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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggctccgatcgagacctatccattccagagcagtctcgatctcgtcacccatggatttcgagatttgatgcgcccttttttttggctcgcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGCGAGCTCGCGGAGGACGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCA

Basic information

species Oryza sativa
transcript LOC_Os07g41750.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g41750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G093902_T02 (Zea mays), 3'ss of exon 1
gtaaggctccgatcgagacctatccattccagagcagtctcgatctcgtcacccatggatttcgagatttgatgcgcccttttttttggctcgcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGCGAGCTCGCGGAGGACGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCA
||| |||||  | |     |  ||  || |   || |  | | |   ||     |||  |    |    |     || |      |||| |||||||||||||||||||| |||||||||||||||||||| ||||||||||| ||||||||||||||||| ||||||||||||||||||||||||||||||||||
gtatggctcgtacccgtctccgtcttttgcgtggc-gcatgggttctgt-----atgtctcatcatgcgtcgcttgctcacccgcttgg-tcgcagTTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGCGAGCTCGCGGAGGATGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCA

upper sequence: LOC_Os07g41750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G26790.1 (Glycine max), 3'ss of exon 1
gtaaggctccgatcgagacc-tatccattccagagcagtc-----tcgatctcgtcacccatggatttcgagat---ttgatgcgcccttttttttggctcgcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGCGAGCTCGCGGAGGACGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCA
|| |  | |  ||  | |||  |  ||| |   | || |      |  | ||| |||   |   | |   |  |   ||  |      | ||| |  |  |||||||||| || ||||| ||||||||||| || ||||||||| | |||||  | ||| | || |||||||| ||||||||||| || ||  | || || || |
gtgactcactcattcataccacaatcatccttcaccaattgaaattaaacctcatcaattaataactataatttcaatttttatcgtgtgtttctgtgtgcgcagTTCGTAGCTGATGGAGTGTTCTTCGCTGAACTGAACGAGGTTCTGACAAGAGAGTTGGCCGAGGACGGTTACTCCGGCGTGGAAGTTAGGGTTACGCCGA

upper sequence: LOC_Os07g41750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G26890.1 (Glycine max), 3'ss of exon 1
------------gtaaggctccgatcgagacctatccattccagagcagtctcgatc--tcgtcacccatggatttcgagatttgatgcgcccttttttttggctcgcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGCGAGCTCGCGGAGGACGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCA
             | |  |  | ||| || | |  ||| |  | |  |  |   |||  |    | | ||| ||||| |  ||| || ||    ||| | ||   |||||||||| || ||||| ||||||||||| || ||||||||| | |||||  | ||| | || |||||||| ||||||||||| || ||  | || || || |
gtgactcactcattcataccacaatc-agccttcaccaattgaaattaaacctcatcaattaataactatg-atttcaattttttat-cgtgtgtttctgtg-tgcgcagTTCGTAGCTGATGGAGTGTTCTTCGCTGAACTGAACGAGGTTCTGACAAGAGAGTTGGCCGAGGACGGTTACTCCGGCGTGGAAGTTAGGGTTACGCCGA

upper sequence: LOC_Os07g41750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA09G28440.1 (Glycine max), 3'ss of exon 1
gtaag-gctccgatcgagacctatccattccagagcagtctcgatctcgtcacccatggatttcgagatttgatgcgccctttttt-ttggctcgcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGCGAGCTCGCGGAGGACGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCA
|| || | | | ||    | ||||  |||         | |   |    |      || |  |  |  | | |   |     | || ||     |||||| ||||||||||| ||||||||||| || ||||||||| | ||||| || ||| | ||||||||||| ||||||||||| |||||  | || || || |
gtcagtggtacaat--gaatctatgaatttttattttatttt--ttctattgtgtttgaaagtgaaactgtaaattgaatagtgttattaatgtgcagTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGTGAGTTGGCGGAGGACGGTTACTCCGGCGTGGAGGTTAGGGTTACGCCGA

upper sequence: LOC_Os07g41750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA20G21190.1 (Glycine max), 3'ss of exon 1
gtaaggctccgat-cgagacctatccattccagagcagtctcgatctcgtcacccatggatttcgagatttgatgcgcccttttttttg-gctcgcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGCGAGCTCGCGGAGGACGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCA
|| |  | |  || |   |   | || |  |  |      | || | | |||       |  |    |||   |   |   | |||||| |  |||||||||| || ||||| ||||||||||| || ||||||||| | |||||  | ||| | || |||||||| ||||||||||| || ||  | || || || |
gtgactcactcattcctcaatcaaccttcaccaattgcaattgaccacatcaatagctaacatttcaattgttttttcgtgtgtttttgtgtgcgcagTTCGTAGCTGATGGAGTGTTCTTCGCTGAACTGAACGAGGTTCTGACAAGGGAGTTAGCCGAGGACGGATACTCCGGCGTGGAAGTTAGGGTTACGCCGA

upper sequence: LOC_Os07g41750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G33230.1 (Glycine max), 3'ss of exon 1
------------gtaaggctccgatcgagacctatccattccagagcagtctcgatctcgtcacccatggatttcgagatttgatgcgcccttttttttggctcgcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGCGAGCTCGCGGAGGACGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCA
             | |  | |  |  |  || | | |  |     |   | ||    || |  ||  ||  | |    |||  |        |    ||     | |||| || ||||| || |||||||| || || ||||||||| | ||||| || ||  | ||||||||||| |||||||||||||| ||  | || || || |
gtcagtggttcaatgaatcgcaaacagcaacattttctatttgtggttttttcttcttcatt-cctttgtgtatgctaattgaacatttgaatggcgttaatgtgtagTTTGTTGCGGACGGAGTGTTCTTTGCCGAACTGAACGAGGTTCTGACACGTGAATTGGCGGAGGACGGTTACTCCGGCGTCGAAGTTAGGGTTACGCCGA

upper sequence: LOC_Os07g41750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G33240.1 (Glycine max), 3'ss of exon 1
------------gtaaggctccgatcgagacctatccattccagagcagtctcgatctcgtcacccatggatttcgagatttga-tgcgcccttttttttggctcgcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGCGAGCTCGCGGAGGACGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCA
            |  |  |    |  |   | | | |  |         | |     || |      ||  | |    ||||||         |    ||     | |||| || ||||| || ||||||||||| || ||||||||| | ||||| || ||  | ||||||||||| ||||||||||| || ||  | || || || |
gtaagtgctagagagaatcgaaaacagcagcattttctatttgtgtttattttttcttcattcttgttgtgtatgtgaatttgaacatttgaatggcgttaatgtgtagTTTGTTGCGGACGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGTGAATTGGCGGAGGACGGTTACTCCGGCGTGGAAGTTAGGGTTACGCCGA

upper sequence: LOC_Os07g41750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EDP07493 (Chlamydomonas reinhardtii), 3'ss of exon 1
----gtaaggctcc-gatcgagacctatccattccagagcagtctcgatctcgt-cacccatggatttcgagatttgatgcgcccttttttt-----tggctcgcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGCGAGCTCGCGGAGGACGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCA
    |  ||||| | ||    |      |  |    | |      ||  | | | |    |  | |  | |  | | | |    || ||  |     || | | ||||||||   ||| || ||||||| ||| |||||||||||| | ||||| |||||||| || ||||| ||||||||||| || ||||||||||| |||||||
gtaggccaggcttctgaatatgttgcggctgtgagcgcgggcggccggccccttgcgaggacaggtggctaagtct-acgtattctattgctccatgtgccacacagTTCGTCCAGGACGGCGTGTTCTACGCCGAGCTGAACGAGCTCCTGACCCGCGAGCTGGCCGAGGATGGCTACTCCGGTGTGGAGGTCCGCGTGACCCCCA

upper sequence: LOC_Os07g41750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S29_222V6.1 (Physcomitrella patens), 3'ss of exon 1
--gtaaggctccgatcgagacctatccattccagagcagtctcgatctcgtcacccatggatttcgagatt--tgatgcgcccttttttttggctc---gcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGCGAGCTCGCGGAGGACGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCA
  ||  |   || |||    |   |   | | |      |     |  | |      |  | ||    | |  || | | |||||   |||  ||    ||||||||| |||||||| || ||||| ||||||||||||||| | || || || |||||||| || || || ||||||||||| ||||| |||||||||||||
gtgtgtgtaacccatcatcgctcttttctgcaaatctgataatactaccctgcttggttcacttgctcactgctggttctcccttccctttttctatgagcagTTCGTAGCGGATGGAGTTTTCTTTGCGGAGCTGAACGAGCTCCTCACCCGGGAGCTCGCCGAAGATGGGTACTCCGGCGTTGAGGTGCGCGTCACCCCCA

upper sequence: LOC_Os07g41750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S136_175V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------gtaaggctccgatcgagacctatccattccagagcagtctcgatctcgtcacccatgg------atttcgagatttgatgcgc------ccttttttttg-------gctcg--cagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGCGAGCTCGCGGAGGACGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCA
              |  || |  ||  |     |     |||  | | | | |   |    |||  || |       | ||||||||    | | |      |||| | ||||       |||||  ||||| || || || || || |||||||| ||||| |||||| | || || ||||||||||| || || || ||||| ||||| ||||| || ||||||||||
gtgagagaattctatttggttgggagaggagtttgga-gttctggtgaaatgtaagtagaatcatgcacgagctcttacttcgagatgcacttcccttactgccttgtgtttgtggtcgcgctcgtgcagTTTGTAGCAGACGGAGTTTTCTTCGCTGAGCTCAACGAGCTTCTCACCCGCGAGCTCGCTGAAGATGGTTACTCTGGCGTGGAGGTGCGTGTCACCCCCA

upper sequence: LOC_Os07g41750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S454_3V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaaggctccgatcgagacctatccattccagagcagtctcgatctcgtcacccatggatttcgagatttgatgcgcccttttttttggctcgcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGCGAGCTCGCGGAGGACGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCA
       |  |   |   || ||   | || |  || | | |    |         ||||||      ||  |     || ||||||     ||||||||| |||||||| || ||||| ||||||||||||||| | || || || ||||| || || || || ||||| ||||| || || |||||||| ||||
------gtgtgtgtgtagcc-attgttccccgctcatttttg---ccaatgggttgggatttttttgcttatta--ttctgttttttcatgagcagTTCGTAGCGGATGGAGTCTTCTTTGCGGAGCTGAACGAGCTTCTCACCCGGGAGCTTGCTGAAGATGGGTACTCTGGCGTGGAAGTGCGCGTCACTCCCA

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|218502938|gb|FG945478.1|FG945478
EST:     AGAAGCGCAAG                         TTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGC
genomic: AGAAGCGCAAGgtaaggctcc ... tggctcgcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGC
EST: gi|58676042|gb|CK064729.1|CK064729
EST:     CACTCTCCACTCCAATGGCGACTCACACGCAGATCAGCAAGAAGCGCAAG                         TTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGC
genomic: CACTCTCCACTCCAATGGCGACTCACACGCAGATCAGCAAGAAGCGCAAGgtaaggctcc ... tggctcgcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGC
EST: gi|38477436|gb|CF961569.1|CF961569
EST:     CCAATGGCGACTCACACGCAGATCAGCAAGAAGCGCAAG                         TTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGC
genomic: CCAATGGCGACTCACACGCAGATCAGCAAGAAGCGCAAGgtaaggctcc ... tggctcgcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGC
EST: gi|58586460|gb|CF984768.1|CF984768
EST:     AGATCAGCAAGAAGCGCAAG                         TTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGAGGGTGACGCGC
genomic: AGATCAGCAAGAAGCGCAAGgtaaggctcc ... tggctcgcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGC
EST: gi|25801300|gb|CA757261.1|CA757261
EST:     ATGGCGATTCACACGCAGATCAGCAAGAAGCGCAAG                         TTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGC
genomic: ATGGCGACTCACACGCAGATCAGCAAGAAGCGCAAGgtaaggctcc ... tggctcgcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGC
EST: gi|38477659|gb|CF961792.1|CF961792
EST:     CACTCTCCACTCCAATGGCGACTCACACGCAGATCAGCAGGAAGCGCAAG                         TTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGC
genomic: CACTCTCCACTCCAATGGCGACTCACACGCAGATCAGCAAGAAGCGCAAGgtaaggctcc ... tggctcgcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctcgtcacccatggatttcgagatttgatgcgcccttttttttggctcgcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGCGAGCTCGCGGAGGACGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCA
                         atttgat  putative branch site (score: 5)
                                   cccttttttttggctc  putative PPT
                                      tttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggctccgatcgagacctatccattccagagcagtctcgatctcgtcacccatggatttcgagatttgatgcgcccttttttttggctcgcagTTCGTGGCGGATGGGGTGTTCTTCGCGGAGCTGAACGAGATGCTGACGCGCGAGCTCGCGGAGGACGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA