGCCATTCTGATCCCGCG                         GTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAG
genomic: TGTTCCGGCAGCCATTCTGATCCCGCGgtaagcaaca ... ttgcatgcagGTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAG
EST: gi|60357556|gb|DN224529.1|DN224529
EST:     AGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCG                         GTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAG
genomic: AGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCGgtaagcaaca ... ttgcatgcagGTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAG
EST: gi|211041651|gb|FL024100.1|FL024100
EST:     GCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCNG                         GTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGGCGGCCAA
genomic: GCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGC-Ggtaagcaaca ... ttgcatgcagGTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAA

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: 59

GGTGAGCAAAGCGGGGCATGAGTGGCGGGCCTTTGCCGTTGCGCAACCGGAGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCGgtaagcaaca ... ttgcatgcagGTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAGGAGGAGTTCATCCGGGCGACGGCCGGCGTGTGGAAGGAGCAGAAGCTGC


Block sizes: 44 (upstream exon), 42 (downstream exon)
Score: 10

GGTGAGCAAAGCGGGGCATGAGTGGCGGGCCTTTGCCGTTGCGCAACCGGAGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCGgtaagcaaca ... ttgcatgcagGTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAGGAGGAGTTCATCCGGGCGACGGCCGGCGTGTGGAAGGAGCAGAAGCTGC


Block sizes: 49 (upstream exon), 32 (downstream exon)
Score: 10

GGTGAGCAAAGCGGGGCATGAGTGGCGGGCCTTTGCCGTTGCGCAACCGGAGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCGgtaagcaaca ... ttgcatgcagGTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAGGAGGAGTTCATCCGGGCGACGGCCGGCGTGTGGAAGGAGCAGAAGCTGC


Block sizes: 47 (upstream exon), 32 (downstream exon)
Score: 7

GGTGAGCAAAGCGGGGCATGAGTGGCGGGCCTTTGCCGTTGCGCAACCGGAGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCGgtaagcaaca ... ttgcatgcagGTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAGGAGGAGTTCATCCGGGCGACGGCCGGCGTGTGGAAGGAGCAGAAGCTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggcagcaggatcatcatctcacttcgctttgcttttgttggcattgcatgcagGTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAGGAGGAGTTCATCCGGGCGACGGCCGGCGTGTGGAAGGAGCAGAAGCTGC
                 atctcac  putative branch site (score: 7)
                                  ttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attactgggtgtgcgtgccaagctggccctcttttctgaattctggaggcagcaggatcatcatctcacttcgctttgcttttgttggcattgcatgcagGTGAGGGTGTACACTCCGAAGCGGCTGTTCCACCAGCTGGAGTCGGCCAAGGAGGAGTTCATCCGGGCGACGGCCGGCGTGTGGAAGGAGCAGAAGCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- tactggg
- - - - - -tgcgtgc
- - - - - - - - - - agctggc
- - - - - - - - - - - - - - - -ttttctg
- - - - - - - - - - - - - - - - - - - - - - - - gcagcag