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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agggcttgagttagatgtctacaatttgtagtcctcaacattcagctactagtactacatactgtatttaagtaaattttattttaattttttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGATGACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACG

Basic information

species Oryza sativa
transcript LOC_Os07g26940.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g26940.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G044720_T01 (Zea mays), 3'ss of exon 1
agggcttgagttagatgtctacaatttgtagtcctcaacattcagctactagtactacatac----tgtatttaagtaaattttattttaattttttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGATGACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACG
      || ||  || | ||  || |   || | |||||     |||| |  |  | | | |    || |||| |||  |    | || ||| | ||||  ||||||||||| |||||||||||||||||||| ||||| || |||||||||||||||||||||||||||| |||| | || |||||||| |||||||| || |
gtcaaatgggtaggaggact-taagtgaaagacgtcaactccttgctattcatgttccttgccaattgaatttcagttgacac-acttgaatctatttt--cagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGATGACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATG

upper sequence: LOC_Os07g26940.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G558324_T01 (Zea mays), 3'ss of exon 2
agggcttgagttagatgtctacaatttgtagtcctcaacattcagctactagtactacatactgtatttaagtaaatttt----------attttaattttttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGATGACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACG---
          || | | |||  |||||  |    | | |  | |   | |  |   |   ||| | |  |  |||   ||          || | ||| || |||   ||||||| || ||||| |||||||||||||| || || || |||||||   ||||||| || || ||||||  | | ||||||||||||||||| ||||| |   
----------tttggtttcttgaattttcatgtattatctattaaacatttctctaagcaactttgtccagataacacttgccatctggaatgtgaatcttattttttagATCACATACCACTTTTTCCATTGGAAGAAAGGGACACCTTTTGCTG---ATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAACAAATGGATAATGGCA

upper sequence: LOC_Os07g26940.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G064898_T02 (Zea mays), 3'ss of exon 1
agggcttgagttagatgtctacaatttgtagtcctcaacattcagctactagtactacatac----tgtatttaagtaaattttattttaatttttt-ttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGATGACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACG
      || ||  ||       || |   ||  ||||||     |||| |  |  | | | |    || |||| |||  |     ||  ||| || | ||  ||||||||||| |||||||||||||||||||| ||||| || |||||||||||||||||||||||||||| |||| | || |||||||| |||||||| || |
-----atgggtaggaaagacttaagtgaaagaactcaaccccttgctattcatgttccttgcctgttgaatttcagttgacacacttgaaatgttctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGATGACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATG

upper sequence: LOC_Os07g26940.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G02540.1 (Glycine max), 3'ss of exon 1
agggcttgagttagatgtctacaatttgtagtcctcaacattcagctactagtactacatactgtatttaagtaaattttattttaattttttttggc----agATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGATGACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACG---
|||   | | ||| || | |    ||||||    |    | |  | |  ||  |  |  ||   | | ||  |     ||| || | | | || || |    || | || |||||||| || || |||||||| |||||||||||||| |   | |||||||| |||||||| ||| | ||||||||||| ||  | || || |   
aggttataaatta-atatttt--gtttgtaaatattgttaat-ggatgttaaaataatttaacttctctacatggcgcttaattgattatgttgtgtccatcagGTAACATATCACTTTTTTCACTGGAAGAAAGGAACTCCATTTGCGG---AGGACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAA

upper sequence: LOC_Os07g26940.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA07G05940.1 (Glycine max), 3'ss of exon 1
-agggcttgagttagatgtctacaatttgtagtcctcaacattcagctactagtactacatactgtatttaagtaaatt--ttattttaattttttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGATGACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACG---
 |||   | | |||    |||    ||||||              | | |||  || |  ||   | | ||| |    |  ||  ||   || | |    ||| | || |||||||| || || |||||||| |||||||||||||| |   | |||||||| |||||||| ||| | ||||||||||| ||  | || || |   
caggttataaattaa---tctgttgtttgtaaattattgttaatggatgctaaaacaatttaacttctctaaatggcctaattgattatgttgtgtccatcagGTAACATATCACTTTTTTCACTGGAAGAAAGGAACTCCATTTGCAG---AGGACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAA

upper sequence: LOC_Os07g26940.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G42000.2 (Arabidopsis thaliana), 3'ss of exon 1
agggcttgagttagatgtctacaatttgtagtcctcaacattcagctactagtactacatactgtatttaagtaaattttattttaattttttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGATGACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACG---
                   ||  |||     ||  |  |  ||   |      | |   |  | | |  |  | ||||||    |  |||| |||   || |||| ||||| | ||||||||||||||||||||| |||||||  |   |||| |||||  |||| || ||| | |||||||||||||| |||||||| |   
------------------gtattattcccgatctcctccgatccaatttcgaaattgt-tggtttctagatttgaatttttgagtttttttgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTTGGAG---ATGATCAAGGAGTCTATAATAGATTGACTTGGTGGGAACAGATTGATAATGGCA

upper sequence: LOC_Os07g26940.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv15s0046g00140.t01 (Vitis vinifera), 3'ss of exon 1
-----agggcttgagttagatgtctacaatttgtagtcctcaacattcagctactagtactacatactgtatttaagtaaattttatttta-attttttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGATGACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACG---
           |   ||   ||| |||  ||  |  | ||  |||||    ||||     || || || | | | |    |||       |   ||        || |||| ||||||||||||||||||||||| |||||||| |||||||   | ||||| || |||||||| ||  | || |||||||| || || || || |   
gtttgtttatcttctttgtctgtatacccttcctgatgct--acattagattact----ttatatcctctctatgacctgattgaggagcatgcttcacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTG---AAGACCAGGGAATCTACAATAGGTTGACGTGGTGGGAGCAGATAGACAATGGAA

upper sequence: LOC_Os07g26940.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0025g02260.t01 (Vitis vinifera), 3'ss of exon 1
agggcttgagtta--gatgtctacaatttgtagtcctcaacattcagctactagtactacatactgtatttaagtaaattttattttaattttttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGATGACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACG---
| |   ||| ||   |   ||| | ||  |   | ||  | ||     |  |  |  ||  |  |||   | | || | |||   ||  | |  |   |||| | |||||||||| ||| || |||||||||||||| ||||| || |   ||||||| || |||||||| || ||||| |||||||| ||||| || |  |   
aagaaatgaattcttgtcatcttccatc-gcgattct-gatatgtcatttttgcttgtagttcatgttacttaatacaatttgggtttttgtcgtcctgcagGTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGG---ATGACCAGGGTATCTACAATAGGCTAACCTGGTGGGAGCAAATAGACAGTGGGA

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|218487860|gb|FG958482.1|FG958482
EST:     CTGCTCCCCCTGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCC                         ATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGAT
genomic: CTGCTCCCCC-GGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCCgtacgtcccg ... tttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGAT
EST: gi|58688367|gb|CK077054.1|CK077054
EST:     CCTGCTCCCCCGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCC                         ATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGAT
genomic: CCTGCTCCCCCGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCCgtacgtcccg ... tttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctactagtactacatactgtatttaagtaaattttattttaattttttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGATGACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACG
                                    ttttaat  putative branch site (score: 3)
                                    ttttaatttttttt  CT-rich tract
          tacatactgtatttaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agggcttgagttagatgtctacaatttgtagtcctcaacattcagctactagtactacatactgtatttaagtaaattttattttaattttttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGATGACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG