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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGATAAATCGATTAAGATAGCAGACTTTGGAGTTGCCAGGATTGAAGTCAAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaataaaacaactacattaatactatttaccatattatctgttagttctagccgcgtgcaacactttattttagttaagagaattttgtttgg...

Basic information

species Oryza sativa
transcript LOC_Os04g51950.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G102088_T02 (Zea mays), 5'ss of exon 2
GCGATAAATCGATTAAGATAGCAGACTTTGGAGTTGCCAGGATTGAAGTCAAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaataaaacaactacattaatactatttaccata-ttatctgttagttctagccgcgtgcaacactttattttagt--taagagaattttgtttgg
| |||||||| || |||||||| ||||||||||| ||  |||||||||| ||||| |||||||||||||||||||| |||||||||||||||||||| |||||||||||| |     ||     |  |  || |||  | | |||   || |  ||       |  ||    | |   | | |  ||  | ||| | | |   
GTGATAAATCTATCAAGATAGCTGACTTTGGAGTAGCTCGGATTGAAGTAAAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACCgtaagttgaacac--tgacattgctggtgttacttattaaaattagaagtcacatcatatattgaacatttatgtcaatcaatagtacaaaaatgtgggtca-

upper sequence: LOC_Os04g51950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G156013_T01 (Zea mays), 5'ss of exon 2
GCGATAAATCGATTAAGATAGCAGACTTTGGAGTTGCCAGGATTGAAGTCAAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaataaaacaactacattaatactatttac----catattatc-------tgttagttctagccgcgtgcaacactttattttagttaagagaattttgtttgg
| |||||||| || |||||||| ||||||||||| ||  | |||||||| ||||| |||||||||||||||||||| |||||||| ||||||||||| |||||||||||| |     ||  ||||| | ||  ||||    | | ||| |       | ||| ||  |       |  |||  | || ||||| | || |           
GTGATAAATCTATCAAGATAGCTGACTTTGGAGTAGCTCGCATTGAAGTAAAAACTGAGGGGATGACACCTGAAACGGGAACCTACCGTTGGATGGCACCgtaagttgaacactctgacatcattagttctgcttacagatcttgttagccacacgatattaattaaaattataagtcacatctcatattagt-atgaaag----------

upper sequence: LOC_Os04g51950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G03010.2 (Glycine max), 5'ss of exon 3
GCGATAAATCGATTAAGATAGCAGACTTTGGAGTTGCCAGGATTGAAGTCAAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaataaaacaactacattaatactatttaccatattatctgttagttctagccgcgtgcaacactttattttagttaagagaattttgtttgg-----
| || || || ||||| || || ||||||||||||||  | ||||| ||  |||| || || ||||||||||| || ||||| || ||||||||||| ||||||| | | |     |    | ||  |  || |||  || |||| ||    |||||||  | |        | ||||| |   ||||  | | | ||       
GTGACAAGTCAATTAAAATTGCTGACTTTGGAGTTGCTCGTATTGAGGTGCAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatcatttgc-tattctctttttttatacttataattttatatgc--attctagcttcttttttggaatgatttttg--gagagcttctcgattatggtta

upper sequence: LOC_Os04g51950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA05G36540.2 (Glycine max), 5'ss of exon 2
GCGATAAATCGATTAAGATAGCAGACTTTGGAGTTGCCAGGATTGAAGTCAAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaataaaacaactacattaatactatttaccatattatctgttagttctagccgcgtgcaacactttattttagttaagagaattttgtttgg-
| || || || ||||| || || ||||||||||||||| | ||||| ||  |||| || || ||||||||||| || ||||| || ||||||||||| ||||||| |   |       ||   ||  || ||||||     || | | |   |||||||  | |        | ||||| |   ||    | |  | ||| 
GTGACAAGTCAATTAAAATTGCTGACTTTGGAGTTGCCCGTATTGAGGTGCAAACTGAAGGAATGACACCTGAGACTGGAACATACCGTTGGATGGCTCCgtaagatcttttgctgttctctcttttta-tatttatatagttttatatgcattctagcttcatttttggaatgatttttggagagcttctctattatggt

upper sequence: LOC_Os04g51950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT4G31170.1 (Arabidopsis thaliana), 5'ss of exon 3
GCGATAAATCGATTAAGATAGCAGACTTTGGAGTTGCCAGGATTGAAGTCAAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaataaaacaactacattaatactatttaccatattatctgttagttc-tagccgcgtgcaacactttattttagttaagagaattttgtttgg----------
  |||   || || ||||| || || ||||| ||||| || ||||||||  ||||||| ||||||||||| || || ||||| ||  | |||||||| ||||||||||||||||   |   | ||     |  ||  | | |  |   | |  |  ||      |||||  | |  ||  |    | |     || ||| |          
CTGATCGGTCCATCAAGATTGCTGATTTTGGTGTTGCAAGAATTGAAGTTCAAACCGAAGGGATGACACCAGAGACTGGAACTTACAGATGGATGGCACCgtaagttgaataaat--atctcgttttccatccttgtcttgtccttaataaccttatatatctctgcaagtcatatttagacactatattcccttattttgatcgatgcag

upper sequence: LOC_Os04g51950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT4G31170.4 (Arabidopsis thaliana), 5'ss of exon 2
GCGATAAATCGATTAAGATAGCAGACTTTGGAGTTGCCAGGATTGAAGTCAAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaataaaacaactacattaatactatttaccatattatctgttagttc-tagccgcgtgcaacactttattttagttaagagaattttgtttgg-
  |||   || || ||||| || || ||||| ||||| || ||||||||  ||||||| ||||||||||| || || ||||| ||  | |||||||| ||||||||||||||||   |   | ||     |  ||  | | |  |   | |  |  ||      |||||  | |  ||  |    | |     || ||| | 
CTGATCGGTCCATCAAGATTGCTGATTTTGGTGTTGCAAGAATTGAAGTTCAAACCGAAGGGATGACACCAGAGACTGGAACTTACAGATGGATGGCACCgtaagttgaataaat--atctcgttttccatccttgtcttgtccttaataaccttatatatctctgcaagtcatatttagacactatattcccttattttga

upper sequence: LOC_Os04g51950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv04s0008g03020.t01 (Vitis vinifera), 5'ss of exon 2
GCGATAAATCGATTAAGATAGCAGACTTTGGAGTTGCCAGGATTGAAGTCAAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaataa--aacaactacattaatactatttaccatattatctgtta-gttctagccgcgtgcaacactttattttagttaagagaattttgtttgg
  |||||||| |||||||| || || ||||| |||||| ||||||| ||  ||||||| || |||||||| || ||||| || ||||| ||||||||||||||||     |||    |   ||  ||  ||  ||||    |  | | | ||   | || |  |  | |  ||| || || | |      |||||  |||   
CTGATAAATCCATTAAGATTGCTGATTTTGGTGTTGCCCGGATTGAGGTGCAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattttaaccgtcttttaagttgttaagatttcttctcctctatattttatgctggatg-attcttcacattgttcttgcattctgaattgggtta--

upper sequence: LOC_Os04g51950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S120_103V6.1 (Physcomitrella patens), 5'ss of exon 2
GCGATAAATCGATTAAGATAGCAGACTTTGGAGTTGCCAGGATTGAAGTCAAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaataaaacaactacattaatactatttaccatattatctgttagttctagccgcgtgcaacactttattttagttaagagaattttgtttgg---
  || ||||| |||||||| ||||| ||||| | ||| ||||| |||||  ||   ||||| ||||| || ||||| ||||||||||| |||||||| |||| |||  |   ||      || ||  |  | | ||   | || | | ||   ||  || | || ||    ||| |||  ||    |  ||  | |       
CGGACAAATCAATTAAGATTGCAGATTTTGGTGCTGCTAGGATAGAAGTGCAAGTTGAGGGCATGACTCCAGAAACGGGAACCTATCGATGGATGGCTCCgtgagt--atctaactgttgacgtttgtgttttgtattcttttttgttttccctcacgctg-gtacatgtttttttttctgtgtgaatgatcatatcaatcta

upper sequence: LOC_Os04g51950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ13809 (Selaginella moellendorffii), 5'ss of exon 1
GCGATAAATCGATTAAGATAGCAGACTTTGGAGTTGCCAGGATTGAAGTCAAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaataaaacaactacattaatactatttaccatattatctgttagttc--tagccgcg-tgcaacactttattt-tagttaagagaattttgtttgg
 |||||| ||||| ||||| || |||||||| || |||||||| || ||| | |||||||||||||| || || || || || ||||| |||||||| |||||||   | |       ||   ||  | || ||  |  | |  | |  |   ||  ||||     | |||  | | | |    |||      |||        
CCGATAAGTCGATCAAGATTGCCGACTTTGGCGTGGCCAGGATCGAGGTCCAGACCGAGGGGATGACGCCCGAGACCGGGACGTATCGCTGGATGGCACCgtaagcgcattt------ctctcttcgttctcttcgcgttttcgtgttcttcctccatagctagacttcaaagcctcactaaccgtttcattcattgcag----

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|66917134|gb|CX103982.1|CX103982
EST:     AAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCC                         AGAAATGATTCAGCACAGGCCATATGACCAGAAAGTAGATGTCTATAGCTT
genomic: AAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaa ... gatcctgcagAGAAATGATTCAGCACAGGCCATATGACCAGAAAGTAGATGTCTATAGCTT
EST: gi|396941486|gb|HO188695.1|HO188695
EST:     AAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCC                         AGAAATGATTCAGCACAGGCCATATGACCAGAAAGTATATGTCTATAGCTT
genomic: AAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaa ... gatcctgcagAGAAATGATTCAGCACAGGCCATATGACCAGAAAGTAGATGTCTATAGCTT
EST: gi|218491270|gb|FG950313.1|FG950313
EST:     AAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCC                         AGAAATGATTCAGCACAGGCCATATGACCAGAAAGTAGATGTCTATAGCTT
genomic: AAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaa ... gatcctgcagAGAAATGATTCAGCACAGGCCATATGACCAGAAAGTAGATGTCTATAGCTT
EST: gi|58608053|gb|CK036086.1|CK036086
EST:     AAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCC                         AGAAATGATTCAGCACAGGCCATATGACCAGAAAGTAGATGTCTATAGCTT
genomic: AAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaa ... gatcctgcagAGAAATGATTCAGCACAGGCCATATGACCAGAAAGTAGATGTCTATAGCTT
EST: gi|86495908|gb|CI138541.1|CI138541
EST:     AAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCC                         AGAAATGATTCAGCACAGGCCATATGACCAGAAAGTAGATGTCTATAGCTT
genomic: AAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaa ... gatcctgcagAGAAATGATTCAGCACAGGCCATATGACCAGAAAGTAGATGTCTATAGCTT
EST: gi|33681588|gb|CF309827.1|CF309827
EST:     AAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCC                         AGAAATGATTTAGCACAGGCCATATGACCAGAAAGTAGATGTCTATAGCTT
genomic: AAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaa ... gatcctgcagAGAAATGATTCAGCACAGGCCATATGACCAGAAAGTAGATGTCTATAGCTT

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: 52 (upstream exon), 25 (downstream exon)
Score: 2

GCGATAAATCGATTAAGATAGCAGACTTTGGAGTTGCCAGGATTGAAGTCAAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaa ... gatcctgcagAGAAATGATTCAGCACAGGCCATATGACCAGAAAGTAGATGTCTATAGCTTTGGCATTGTTCTATGGGAGCTCATTACTGGCATGCTCCCTTTCGCTAAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGATAAATCGATTAAGATAGCAGACTTTGGAGTTGCCAGGATTGAAGTCAAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaataaaacaactacattaatactatttaccatattatctgttagttctagccgcgtgcaacactttattttagttaagagaattttgtttgg

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