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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATACTCGGCATCCTAATTGCAGTAGTTGGAATGGTCTTATACTCATACTTCTGCACATTGGAGGGCCAGCAAAAAAACGCCGAAGTCTCCCCACAACAGgtagcttccagtctgaattttattgcttgcaaatggttcaccattagttctggaatcgtttcaattgttcccacatatcttatcagctcttcaaaacgccatatattacag

Basic information

species Oryza sativa
transcript LOC_Os05g07670.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g07670.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G063511_T02 (Zea mays), 5'ss of exon 7
CATACTCGGCATCCTAATTGCAGTAGTTGGAATGGTCTTATACTCATACTTCTGCACATTGGAGGGCCAGCAAAAAAACGCCGAAGTCTCCCCACAACAGgtagcttccagtctgaattttattgcttgcaaatggttcaccattagttctggaatcgtttcaattgttcccacatatcttatcagctcttcaaaacgccatat-attacag
|||||| || |||||||||||||||||||||||||||||||| ||||||||||||||| |||||  |||||| || ||| | |||||||||||||| |||||| |||          | | ||    || | |   ||||   | |    |  |||  ||       |||      |      |||    | || | |  |||  | |||  
CATACTTGGGATCCTAATTGCAGTAGTTGGAATGGTCTTATATTCATACTTCTGCACAGTGGAGACCCAGCATAAGAACACTGAAGTCTCCCCACAGCAGgtacctt----------tctcatgcactggagaaatttcagtgtgaaccattaaattcttctgccctttcattggcagtgacccagtgtgtaaatatgttatacgagtac--

upper sequence: LOC_Os05g07670.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G063253_T09 (Zea mays), 5'ss of exon 5
CATACTCGGCATCCTAATTGCAGTAGTTGGAATGGTCTTATACTCATACTTCTGCACATTGGAGGGCCAGCAAAAAAACGCCGAAGTCTCCCCACAACAGgtagcttccagtctgaattttattgcttgcaaatggttcaccattagttctggaatcgtttcaattgttcccacatatcttatcagctcttcaaaacgccatatattacag
|||||| || ||||||||||| ||||||||||||||||| || ||||||||||||||| |||||  |||||||||||| |  ||||||||||||||||||||| ||| |    || | |  |   || | | | | | ||          |  |||  | |      |||  |  | | | ||  |   |     || |  | | |     
CATACTTGGAATCCTAATTGCTGTAGTTGGAATGGTCTTGTATTCATACTTCTGCACAGTGGAGACCCAGCAAAAAAATGTTGAAGTCTCCCCACAACAGgtaactttct-catgcactacagcactag-agaagttccagtgcgcaccattaaattctgttgccctttcagaattctgtcattggtagt----gacccagtgtgt-----
















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|86497394|gb|CI140027.1|CI140027
EST:     TCTGCACATTGGAGGGCCAGCNNNNNNNCGCCGAAGTCTCCCCACAACAG                         GCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
genomic: TCTGCACATTGGAGGGCCAGCAAAAAAACGCCGAAGTCTCCCCACAACAGgtagcttcca ... tatattacagGCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
EST: gi|88228626|gb|CI228106.1|CI228106
EST:     TCTGCACATTGGAGGGCCAGCNNNNNNNCGCCGAAGTCTCCCCACAACAG                         GCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
genomic: TCTGCACATTGGAGGGCCAGCAAAAAAACGCCGAAGTCTCCCCACAACAGgtagcttcca ... tatattacagGCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
EST: gi|89192784|gb|CI050082.1|CI050082
EST:     TCTGCACATTGGAGGGCCAGCNNNNNNNCGCCGAAGTCTCCCCACAACAG                         GCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
genomic: TCTGCACATTGGAGGGCCAGCAAAAAAACGCCGAAGTCTCCCCACAACAGgtagcttcca ... tatattacagGCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
EST: gi|87029250|gb|CI276518.1|CI276518
EST:     CGCCGAAGTCTCCCCACAACAG                         GCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
genomic: CGCCGAAGTCTCCCCACAACAGgtagcttcca ... tatattacagGCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
EST: gi|58676032|gb|CK064719.1|CK064719
EST:     TCTGCACATTGGAGGGCCAGCNNNNNNNCGCCGAAGTCTCCCCACAACAG                         GCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
genomic: TCTGCACATTGGAGGGCCAGCAAAAAAACGCCGAAGTCTCCCCACAACAGgtagcttcca ... tatattacagGCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
EST: gi|86494251|gb|CI136884.1|CI136884
EST:     TCTGCACATTGGAGGGCCAGCNNNNNNNCGCCGAAGTCTCCCCACAACAG                         GCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
genomic: TCTGCACATTGGAGGGCCAGCAAAAAAACGCCGAAGTCTCCCCACAACAGgtagcttcca ... tatattacagGCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
EST: gi|218493898|gb|FG949293.1|FG949293
EST:     TCTGCACATTGGAGGGCCAGCNNNNNNNCGCCGAAGTCTCCCCACAACAG                         GCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
genomic: TCTGCACATTGGAGGGCCAGCAAAAAAACGCCGAAGTCTCCCCACAACAGgtagcttcca ... tatattacagGCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
EST: gi|88270274|gb|CI385532.1|CI385532
EST:     AAAAACTCCGAAGTCTCCCCACAACAG                         GCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAATTT
genomic: AAAAACGCCGAAGTCTCCCCACAACAGgtagcttcca ... tatattacagGCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
EST: gi|86504458|gb|CI147091.1|CI147091
EST:     TCTGCACATTGGAGGGCCAGCNNNNNNNCGCCGAAGTCTCCCCACAACAG                         GCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
genomic: TCTGCACATTGGAGGGCCAGCAAAAAAACGCCGAAGTCTCCCCACAACAGgtagcttcca ... tatattacagGCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
EST: gi|58676230|gb|CK064917.1|CK064917
EST:     TCTGCACATTGGAGGGCCAGCNNNNNNNCGCCGAAGTCTCCCCACAACAG                         GCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
genomic: TCTGCACATTGGAGGGCCAGCAAAAAAACGCCGAAGTCTCCCCACAACAGgtagcttcca ... tatattacagGCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
EST: gi|88228565|gb|CI228045.1|CI228045
EST:     TCTGCACATTGGAGGGCCAGCNNNNNNNCGCCGAAGTCTCCCCACAACAG                         GCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT
genomic: TCTGCACATTGGAGGGCCAGCAAAAAAACGCCGAAGTCTCCCCACAACAGgtagcttcca ... tatattacagGCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTT

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), 58 (downstream exon)
Score: 4

CATACTCGGCATCCTAATTGCAGTAGTTGGAATGGTCTTATACTCATACTTCTGCACATTGGAGGGCCAGCAAAAAAACGCCGAAGTCTCCCCACAACAGgtagcttcca ... tatattacagGCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTTGAGAATGGAGGTGGAGTGGTTGATGATGAGCCTCTCAAGGTACCGATGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATACTCGGCATCCTAATTGCAGTAGTTGGAATGGTCTTATACTCATACTTCTGCACATTGGAGGGCCAGCAAAAAAACGCCGAAGTCTCCCCACAACAGgtagcttccagtctgaattttattgcttgcaaatggttcaccattagttctggaatcgtttcaattgttcccacatatcttatcagctcttcaaaacgccatatattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG