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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGAAAAAATATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAGgttctattctgatcattctgtaaaatcctgaacaatatctgccctggtgacaatatttttcttgtttgatggcag

Basic information

species Oryza sativa
transcript LOC_Os01g13190.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g13190.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G058584_T01 (Zea mays), 5'ss of exon 11
GTTGAAAAAATATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAGgttctattctgatcattc--tgtaaaatcctgaacaatatctgccctggtgaca-atatttttcttgtttgatggcag-----------------------------
| ||| || || ||||||||||| || |||||||| || ||||| ||||||||||||||||||   |  || || | |  ||||||| | | | || || || |  ||   | | || ||||   || |  || |                                
GCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAGgtttgttcttgttcttccattgtaaaa-ctttaccattaccttctttgccaatacatcttttctatggtaaattgtttttgcggttctaatttttattttactgcag

upper sequence: LOC_Os01g13190.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA09G02960.1 (Glycine max), 5'ss of exon 9
GTTGAAAAAATATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAGgt---tctattctgatcattctgtaaaatcctgaacaatatctgccctggtgacaatatttttcttgtttgatggcag---------------------------------------
|||||||| || ||||| |||||||| || |||||||| |||||||||||||| ||||| ||     | ||   ||||   |  ||  |   || |  ||||  |       |  | ||||   |||||  ||   ||                                       
GTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAAgtaagcatgtttatatcacattagaatttatggatccgtatccact------attacatttcgtttgttgaatcttagatcttctgcatttctttaccttttgaaaatcttatgcag

upper sequence: LOC_Os01g13190.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA15G13910.1 (Glycine max), 5'ss of exon 9
GTTGAAAAAATATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAGgttctattctgatcattctgtaaaatcctgaacaatatctgccctggtgacaatatttttcttgtttgatggcag-----------
|||||||| || ||||| |||||||| || |||||||| |||||||||||||| ||||| ||   |   || | ||  || |  |   |  |    |||||        |  | ||||   || ||  ||   |            
GTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAAgt--aagcatgtttatattgcattaaaatttatgg-atctgtatccactattacatttcatttcttgaatcttaaatcttctgcag

upper sequence: LOC_Os01g13190.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA08G08630.1 (Glycine max), 5'ss of exon 8
GTTGAAAAAATATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAGgttctattctgatcattctgtaaa-atcctgaacaatatctgcc-ctggtgacaatatttttcttgtttgatggcag-----------------------------
||||| ||||| ||||| || ||||| || |||||||| |||||||||||||| || || ||    ||   |||  ||| ||   ||  |  ||| | | |  | ||  | | |   | | |  |  || ||  |                               
GTTGAGAAAATTTTTGGCCCAGGAAACCAATATGTCACAGCTGCAAAAATGATACTACAAgtgagctttgaatctctctctatctattttatacattgtgtttcactcttcagatcttatattatagtttatcccgctttacattattgttgaaaatattctgcag

upper sequence: LOC_Os01g13190.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv18s0166g00300.t01 (Vitis vinifera), 5'ss of exon 11
GTTGAAAAAATATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAGgttc-tattctgatcattctgtaaaatcctgaacaatat-ctgccctggtgacaatatttttcttgtttgatggcag--------------------------------------
|| ||||| || ||||| |||||||||||||||||||||||||||||||||||||| || ||    |  |   || |||   || ||  |    | | | ||    || || | ||||  | |   | | ||                                           
GTGGAAAAGATTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAAgtaggcacacatttccttccaaaagattattggaactctacttttttgctgtctatatgatacacatcttatcttgatatgattctgttgcttttctttttttattcatcaacag

upper sequence: LOC_Os01g13190.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S233_40V6.1 (Physcomitrella patens), 5'ss of exon 10
GTTGAAAAAATATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAGg------ttctattctgatca-ttctgtaaaatcctgaacaatatctgc--cctggtga---caatatttttcttgtttgatggcag-------------
|| || ||| | ||||||||||||||||||||||| ||||||||||||||| | |||||||      |   |  || || |  ||| |   ||   |     |  |  |  |||   ||     | |||| ||   | || |                  
GTGGATAAAGTTTTTGGACCTGGAAATCAGTATGTTACGGCTGCAAAAATGTTGCTTCAGgcatgtctcacacactcattagctcttttccatttcgtgttgttccctctgcctatcgaatgtgaaatttatcgcatctgctcatttcttcagtgcagat

upper sequence: LOC_Os01g13190.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S15_472V6.1 (Physcomitrella patens), 5'ss of exon 10
GTTGAAAAAATATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAGgttctattc---tgatcatt----ctgtaaaatcctgaacaata---tctgccct--ggtgacaatatttttcttgtttgatggcag-------------------------------------------------------------------------------------------------
|| || ||| |  |||||||||||||||||||||| |||||||| || ||| |  | |||||    |     || |||||    ||||    |     |  ||    ||||| ||  |   |  | || |  |   |||| |   |                                                                                                  
GTCGATAAAGTTCTTGGACCTGGAAATCAGTATGTTACGGCTGCGAAGATGTTGTTGCAGgtatggtctatgtgctcattagccctgttctttgtcagattattgcttctgctctttgaatatgaaatgtaccacttttgctcatatttttagtttggatttcagagtgtatgggccttcagtttcaaccaatcaatgtacgagagtgctgacttctacttgccaatcaatctgtggtcaacag

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|32948183|gb|BP184755.1|BP184755
EST:     TATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAG                         AACAGTGAAGCCATGGTTTCTATAGACATGCCTGCTGGCCCTT-AGAAGTA
genomic: TATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAGgttctattct ... ttgatggcagAACAGTGAAGCCATGGTTTCTATAGACATGCCTGCTGGCCCTTCAGAAGTA
EST: gi|29685418|gb|CB681693.1|CB681693
EST:     TATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAG                         AACAGTGAAGCCATGGTTTCTATAGACATGCCTGCTGGCCCTTCAGAAGTA
genomic: TATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAGgttctattct ... ttgatggcagAACAGTGAAGCCATGGTTTCTATAGACATGCCTGCTGGCCCTTCAGAAGTA
EST: gi|58678012|gb|CK066699.1|CK066699
EST:     TATTTGGACCTGGTAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAG                         AACAGTGAAGCCATGGTTTCTATAGACATGCCTGCTGGCCCTTCAGAAGTA
genomic: TATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAGgttctattct ... ttgatggcagAACAGTGAAGCCATGGTTTCTATAGACATGCCTGCTGGCCCTTCAGAAGTA
EST: gi|29683233|gb|CB679508.1|CB679508
EST:     TATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAG                         AACAGTGAAGCCATGGTTTCTATAGACATGCCTGCTGGCCCTTCAGAAGTA
genomic: TATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAGgttctattct ... ttgatggcagAACAGTGAAGCCATGGTTTCTATAGACATGCCTGCTGGCCCTTCAGAAGTA
EST: gi|87017573|gb|CI289706.1|CI289706
EST:     TATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAG                         AACAGTGAAGCCATGGTTTCTATAGACATGCCTGCTGGCCCTTCAGAAGTA
genomic: TATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAGgttctattct ... ttgatggcagAACAGTGAAGCCATGGTTTCTATAGACATGCCTGCTGGCCCTTCAGAAGTA
EST: gi|58666767|gb|CK055453.1|CK055453
EST:     TATTTGGACCTGGTAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAG                         AACAGTGAAGCCATGGTTTCTATAGACATGCCTGCTGGCCCTTCAGAAGTA
genomic: TATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAGgttctattct ... ttgatggcagAACAGTGAAGCCATGGTTTCTATAGACATGCCTGCTGGCCCTTCAGAAGTA

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: 60 (upstream exon), 74 (downstream exon)
Score: 17

GTTGAAAAAATATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAGgttctattct ... ttgatggcagAACAGTGAAGCCATGGTTTCTATAGACATGCCTGCTGGCCCTTCAGAAGTATTAGTGATAGCGGATAAATATGCAAACCCAGTTCATGTTGCTGCTGATT




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