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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGGGAAGAGCTTCACTTACAACACCAACATCAACATCGCGGTGGCTGTCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggatatctgtgtgtttaatgtcgtttcatttaggaattgaatcatatgagttcactgaatagcttgagcaatggcatgatgcag

Basic information

species Oryza sativa
transcript LOC_Os08g33440.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g33440.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G117786_T01 (Zea mays), 5'ss of exon 2
GGATGGGAAGAGCTTCACTTACAACACCAACATCAACATCGCGGTGGCTGTCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggatatctgtgtgtttaatgtcgtttcatttaggaatt--gaat-----catatgagttcactgaatagcttgagcaatggcatgatgcag
|||||| ||||||||||| |||||||  || |||||||| || |||||||| ||||| |||||||| || ||||||||||| ||  ||||||| || |||||| |   ||||| |||| | ||| | | |||| |  ||| ||  || |     || |  |||||||  || || |||   ||||  |   || ||
GGATGGAAAGAGCTTCACATACAACAGTAATATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagtatctttgtgataaatttggcttcactccggagttcggagttttagcaaacaagttcaccaaacagtttgttgaatgttacactgtag

upper sequence: LOC_Os08g33440.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G058702_T01 (Zea mays), 5'ss of exon 2
GGATGGGAAGAGCTTCACTTACAACACCAACATCAACATCGCGGTGGCTGTCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggatatctgtgtgtttaatgtcgtttcatttaggaattgaatcatatgagttcactgaatagcttgagcaatggcatgatgcag
|||||| ||||||||||| |||||||  ||||||||||| || |||||||| ||||| |||||||| || ||||||||||||||  |||||||||| |||||||     |||| |||| | |||   | |||| || | | ||  | || |  ||||||   || ||||||   ||||  |   || ||
GGATGGAAAGAGCTTCACATACAACAGTAACATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgtacaatctttgtgataaattcggcttcaattcgcagttttagcaaacaagttcatcaaacagcttgttgaatgttacactgtag

upper sequence: LOC_Os08g33440.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv01s0011g03380.t01 (Vitis vinifera), 5'ss of exon 2
GGATGGGAAGAGCTTCACTTACAACACCAACATCAACATCGCGGTGGCTGTCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggatatctgtgtgtttaatgtcgtttcatttaggaatt---gaatcatatgagttcactga--atagcttgagcaatggcat--gatgcag-------------------------------
 ||||||||||  || || || |||| ||  || ||||| ||||| || || |||||| |||||||| | || || ||||||||  ||||||||||||||||| | || ||  |  | ||   ||    ||| |  |  ||||   | ||| | | |  | |   |  ||   ||||    |    |   |   ||                               
AGATGGGAAGACTTTTACATATAACAGCAGTATAAACATTGCGGTAGCAGTGGCAATCAATGGTGGGTTGATAACCCCTGTTCTTCAGGATGCTGATAAGgtaaatgacat--gcattttctgtggaaattcgtgaaaaaattcttgtatcctgtcaagttatgaatgatgttttgatttttaatttcgaaattagtttagttaataatttgtttttgatggtgtag

upper sequence: LOC_Os08g33440.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ37696 (Selaginella moellendorffii), 5'ss of exon 2
GGATGGGAAGAGCTTCACTTACAACACCAACATCAACATCGCGGTGGCTGTCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtaca-ggatatctgtgtgtttaatgtcgtttcatttaggaattgaatcatatgagttcactgaatagcttgagcaatggcatgatgcag
|||||||||||||||||| |||||| ||| |||||||||||| || || || || || || || || || || || || |||||| | || || || |||||||    | |||| | | ||    ||  |    || |       | || | || |||    |   ||                      
GGATGGGAAGAGCTTCACGTACAACGCCAGCATCAACATCGCCGTTGCAGTAGCGATTGACGGCGGACTTATCACCCCCGTTCTGCAAGACGCCGACAAGgtacgcaaaaatctttctattcctcgttttcgagttcat------agtcttgtgtgttggtggtgcag----------------------

upper sequence: LOC_Os08g33440.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ14990 (Selaginella moellendorffii), 5'ss of exon 2
GGATGGGAAGAGCTTCACTTACAACACCAACATCAACATCGCGGTGGCTGTCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtaca-ggatatctgtgtgtttaatgtcgtttcatttaggaattgaatcatatgagttcactgaatagcttgagcaatggcatgatgcag
|||||||||||||||||| |||||| ||| |||||||||||| || || || || || || || || || || || || |||||| | || || || |||||||    | |||| | | ||     ||||||   |   |   | | || | || |||    |   ||                      
GGATGGGAAGAGCTTCACGTACAACGCCAGCATCAACATCGCCGTTGCAGTAGCGATTGACGGCGGACTTATCACCCCCGTTCTGCAAGACGCCGACAAGgtacgcaaaaatctttctatt---cctcgttt---tcgagttcttagtcttgtgtgttggtggtgcag----------------------

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|86498267|gb|CI140900.1|CI140900
EST:     TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAG                         TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
genomic: TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggata ... catgatgcagTTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
EST: gi|86502788|gb|CI145421.1|CI145421
EST:     TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAG                         TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
genomic: TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggata ... catgatgcagTTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
EST: gi|58585893|gb|CF984201.1|CF984201
EST:     TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAG                         TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
genomic: TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggata ... catgatgcagTTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
EST: gi|88740335|gb|CI763843.1|CI763843
EST:     TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAG                         TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
genomic: TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggata ... catgatgcagTTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
EST: gi|86499821|gb|CI142454.1|CI142454
EST:     GATGCTGATAAG                         TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
genomic: GATGCTGATAAGgtacaggata ... catgatgcagTTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
EST: gi|86493670|gb|CI136303.1|CI136303
EST:     TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAG                         TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
genomic: TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggata ... catgatgcagTTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
EST: gi|27920911|gb|CB096719.1|CB096719
EST:     TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAG                         TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
genomic: TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggata ... catgatgcagTTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
EST: gi|86497312|gb|CI139945.1|CI139945
EST:     TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAG                         TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
genomic: TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggata ... catgatgcagTTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
EST: gi|86504362|gb|CI146995.1|CI146995
EST:     TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAG                         TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCCAAGAAAGC
genomic: TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggata ... catgatgcagTTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGT-CAAGAAAGC
EST: gi|86858948|gb|CI275150.1|CI275150
EST:     TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAG                         TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
genomic: TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggata ... catgatgcagTTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
EST: gi|86597928|gb|CI276714.1|CI276714
EST:     TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAG                         TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
genomic: TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggata ... catgatgcagTTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
EST: gi|86499205|gb|CI141838.1|CI141838
EST:     TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAG                         TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
genomic: TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggata ... catgatgcagTTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
EST: gi|86501092|gb|CI143725.1|CI143725
EST:     TTGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAG                         TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
genomic: TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggata ... catgatgcagTTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
EST: gi|66912791|gb|CX099639.1|CX099639
EST:     TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAG                         TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
genomic: TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggata ... catgatgcagTTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
EST: gi|58688879|gb|CK077566.1|CK077566
EST:     TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAG                         TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
genomic: TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggata ... catgatgcagTTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
EST: gi|86501837|gb|CI144470.1|CI144470
EST:     TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAG                         TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
genomic: TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggata ... catgatgcagTTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
EST: gi|86859001|gb|CI276951.1|CI276951
EST:     TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAG                         TTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT
genomic: TCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggata ... catgatgcagTTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCT

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: 71 (upstream exon), 71 (downstream exon)
Score: 16

GGATGGGAAGAGCTTCACTTACAACACCAACATCAACATCGCGGTGGCTGTCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggata ... catgatgcagTTGGATATATATTTGCTCTCACAAAAATGGAAGGAACTAGTCAAGAAAGCTCGTGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGGGAAGAGCTTCACTTACAACACCAACATCAACATCGCGGTGGCTGTCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggatatctgtgtgtttaatgtcgtttcatttaggaattgaatcatatgagttcactgaatagcttgagcaatggcatgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT