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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATGAGTACTTTGCTTGGGGTCTTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTTgtaagccctccccccccctctctctctctctcacacacacacacactctctctctctctctctctctctctctcaaacggagtacaatcgcataatgcaa...

Basic information

species Oryza sativa
transcript LOC_Os01g60440.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AC218972.3_FGT001 (Zea mays), 5'ss of exon 4
AGATGAGTACTTTGCTTGGGGTCTTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTTgtaagccctccccccccctctctctctctctcacacacacacacactctctctctctctctctctctctctctcaaacggagtacaatcgcataatgcaa---
||||||||||||||| ||||| ||||| |||||||| |||||||||||||||||||| || |||||||| ||||||||  |   |  |   |     | |       | | |  || |  |    | | |   ||||||  |   |  ||   |  ||| ||  ||  ||      
AGATGAGTACTTTGCATGGGGGCTTCATCAGATATCCAAAGCTGTGAGCTTTCTCAATAATGACTGCAAACTTgtaagttcctgcatcaagttgaagtttgcagtgta-atatgca-atccggcttgttttaatctctccttagatgcaagataaaacattca-attttgttgatt

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G098078_T01 (Zea mays), 5'ss of exon 4
AGATGAGTACTTTGCTTGGGGTCTTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTTgtaagccctccccccccctctctctctctctcacacacacacacactctctctctctctctctctctctctctcaaacggagtacaatcgcataatgcaa-----
||||||||||||||| ||||| ||||| |||||||| |||||||||||||||||||| || || ||||| ||||||||   |||  |  |   |     | |   ||| | | |  || |||  |||  | | | ||||| |   |  ||   |  ||| || |||  ||        
AGATGAGTACTTTGCATGGGGGCTTCATCAGATATCCAAAGCTGTGAGCTTTCTCAATAATGATTGCAAACTTgtaag--ttcctgcatcaagttgaagttttgaacataaa-atgcaatctggctcgttttat-tctctttagatgcaagataaaacattc-cattttgttgctttg

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT2G40730.1 (Arabidopsis thaliana), 5'ss of exon 4
AGATGAGTACTTTGCTTGGGGTCTTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTTgtaagc-cctccccccccctctctctctctctcacacacacacacactctctctctctctctctctctctctctcaaacg-gagtacaatcgcataatgcaa
 ||||||||||||||   ||| || |||||||||   ||||||||||||||||| ||||| |||||||| ||||||||   ||        | || |   ||    |       | | |  |  |  ||       | | |   |   |  |   ||| | |  |  | |  || 
GGATGAGTACTTTGCACTGGGGCTACACCAGATAGGTAAAGCTGTGAGCTTTCTGAACAATGACTGCAAACTTgtaagtatctgtttataacactataattcagctattagagtatataaccggtggctagtcgattttttagttaaaactcttaagttctactgtctta-acag

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|117245083|gb|CT843332.1|CT843332
EST:     TTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTT                         GTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCAAACTCTAGAT
genomic: TTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTTgtaagccctc ... tcaatttcagGTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCAAACTCTAGAT
EST: gi|58695768|gb|CK084455.1|CK084455
EST:     TTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTT                         GTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCAAACTCTAGAT
genomic: TTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTTgtaagccctc ... tcaatttcagGTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCAAACTCTAGAT
EST: gi|58695973|gb|CK084660.1|CK084660
EST:     TTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTT                         GTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTT
genomic: TTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTTgtaagccctc ... tcaatttcagGTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTT
EST: gi|25804372|gb|CA760333.1|CA760333
EST:     TTCACCAGATATCANAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTT                         GTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCANACTCTAGAT
genomic: TTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTTgtaagccctc ... tcaatttcagGTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCAAACTCTAGAT
EST: gi|29636110|gb|CB641119.1|CB641119
EST:     TTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTT                         GTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCAAACTCTAGAT
genomic: TTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTTgtaagccctc ... tcaatttcagGTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCAAACTCTAGAT
EST: gi|29622867|gb|CB627878.1|CB627878
EST:     TTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTT                         GTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCAAACTCTAGAT
genomic: TTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTTgtaagccctc ... tcaatttcagGTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCAAACTCTAGAT
EST: gi|58684299|gb|CK072986.1|CK072986
EST:     TTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTT                         GTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCAAACTCTAGAT
genomic: TTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTTgtaagccctc ... tcaatttcagGTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCAAACTCTAGAT
EST: gi|58658376|gb|CK047056.1|CK047056
EST:     TTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTT                         GTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCAAACT
genomic: TTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTTgtaagccctc ... tcaatttcagGTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCAAACT
EST: gi|29676650|gb|CB672925.1|CB672925
EST:     TTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTT                         GTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCAAACTCTAGAT
genomic: TTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTTgtaagccctc ... tcaatttcagGTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCAAACTCTAGAT
EST: gi|29623070|gb|CB628081.1|CB628081
EST:     TTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTT                         GTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCAAACTCTAGAT
genomic: TTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTTgtaagccctc ... tcaatttcagGTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCAAACTCTAGAT

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 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 70 (downstream exon)
Score: 41

AGATGAGTACTTTGCTTGGGGTCTTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTTgtaagccctc ... tcaatttcagGTTCACGGGAATGTATGCGTGACGAGCGTAGTTGTTACTCAAACTCTAGATTGGAAGCTTCATGCTTTTGATGTTCTTTCTGAATTTGATGCTAACAACG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATGAGTACTTTGCTTGGGGTCTTCACCAGATATCAAAAGCTGTGAGCTTTCTCAACAACGACTGCAAGCTTgtaagccctccccccccctctctctctctctcacacacacacacactctctctctctctctctctctctctctcaaacggagtacaatcgcataatgcaa

- - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctct