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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTGAGCTAGTAGGGAGGTGTTCAATTGTCCGTGAACTTCATGTATATGGAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatagtacatgtgatattattagcataccatgtttgggaaatggatcggtgccatgacagtattagtagcagttagcaccaacgactttgctatg...

Basic information

species Oryza sativa
transcript LOC_Os04g40840.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G359735_T01 (Zea mays), 5'ss of exon 8
CCCTGAGCTAGTAGGGAGGTGTTCAATTGTCCGTGAACTTCATGTATATGGAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatagtacatgtgatattattagcatacca-tgtttgggaaatggatcggt-gccatgacagta-ttagtagcagttagcaccaacgactttgctatg
|||||| || |||||||||||||||||||| ||||| |||||||| |||||||||||||||||||| ||||| |||||||  |||||||| || ||||||||||     |||  |   || |    ||  |  || ||  ||       |||     |||| | |  |  | |   ||| || || | | |   |||   |  
CCCTGAACTTGTAGGGAGGTGTTCAATTGTGCGTGAGCTTCATGTCTATGGAACTGCAGTCCCTGTGCATGGCCGTGATGTGGACAAACTGCAGCACCAGgtgattcacgtatttac-atgtagacagtgtgacagtgagtgaatgtatgataaccagccaaggctttggtcatcggcaattggcgctaccatgtttagaa--

upper sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 8
CCCTGAGCTAGTAGGGAGGTGTTCAATTGTCCGTGAACTTCATGTATATGGAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatagtacatgtgatattattagcataccatgtttgggaaatggatcggtgc-catgacagta-ttagtagcagttagcaccaacgactttgctatg------
|||||| || |||||||||||||||||||| ||||| |||||||| |||||||||||||||||||| ||||| ||||||| |||||| ||||| ||||||||||       || | |    |||   | | ||  ||| ||       ||||    | || |    |  | |  ||||||| |||| | |   ||||  ||       
CCCTGAACTTGTAGGGAGGTGTTCAATTGTTCGTGAGCTTCATGTCTATGGAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAGgtgatt----cacttat----ttacatgtagacagtgtatgaatgtatgatcatcacacaaggttttggtcatcagcagttggcactaccatgtttgaaatttatgta

upper sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA06G18150.1 (Glycine max), 5'ss of exon 8
CCCTGAGCTAGTAGGGAGGTGTTCAATTGTCCGTGAACTTCATGTATATGGAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccat-agtacatgtgatattattagcataccatgtttgggaaatggatcggtgccatgacagtattagtagcagtt-agcaccaacgactttgctatg
 || |||||  | |||| |||||| ||||| |||||||| ||||| ||||||||||| || || || ||||| || ||||| ||||| |||||||||||||| |   | |||   | || |   | |    ||      |       |   |   |   || | |  |||  |     || ||       | ||   ||   
TCCAGAGCTTATGGGGAAGTGTTCTATTGTTCGTGAACTCCATGTTTATGGAACTGCTGTACCAGTTCATGGACGGGATGCTGACAAGCTACAACACCAGgtaatactgagtcagtttgtttaaacttatttattgaaataaatgcttattttaataaaataagaaaatttctgtttttttagtgtgtttgtctcaactg--

upper sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA04G36790.1 (Glycine max), 5'ss of exon 8
CCCTGAGCTAGTAGGGAGGTGTTCAATTGTCCGTGAACTTCATGTATATGGAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatagtacatgtgatattattagcataccatgtttgggaaatggatcggtgccatgacagtattagtagcagttagcaccaacgactttgctatg------
 || |||||  | |||| |||||| ||||| |||||||| || || ||||||||||| || || || ||||| || ||||| ||||| |||||||||||||| ||   | |   | || || |||    ||  |||      |||  | |    |  |||||    ||| |    | | |  |  ||     |   ||        
TCCAGAGCTTATGGGGAAGTGTTCTATTGTTCGTGAACTCCACGTTTATGGAACTGCTGTACCAGTTCATGGACGGGATGCTGACAAGCTACAACACCAGgtaac---actgtct-tgctaatatggaaatgacataaacatgaatagaagttttcacatgatttcattggattaaatcatta--aaaagtctgattaaattcgtt

upper sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv17s0000g10190.t01 (Vitis vinifera), 5'ss of exon 8
CCCTGAGCTAGTAGGGAGGTGTTCAATTGTCCGTGAACTTCATGTATATGGAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatagtacatg--tgatattattagcataccatgtt-------tgggaaatggatcggtgccatgacagtattagtagcagttagcaccaacgactttgctatg------------
||| |||||  | || || ||||||||||| |||||||| ||||| ||||| ||||||||||| || ||||| || ||||| ||||| || ||||||||||| |    ||||   |  | | ||| | | ||  | ||||         || |||   |  | | || |||     ||||   |   | | |  |  |  ||   | |             
CCCAGAGCTGATTGGCAGATGTTCAATTGTTCGTGAACTCCATGTTTATGGGACTGCAGTCCCAGTCCATGGACGGGATGCTGACAAGCTTCAACACCAGgtaaatgcagtaatagcctcacattttcaacaatcaatgtaaaaacagcggaaaaaaaaatgcttccttgatttctttagccacttattggatgattgttttccatttcaatgtttgatag

upper sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S167_46V6.1 (Physcomitrella patens), 5'ss of exon 11
CCCTGAGCTAGTAGGGAGGTGTTCAATTGTCCGTGAACTTCATGTATATGGAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatagtacatgtgatattattag--cataccatgtttgggaaatgg------------atcggtgccatgacagtattagtagcagttagcacc----aacgactttgctatg---
                  ||||||  | || || || |||||||| ||||||||||| |||||||| |||||||| ||  | ||||| || ||||| ||||| || ||  | | |   |   |||||   |||   |   |  |||  | |            || |    | |   ||| |||  || | ||  ||      | ||| |||| | ||   
------------------GTGTTCTGTGGTGCGAGAGCTTCATGTTTATGGAACTGCTGTCCCTGTCCATGGTCGAGAAACTGACAAGCTGCAACATCAGgt-actatttttcgttcaagcatattacttcatgtgaaaatctggatgttgtcagtcttggtcatagaaatcctattagtcttaagagaatttctcaattttgatcgattttggtgtgaag

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|33810915|gb|CF331348.1|CF331348
EST:     GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAG                         GGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
genomic: GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatag ... acatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
EST: gi|88907490|gb|CI090284.1|CI090284
EST:     GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAG                         GGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
genomic: GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatag ... acatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
EST: gi|86887320|gb|CI313223.1|CI313223
EST:     GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAG                         GGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
genomic: GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatag ... acatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
EST: gi|29682940|gb|CB679215.1|CB679215
EST:     GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAG                         GGTTATGGTACTCTTTTGATGGAAGAAGCAGACAGAATTGCTCGCAAGGAG
genomic: GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatag ... acatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
EST: gi|29666831|gb|CB663106.1|CB663106
EST:     GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAG                         GGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
genomic: GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatag ... acatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
EST: gi|88553089|gb|CI483162.1|CI483162
EST:     GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAG                         GGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
genomic: GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatag ... acatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
EST: gi|29682941|gb|CB679216.1|CB679216
EST:     GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAG                         GGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
genomic: GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatag ... acatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
EST: gi|89186014|gb|CI047883.1|CI047883
EST:     GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAG                         GGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
genomic: GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatag ... acatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
EST: gi|27577984|gb|CB000679.1|CB000679
EST:     GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAG                         GGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGC
genomic: GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatag ... acatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGC
EST: gi|88226125|gb|CI226041.1|CI226041
EST:     GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAG                         GGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
genomic: GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatag ... acatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
EST: gi|218500846|gb|FG954979.1|FG954979
EST:     GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAG                         GGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
genomic: GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatag ... acatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
EST: gi|27576345|gb|CA999039.1|CA999039
EST:     GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAG                         GGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
genomic: GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatag ... acatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
EST: gi|88983019|gb|CI250623.1|CI250623
EST:     GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAG                         GGTTACGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
genomic: GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatag ... acatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
EST: gi|33810913|gb|CF331347.1|CF331347
EST:     GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAG                         GGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
genomic: GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatag ... acatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
EST: gi|86543899|gb|CI184105.1|CI184105
EST:     GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAG                         GGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
genomic: GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatag ... acatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
EST: gi|86485804|gb|CI128437.1|CI128437
EST:     GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAG                         GGTTATGGTACTCTTTTGATGGAAGAAGCAGAGAGAATTGCTCGCAAGGAG
genomic: GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatag ... acatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
EST: gi|87035159|gb|CI189781.1|CI189781
EST:     GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAG                         GGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
genomic: GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatag ... acatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
EST: gi|88264899|gb|CI367550.1|CI367550
EST:     GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAG                         GGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG
genomic: GAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatag ... acatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAG

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: 70 (upstream exon), 70 (downstream exon)
Score: 13

CCCTGAGCTAGTAGGGAGGTGTTCAATTGTCCGTGAACTTCATGTATATGGAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatag ... acatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAGCATCGTTCAAAGAAAATCGCTGTTATATCAGGAGTTGGGACTCGCCACT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCTGAGCTAGTAGGGAGGTGTTCAATTGTCCGTGAACTTCATGTATATGGAACTGCAGTCCCTGTACATGGTCGTGATGCAGACAAACTACAACACCAGgtgaccatagtacatgtgatattattagcataccatgtttgggaaatggatcggtgccatgacagtattagtagcagttagcaccaacgactttgctatg

- - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cggtgcc