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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacatgaaaaatattaccaagttcaatacagaagcatactactattagatcaagcatgcgtttagttgaaattttttgtaacagcttgcacttatcaatgcag

Basic information

species Oryza sativa
transcript LOC_Os03g16900.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16900.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G084440_T01 (Zea mays), 5'ss of exon 11
AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacatgaaaaatattaccaagttcaatacagaagcatactactattagatcaagcatgcgtttagttgaaattttttgtaacagcttgcacttatcaatgcag
|| || ||  | || || ||||||||||| ||||| ||||||||||| || ||||||| |||||||||||| |||||||   ||  | | |||||           | |||  | ||  |    ||| |  |   || | || || | |    ||    ||||     |    |  |||||||
AGCTATGACTCCACCACCCATTTTGAGACGACGGTCAAGGATGTGCTCGCCTTGTACAACAAGATCACTGGAAAGgtaactgca-aatatatattgt---------ttcaggtg-atgtt----ttacagtacaaattccttcagctaacgactt----aacaa---acgtgcaataatgcag
















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|86602820|gb|CI357184.1|CI357184
EST:     AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG                         GAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
genomic: AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacat ... atcaatgcagGAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
EST: gi|8856777|gb|AU094095.1|AU094095
EST:     AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG                         GAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
genomic: AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacat ... atcaatgcagGAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
EST: gi|10109151|gb|AU063867.2|AU063867
EST:     AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG                         GAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
genomic: AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacat ... atcaatgcagGAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
EST: gi|88258259|gb|CI360845.1|CI360845
EST:     AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAAATCACTGGGAAG                         GAACTTGATCTTTCTGTGGATCTGAATCCTGCTAGTGCTGCTGAATCTGAA
genomic: AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacat ... atcaatgcagGAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
EST: gi|33693913|gb|CF322152.1|CF322152
EST:     AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG                         GAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCT
genomic: AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacat ... atcaatgcagGAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCT
EST: gi|89197962|gb|CI117440.1|CI117440
EST:     AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG                         GAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
genomic: AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacat ... atcaatgcagGAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
EST: gi|88254220|gb|CI352846.1|CI352846
EST:     AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG                         GAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
genomic: AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacat ... atcaatgcagGAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
EST: gi|87026816|gb|CI259469.1|CI259469
EST:     AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG                         GAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
genomic: AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacat ... atcaatgcagGAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
EST: gi|87026825|gb|CI259478.1|CI259478
EST:     AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG                         GAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
genomic: AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacat ... atcaatgcagGAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
EST: gi|88259855|gb|CI364346.1|CI364346
EST:     AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG                         GAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
genomic: AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacat ... atcaatgcagGAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
EST: gi|66947289|gb|AU312133.1|AU312133
EST:     AAGATCACTGGGAAG                         GAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
genomic: AAGATCACTGGGAAGgtaatcacat ... atcaatgcagGAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
EST: gi|86879928|gb|CI339995.1|CI339995
EST:     AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG                         GAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
genomic: AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacat ... atcaatgcagGAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
EST: gi|11564810|gb|AU165446.1|AU165446
EST:     AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG                         GAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
genomic: AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacat ... atcaatgcagGAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
EST: gi|3761371|gb|C98619.1|C98619
EST:     AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG                         GAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
genomic: AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacat ... atcaatgcagGAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
EST: gi|89187975|gb|CI115224.1|CI115224
EST:     AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG                         GAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
genomic: AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacat ... atcaatgcagGAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
EST: gi|88996545|gb|CI260049.1|CI260049
EST:     AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG                         GAACTCGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAG
genomic: AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacat ... atcaatgcagGAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
EST: gi|33693914|gb|CF322153.1|CF322153
EST:     AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG                         GAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
genomic: AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacat ... atcaatgcagGAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
EST: gi|86839705|gb|CI343639.1|CI343639
EST:     AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAG                         GAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA
genomic: AGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacat ... atcaatgcagGAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAA

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: 61 (upstream exon), 73 (downstream exon)
Score: 19

AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacat ... atcaatgcagGAACTTGATCTTTCTGTGGATCTGAATGCTGCTAGTGCTGCTGAATCTGAAGCGGCCTGAGCGATAGCTACTTCTTCCAATTCCTTTTATTCTTTCATAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTACGATGCAACTACTCATTTTGAGACAACGGTGAAGGATGTGCTTGCATTGTACAGCAAGATCACTGGGAAGgtaatcacatgaaaaatattaccaagttcaatacagaagcatactactattagatcaagcatgcgtttagttgaaattttttgtaacagcttgcacttatcaatgcag

- - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA