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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttgttcctaccactattcttacttcacctgaattagttcctttcatcacaagttttggtcaagaaggaacacaaatgtttataccttgacattctgttcccttttctgtttgggtaaccacag

Basic information

species Oryza sativa
transcript LOC_Os07g08760.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g08760.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G124965_T01 (Zea mays), 5'ss of exon 5
GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttgttc-------ctaccactattctta---cttcacctgaattagttcctttcatcacaagtttt-ggtcaagaaggaacacaaatgtttataccttgacattctgttccc-ttttctgtttgggtaaccacag
|| ||||| |||||| | ||||| ||||| ||||||||||||||||||||  |||| ||||||||||||||||||||||| |||||    | |||       |||  |  ||| |     ||| | |||  || || |    ||| | | ||||   |||| | | || || ||||| ||| ||||| ||  |    ||   || | |||||| | ||   |||
GGTGTTCCATATCCATCATTGCCCAAGAAAGAAAAACCAAGGCGTGTGGAGTTGTACTTCTCAAGTTGGCGTATTAGAGCTGgtaaacccttttctcagtagctagtatcattttggtgtcttgagctgtgtttgtcctgaacatgaaaggtttccagtcaggcacgagcagaaatgcttagaccttaacgctacaatcatattctttgtttgtg-aaatgcag

upper sequence: LOC_Os07g08760.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G121223_T02 (Zea mays), 5'ss of exon 6
GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaactttt---------gttcctaccactattcttacttcacctgaattagttcctttcatcacaagt-tttggtcaagaaggaacacaaatgtttataccttgacattctgttccc-ttttctgtttgggtaaccacag
|| ||||| |||||| | ||||| ||||| |||||||| ||||||||||| ||||| ||||||||||||||||||||||| ||||||||||         |||  || || |||  |  ||  | |||  || ||||    ||| | | || |   |||| |   ||||||||||| |||  |||| ||  | |  ||   || | ||| |  | ||   |||
GGTGTTCCATATCCATCATTGCCCAAGAAAGAAAAACCGAGGCGTGTGGAGCTGTACTTCTCAAGTTGGCGTATTAGAGCTGgtaacttttttcttagtagttagtatcattatggtgtctagagctgtgtttgttctgaacatgaaaggtatccagtcaggcttgaacacaaatgcttaggccttaacgctataatcatattctttgtctctg-aaatgcag

upper sequence: LOC_Os07g08760.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT4G14500.1 (Arabidopsis thaliana), 5'ss of exon 5
GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttgttcctaccactattcttacttcacctgaattagttcctttcatcacaagttttggtcaagaaggaacacaaatgtttataccttgacattctgttcccttttctgtttgggtaaccacag
|||||||||||||||||| | || |||   || || ||||||||||| || || |||||||||||||||  ||| ||||| |||||   || ||  ||  || | ||||  ||    | |    |   | |  ||    | |||    ||| |   || |||||||                                              
GGAGTTCCTTATCCAGCTCTACCAAAGCGTGATAAGCCAAGGCGTGTTGAGCTTTATTTCTCAAGTTGGGTTATCAGAGCGGgtaagcctt-ttgatat-acaagtctttttttctttaagacggg--catagattttgattttaaagcaa-attcaaaacaaatgcag-------------------------------------------

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|29659937|gb|CB656212.1|CB656212
EST:     AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG                         TTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
genomic: AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttg ... gtaaccacagTTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
EST: gi|86495790|gb|CI138423.1|CI138423
EST:     AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG                         TTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
genomic: AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttg ... gtaaccacagTTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
EST: gi|86494162|gb|CI136795.1|CI136795
EST:     AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG                         TTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
genomic: AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttg ... gtaaccacagTTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
EST: gi|30226837|gb|CB964729.1|CB964729
EST:     AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG                         TTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
genomic: AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttg ... gtaaccacagTTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
EST: gi|14981939|gb|BI306617.1|BI306617
EST:     AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG                         TTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
genomic: AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttg ... gtaaccacagTTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
EST: gi|86503157|gb|CI145790.1|CI145790
EST:     AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG                         TTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
genomic: AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttg ... gtaaccacagTTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
EST: gi|29659876|gb|CB656151.1|CB656151
EST:     AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG                         TTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
genomic: AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttg ... gtaaccacagTTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
EST: gi|29674883|gb|CB671158.1|CB671158
EST:     TATTAGAGCAG                         TTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
genomic: TATTAGAGCAGgtaacttttg ... gtaaccacagTTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
EST: gi|30228065|gb|CB965957.1|CB965957
EST:     AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG                         TTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
genomic: AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttg ... gtaaccacagTTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
EST: gi|23512848|gb|BU672864.1|BU672864
EST:     AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG                         TTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
genomic: AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttg ... gtaaccacagTTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
EST: gi|29662657|gb|CB658932.1|CB658932
EST:     TATTAGAGCAG                         TTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
genomic: TATTAGAGCAGgtaacttttg ... gtaaccacagTTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
EST: gi|29621755|gb|CB626766.1|CB626766
EST:     AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGAATTAGAGCAG                         TTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
genomic: AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttg ... gtaaccacagTTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
EST: gi|3763435|gb|AU030187.1|AU030187
EST:     AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG                         TTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
genomic: AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttg ... gtaaccacagTTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
EST: gi|29686576|gb|CB682851.1|CB682851
EST:     AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG                         TTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
genomic: AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttg ... gtaaccacagTTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
EST: gi|30228719|gb|CB966609.1|CB966609
EST:     AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG                         TTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
genomic: AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttg ... gtaaccacagTTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
EST: gi|29612780|gb|CB617793.1|CB617793
EST:     AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGAATTAGAGCAG                         TTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
genomic: AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttg ... gtaaccacagTTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
EST: gi|29686577|gb|CB682852.1|CB682852
EST:     AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG                         TTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
genomic: AAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttg ... gtaaccacagTTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
EST: gi|29659938|gb|CB656213.1|CB656213
EST:     TATTAGAGCAG                         TTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG
genomic: TATTAGAGCAGgtaacttttg ... gtaaccacagTTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGG

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: 58 (upstream exon), 73 (downstream exon)
Score: 13

GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttg ... gtaaccacagTTCAATCACCGAAACAAGATGGACAGCAATCCGCATGTGAAGTAACGCTGGTCCACTACGAGGACATGGGCATCCCTAAAGATGTCGCCAAGGTGGGTGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAGgtaacttttgttcctaccactattcttacttcacctgaattagttcctttcatcacaagttttggtcaagaaggaacacaaatgtttataccttgacattctgttcccttttctgtttgggtaaccacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG