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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGATGAGGGTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgttggtgtctccttgtctctgcttcccatgcctccaaagccaaagtgacaatgtcaaccttagcttttctttggggaaaagaaaaacactaatcataccattccaatgtttcag

Basic information

species Oryza sativa
transcript LOC_Os01g71770.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g71770.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G030902_T02 (Zea mays), 5'ss of exon 12
TAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGATGAGGGTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgttggtgtctccttgtctctgcttcccatgcctccaaagccaaagtgacaatgtcaacct--tagcttttctttggggaaaagaaaaacactaatcataccattc---caatgtttcag
 ||||||||||| || ||||||||||| ||||||||||| |||||||||||||||||||| |||||| |||| ||||| ||||||||||| || ||||||||||||||| |||||| ||||||   ||||| ||   |  || || |  |||   |  |||| |   |  | |   || | |||||  ||    |    |||   ||   |     |  | ||||||
CAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGATGAGGGTGTGGCAGAACGGGTATCTCGTAGAAGCCATGAAATTCTGGGCCATGAGgtaaggctgctggtgt-tccttgctgctgctaccttcgtatcaaatgtaaaacaaattatgttatattatttgtccttgtctggggggaaatgcagagttaaaagtattttctgctctttctttcag

upper sequence: LOC_Os01g71770.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G060977_T05 (Zea mays), 5'ss of exon 13
TAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGATGAGGGTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgttggtgtctccttgtctctgcttcccatgcctccaaagccaaagtgacaatgtcaaccttagcttttctttggggaaaagaaaaacactaatcataccattccaatgtttcag
 |||||||| || || ||||||||||| ||||||||||| |||||||| ||||||||||| || |||||||| ||||| |||||||||||||| ||||||||||||||| || ||| |||||| | ||||| ||  ||  || ||      | ||  ||  | ||   |||  ||    | |      |    |  | | |                     
CAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGATGATGGTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCCATGAGgtaaggctgctgttgt-tccttgcccctgctacctttgtatctaatattctaatgtaaaaataaatgatagtattgtccttgtcttgggggggatgcaagt---------------------

upper sequence: LOC_Os01g71770.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AT4G36960.1 (Arabidopsis thaliana), 5'ss of exon 11
TAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGATGAGGGTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgttggtgtctccttgtctctgcttcccatgcctccaaagccaaagtg---acaatgtcaaccttagcttttctttggggaaaagaaaaacactaatcataccattccaatgtttcag
 || |||||||||||| |||||||||| ||||| |||||||||||  | ||||| |||||||| ||||| || |||  |||||||||    ||||| |||||||        |    |  |  |   |||||   |      |  | | ||  ||   | |    | ||  |   ||   ||| |||   ||                                 
AAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTACCTTTGCTGAAAATGGTGTTGCAGATCGTGTAGCCCGAAGATCTCATGAAATCTGTGGACAAGAGgtaaaaaaacaagc--ttgatacttgatgctttagacaaaaacttatctaagatgtataaagaagctacactgttttgattttcgggtttag---------------------------------

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|88964649|gb|CI069997.1|CI069997
EST:     CTCGCAGAAGTCATGAAATTCTAGGACATGAG                         GTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
genomic: CTCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgt ... aatgtttcagGTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
EST: gi|88993361|gb|CI257789.1|CI257789
EST:     GTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAG                         GTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
genomic: GTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgt ... aatgtttcagGTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
EST: gi|32947891|gb|BP184463.1|BP184463
EST:     GTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAG                         GTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
genomic: GTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgt ... aatgtttcagGTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
EST: gi|8528147|gb|AU092962.1|AU092962
EST:     GTTTGCCAGATCGGTTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAG                         GTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
genomic: GTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgt ... aatgtttcagGTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
EST: gi|29677103|gb|CB673378.1|CB673378
EST:     GTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAG                         GTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
genomic: GTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgt ... aatgtttcagGTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
EST: gi|88828471|gb|CI073341.1|CI073341
EST:     TCGCAGAAGTCATGAAATTCTAGGACATGAG                         GTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
genomic: TCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgt ... aatgtttcagGTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
EST: gi|88964718|gb|CI070064.1|CI070064
EST:     TAGCTCGCAGAAGTCATGAAATTCTAGGACATGAG                         GTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
genomic: TAGCTCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgt ... aatgtttcagGTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
EST: gi|116875665|gb|EC366173.1|EC366173
EST:     GTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAG                         GTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTT
genomic: GTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgt ... aatgtttcagGTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTT
EST: gi|3766847|gb|AU030957.1|AU030957
EST:     TAGCTCGCAGAAGTCATGAAATTCTAGGACATGAG                         GTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
genomic: TAGCTCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgt ... aatgtttcagGTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
EST: gi|86429774|gb|CI082197.1|CI082197
EST:     AAGTCATGAAATTTTAGGACATGAG                         GTTGCAATAGACACTGCTGCACCACTTGGGGGTGACTCTGGTGGTGGTTAC
genomic: AAGTCATGAAATTCTAGGACATGAGgtaaggctgt ... aatgtttcagGTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
EST: gi|116875549|gb|EC366057.1|EC366057
EST:     GTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAG                         GTTGCAATAGACACTGCTGCACCGCTTGAGGGTGACTCTGGTGGTGGTTAC
genomic: GTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgt ... aatgtttcagGTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
EST: gi|3766706|gb|AU030816.1|AU030816
EST:     GTNTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAG                         GTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
genomic: GTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgt ... aatgtttcagGTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
EST: gi|88846949|gb|CI005928.1|CI005928
EST:     GTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAG                         GTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC
genomic: GTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgt ... aatgtttcagGTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTAC

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: 65 (upstream exon), 69 (downstream exon)
Score: 25

TAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGATGAGGGTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgt ... aatgtttcagGTTGCAATAGACACTGCTGCACCACTTGAGGGTGACTCTGGTGGTGGTTACATGGAACCCATGGATCTTTATGGGGCTTATGGTTCAATGCGAACTTATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGATGAGGGTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgttggtgtctccttgtctctgcttcccatgcctccaaagccaaagtgacaatgtcaaccttagcttttctttggggaaaagaaaaacactaatcataccattccaatgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT