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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttccaccaacaatatagttatcttgttagacagtccttgtagtctattcaattactgtgaataaataaagtattgaaaattaaaaggtgaaaatagtttagaacaccattatcatatcatgcatggttacattactgtatcagacatggttatggttacgaggtggtggtaatgaatctatttgttgattcag

Basic information

species Oryza sativa
transcript LOC_Os12g01140.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01140.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GRMZM2G001457_T02 (Zea mays), 5'ss of exon 19
GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttccaccaacaatatagttatcttgttagacagtccttgtagtctattcaattactgtgaataaataaagtattgaaaattaaaaggtgaaaatagtttagaacaccattatcatatcatgcatggttacattactgtatcagacatggttatggttacgaggtggtggtaatgaatctatttgttgattcag
||||||||||| |||||||||||||| || ||||| ||||||||||| |||||||| |  ||       || | |   || |  | | ||||    | ||   || | | || || |   ||      || |                                                                                                                        
GAGATTATTACCGGAGCTGGCCATACGAGTGCTGTAGATTGGTGGGCGCTAGgtaactaatcttgtgctaaaagaaacatgt-atgatacagctactatatgatagtgagtt-ctctttctactggttgtgtcag---------------------------------------------------------------------------------------------------------------------

upper sequence: LOC_Os12g01140.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GRMZM2G001457_T01 (Zea mays), 5'ss of exon 1
GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttccaccaacaatatagttatcttgttagacagtccttgtagtctattca-attactgtgaataaataaagta-ttgaaaat-taaaaggtgaaaatagtttagaacaccattatcatatcatgcatggttacattactgtatcagacatggttatggttacgaggtggtg-gtaatgaatctatttgttgattcag
                                                                     |   |  | ||||  ||   || |||||||| | ||| ||   |   |   || | ||  | |  ||   ||   |  | || | || | |  |  |    | |  | ||| ||  || | | |  |   | |  || |  | ||    ||   | | ||| ||  |   |||| | ||||  ||||
---------------------------------------------------------------------ATAGTCATCATCTGTTTTATCAATCCTTGTATTGTATGCATGCTGTAGGAGATTATTACCGGAGCTGGCCATACGAGTGCTGTAGATTGGTGGGCGCTAGgtaacta-atcttg--tgctaaaagaaacatgtatgatacagctac---tatatgatagtgagttctctttctactggttgtgtcag

upper sequence: LOC_Os12g01140.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA15G04850.1 (Glycine max), 5'ss of exon 20
GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttccaccaacaatatagttatcttgttagacagtccttgtagtctattcaattactgtgaataaataaagtattgaaaattaaaaggtgaaaatagtttagaacaccattatcatatcatgcatggttacattactgtatcagacatggttatggttacgaggtggtggtaatgaatctatttgttgattcag
|| ||||| || ||  | || || ||||| ||||| |||||||||||||||||||||| ||           ||  |||| ||  || | |        | | ||  ||||   | |||| |||  || | |  || |||||||    |||  | |  |||| |   | |    ||                                                                            
GAAATTATAACTGGTTCAGGTCACACAAGTGCTGTGGATTGGTGGGCTCTAGgtaattttta----------attcttatttttataaaaaa-------aatataggcaat---tttgaacaaaataaatttctaacattaaaaa---aaatcaatacagaa-agtttgaatgcat----------------------------------------------------------------------------

upper sequence: LOC_Os12g01140.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA12G07890.2 (Glycine max), 5'ss of exon 21
GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttccaccaacaatatagttatcttgttagacagtccttgtagtctattcaattactgtgaataaataaagtattgaaaattaaaaggtgaaa-atagtttagaacaccattatcatatcatgcatggttacattactgtatcagacatggttatggttacgaggtggtggtaatgaatctatttgttgattcag
|| ||||| || ||  | ||||||||||| ||||| |||||||||||||| ||||||||||            || || |     || | |        || |||||     |||      |||| || | |  |||| |||||    ||| | | |  |    |   ||||  | |                                                                            
GAAATTATAACGGGTTCAGGCCATACAAGTGCTGTGGATTGGTGGGCTCTTGgtaattctt------------taattcttacaataaataa-------aggctattaggcaact------aaatcaattttgaaaaactaaaaaaaaaaatagaatgcattgtatatttattgtgt----------------------------------------------------------------------------

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|29644412|gb|CB649419.1|CB649419
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|25806002|gb|CA761963.1|CA761963
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|66913937|gb|CX100785.1|CX100785
EST:     GATTATTACAGGAGCTGGCAATACAAGCGCTGTTGACTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|29621738|gb|CB626749.1|CB626749
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|58695632|gb|CK084319.1|CK084319
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|29623925|gb|CB628936.1|CB628936
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|29630467|gb|CB635476.1|CB635476
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|29641401|gb|CB646408.1|CB646408
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|29663823|gb|CB660098.1|CB660098
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|29678745|gb|CB675020.1|CB675020
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|18386007|gb|BM419206.1|BM419206
EST:     ATAC-AGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: ATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|88299110|gb|CI570080.1|CI570080
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|29630120|gb|CB635129.1|CB635129
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|29634078|gb|CB639087.1|CB639087
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|29672021|gb|CB668296.1|CB668296
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|58695041|gb|CK083728.1|CK083728
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|29623926|gb|CB628937.1|CB628937
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|29624138|gb|CB629149.1|CB629149
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|29646711|gb|CB651718.1|CB651718
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|33680724|gb|CF308963.1|CF308963
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|29622724|gb|CB627735.1|CB627735
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|29674379|gb|CB670654.1|CB670654
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
EST: gi|29677072|gb|CB673347.1|CB673347
EST:     GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG                         GGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA
genomic: GATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAA

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), 60 (downstream exon)
Score: 19

GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttc ... gttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAACGAGGCAACGGACATTTGCTAATATCTTGCACAAGGATATCAGATTTCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAGgtaattcttccaccaacaatatagttatcttgttagacagtccttgtagtctattcaattactgtgaataaataaagtattgaaaattaaaaggtgaaaatagtttagaacaccattatcatatcatgcatggttacattactgtatcagacatggttatggttacgaggtggtggtaatgaatctatttgttgattcag

- - - - - - GGAGCT
- - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - -  TGGTGG