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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAAGATGATCAATCGGCAACGCTTGACCAAGTCTTGAATGATACGACGAGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACAAGCAATCAAgttagttgattttgcttgctgtttaccacgcgtctaagtgttttctgctaaaaatcaactaatgcaactaactgtatgatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g67220.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67220.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G044092_T01 (Zea mays), 5'ss of exon 12
AGGAAGATGATCAATCGGCAACGCTTGACCAAGTCTTGAATGATACGACGAGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACAAGCAATCAAgttag--ttgattttgctt-gctgtttaccacgcgtctaagtgttttctgctaaaaatc-------aactaatgcaactaactgtatgatgcag------------------------------
| || || |||||||| |||||||||||||| ||| | || || ||||||||||| |||||||||||||| ||||||   |||||||| ||||| ||||||| ||  ||  ||||| || ||||   | |||  |  ||        |    | |   |       | ||| | |||      |   ||  ||                               
AAGAGGACGATCAATCCGCAACGCTTGACCAGGTCCTAAACGACACGACGAGGGTCGGTTACTTCAAAGGGTACCTCAATTCAGTTGCGCAAGCGATCAAgtaagccttttttttgtttcgctgcccatcacatgcatagccaagaccaaggacaggacgtgcgtgagctactacaatatgacgaccgacacaagcaggcactaacgagtggttttgactgcag
















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|88844089|gb|CI001146.1|CI001146
EST:     AGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACAAGCAATCAA                         GGATGGTGCTGATGTTCGTGGGTACTTCGCATGGTCGTTCCTGGACAACTT
genomic: AGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACAAGCAATCAAgttagttgat ... tatgatgcagGGATGGTGCTGATGTTCGTGGGTACTTCGCATGGTCGTTCCTGGACAACTT
EST: gi|3761659|gb|C98907.1|C98907
EST:     AGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACAAGCAATCAA                         GGATGGTGCTGATGTTCGTGGGTACTTCGCATGGTCGTTCCTGGACAACTT
genomic: AGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACAAGCAATCAAgttagttgat ... tatgatgcagGGATGGTGCTGATGTTCGTGGGTACTTCGCATGGTCGTTCCTGGACAACTT
EST: gi|88491677|gb|CI428949.1|CI428949
EST:     AAAGGATACCTCGCGTCAGTTGCACAAGCAATCAA                         GGATGGTGCTGATGTTCGTGGGTACTTCGCATGGTCGTTCCTGGACAACTT
genomic: AAAGGATACCTCGCGTCAGTTGCACAAGCAATCAAgttagttgat ... tatgatgcagGGATGGTGCTGATGTTCGTGGGTACTTCGCATGGTCGTTCCTGGACAACTT
EST: gi|25806962|gb|CA762923.1|CA762923
EST:     AGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACAAGCAATCAA                         GGATGGTGCTGATGTTCGTGGGTACTTCGCATGGTCGTTCCTGGACAACTT
genomic: AGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACAAGCAATCAAgttagttgat ... tatgatgcagGGATGGTGCTGATGTTCGTGGGTACTTCGCATGGTCGTTCCTGGACAACTT
EST: gi|88428839|gb|CI554555.1|CI554555
EST:     ACCTCGCGTCAGTTGCACAAGCAATCAA                         GGATGGTGCTGATGTTCGTGGGTACTTCGCATGGTCGTTCCTGGACAACTT
genomic: ACCTCGCGTCAGTTGCACAAGCAATCAAgttagttgat ... tatgatgcagGGATGGTGCTGATGTTCGTGGGTACTTCGCATGGTCGTTCCTGGACAACTT
EST: gi|58672934|gb|CK061620.1|CK061620
EST:     AGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACAAGCAATCAA                         GGATGGTGCTGATGTTCGTGGGTACTTCGCATGGTCGTTCCTGGACAACTT
genomic: AGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACAAGCAATCAAgttagttgat ... tatgatgcagGGATGGTGCTGATGTTCGTGGGTACTTCGCATGGTCGTTCCTGGACAACTT
EST: gi|88994486|gb|CI117638.1|CI117638
EST:     AGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACAAGCAATCAA                         GGATGGTGCTGATGTTCGTGGGTACTTCGCATGGTCGTTCCTGGACAACTT
genomic: AGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACAAGCAATCAAgttagttgat ... tatgatgcagGGATGGTGCTGATGTTCGTGGGTACTTCGCATGGTCGTTCCTGGACAACTT
EST: gi|88591557|gb|CI709596.1|CI709596
EST:     AGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACAAGCAATCAA                         GGATGGTGCTGATG
genomic: AGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACAAGCAATCAAgttagttgat ... tatgatgcagGGATGGTGCTGATG
EST: gi|396941166|gb|HO188375.1|HO188375
EST:     AGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACAAGCAATCAA                         GGATGGTGCTGATGTTCGTGGGTACTTCGCATGGTCGTTCCTGGACAACTT
genomic: AGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACAAGCAATCAAgttagttgat ... tatgatgcagGGATGGTGCTGATGTTCGTGGGTACTTCGCATGGTCGTTCCTGGACAACTT
EST: gi|88508596|gb|CI436102.1|CI436102
EST:     AAAGGATACCTCGCGTCAGTGGCACAAGCAATCAA                         GGAGGGTGCTGATGTTCGTGGGTACTTCGCATGTTCGTTCCTGGACAACTT
genomic: AAAGGATACCTCGCGTCAGTTGCACAAGCAATCAAgttagttgat ... tatgatgcagGGATGGTGCTGATGTTCGTGGGTACTTCGCATGGTCGTTCCTGGACAACTT

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: 75 (upstream exon), 73 (downstream exon)
Score: 70

AGGAAGATGATCAATCGGCAACGCTTGACCAAGTCTTGAATGATACGACGAGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACAAGCAATCAAgttagttgat ... tatgatgcagGGATGGTGCTGATGTTCGTGGGTACTTCGCATGGTCGTTCCTGGACAACTTCGAGTGGGCTATGGGATACACCAAGAGGTTTGGCATTGTTTATGTTGAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGAAGATGATCAATCGGCAACGCTTGACCAAGTCTTGAATGATACGACGAGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACAAGCAATCAAgttagttgattttgcttgctgtttaccacgcgtctaagtgttttctgctaaaaatcaactaatgcaactaactgtatgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA